1
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Cervantes-Salguero K, Kadrmas M, Ward BM, Lysne D, Wolf A, Piantanida L, Pascual G, Knowlton WB. Minimizing Structural Heterogeneity in DNA Self-Assembled Dye Templating via DNA Origami-Tuned Conformations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:10195-10207. [PMID: 38690801 PMCID: PMC11100016 DOI: 10.1021/acs.langmuir.4c00470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024]
Abstract
With recent advances in DNA-templated dye aggregation for leveraging and engineering molecular excitons, a need exists for minimizing structural heterogeneity. Holliday Junction complexes (HJ) are commonly used to covalently template dye aggregates on their core; however, the global conformation of HJ is detrimentally dynamic. Here, the global conformation of the HJ is selectively tuned by restricting its position and orientation by using a sheet-like DNA origami construct (DOC) physisorbed on glass. The HJ arms are fixed with four different designed interduplex angles (IDAs). Atomic force microscopy confirmed that the HJs are bound to the surface of DOC with tuned IDAs. Dye orientation distributions were determined by combining dipole imaging and super-resolution microscopy. All IDAs led to dye orientations having dispersed distributions along planes perpendicular to the HJ plane, suggesting that stacking occurred between the dye and the neighboring DNA bases. The dye-base stacking interpretation was supported by increasing the size of the core cavity. The narrowest IDA minimizes structural heterogeneity and suggests dye intercalation. A strong correlation is found between the IDA and the orientation of the dye along the HJ plane. These results show that the HJ imposes restrictions on the dye and that the dye-DNA interactions are always present regardless of global conformation. The implications of our results are discussed for the scalability of dye aggregates using DNA self-assembly. Our methodology provides an avenue for the solid-supported single-molecule characterization of molecular assemblies templated on biomolecules─such as DNA and protein templates involved in light-harvesting and catalysis─with tuned conformations and restricted in position and orientation.
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Affiliation(s)
- Keitel Cervantes-Salguero
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Madison Kadrmas
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Brett M. Ward
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Drew Lysne
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Amanda Wolf
- Biomolecular
Sciences Graduate Programs, Boise State
University, Boise, Idaho 83725, United States
| | - Luca Piantanida
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Gissela Pascual
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - William B. Knowlton
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical and Computer Engineering, Boise State University, Boise, Idaho 83725, United States
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2
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Marcus AH, Matsika S, Heussman D, Sorour MI, Maurer J, Albrecht CS, Enkhbaatar L, Herbert P, Kistler KA, von Hippel PH. Spectroscopic approaches for studies of site-specific DNA base and backbone 'breathing' using exciton-coupled dimer-labeled DNA. ARXIV 2024:arXiv:2403.16251v2. [PMID: 38584614 PMCID: PMC10996769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA 'breathing') play a central role in such processes. Here we review the development and application of novel spectroscopic methods and analyses - both at the ensemble and single-molecule levels - to study structural and dynamic properties of exciton-coupled cyanine and fluorescent nucleobase analogue dimer-labeled DNA constructs at key positions involved in protein-DNA complex assembly and function. The exciton-coupled dimer probes act as 'sensors' of the local conformations adopted by the sugar-phosphate backbones and bases immediately surrounding the dimer probes. These methods can be used to study the mechanisms of protein binding and function at these sites.
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Affiliation(s)
- Andrew H. Marcus
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Dylan Heussman
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Mohammed I. Sorour
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Jack Maurer
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Claire S. Albrecht
- Center for Optical, Molecular and Quantum Science, Department of Physics, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Physics, and University of Oregon, Eugene, Oregon 97403
| | - Lulu Enkhbaatar
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Patrick Herbert
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Kurt A. Kistler
- Department of Chemistry, Brandywine Campus, The Pennsylvania State University, Media, Pennsylvania 19063
| | - Peter H. von Hippel
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
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3
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Heussman D, Enkhbaatar L, Sorour MI, Kistler KA, von Hippel PH, Matsika S, Marcus AH. Using transition density models to interpret experimental optical spectra of exciton-coupled cyanine (iCy3)2 dimer probes of local DNA conformations at or near functional protein binding sites. Nucleic Acids Res 2024; 52:1272-1289. [PMID: 38050987 PMCID: PMC10853810 DOI: 10.1093/nar/gkad1163] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/15/2023] [Accepted: 11/18/2023] [Indexed: 12/07/2023] Open
Abstract
Exciton-coupled chromophore dimers are an emerging class of optical probes for studies of site-specific biomolecular interactions. Applying accurate theoretical models for the electrostatic coupling of a molecular dimer probe is a key step for simulating its optical properties and analyzing spectroscopic data. In this work, we compare experimental absorbance and circular dichroism (CD) spectra of 'internally-labeled' (iCy3)2 dimer probes inserted site-specifically into DNA fork constructs to theoretical calculations of the structure and geometry of these exciton-coupled dimers. We compare transition density models of varying levels of approximation to determine conformational parameters of the (iCy3)2 dimer-labeled DNA fork constructs. By applying an atomistically detailed transition charge (TQ) model, we can distinguish between dimer conformations in which the stacking and tilt angles between planar iCy3 monomers are varied. A major strength of this approach is that the local conformations of the (iCy3)2 dimer probes that we determined can be used to infer information about the structures of the DNA framework immediately surrounding the probes at various positions within the constructs, both deep in the duplex DNA sequences and at sites at or near the DNA fork junctions where protein complexes bind to discharge their biological functions.
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Affiliation(s)
- Dylan Heussman
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, OR 97403, USA
| | - Lulu Enkhbaatar
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, OR 97403, USA
| | - Mohammed I Sorour
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Kurt A Kistler
- Department of Chemistry, Brandywine Campus, The Pennsylvania State University, Media, PA 19063, USA
| | - Peter H von Hippel
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, OR 97403, USA
| | | | - Andrew H Marcus
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, OR 97403, USA
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4
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Benham CJ. DNA superhelicity. Nucleic Acids Res 2024; 52:22-48. [PMID: 37994702 PMCID: PMC10783518 DOI: 10.1093/nar/gkad1092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 10/20/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Closing each strand of a DNA duplex upon itself fixes its linking number L. This topological condition couples together the secondary and tertiary structures of the resulting ccDNA topoisomer, a constraint that is not present in otherwise identical nicked or linear DNAs. Fixing L has a range of structural, energetic and functional consequences. Here we consider how L having different integer values (that is, different superhelicities) affects ccDNA molecules. The approaches used are primarily theoretical, and are developed from a historical perspective. In brief, processes that either relax or increase superhelicity, or repartition what is there, may either release or require free energy. The energies involved can be substantial, sufficient to influence many events, directly or indirectly. Here two examples are developed. The changes of unconstrained superhelicity that occur during nucleosome attachment and release are examined. And a simple theoretical model of superhelically driven DNA structural transitions is described that calculates equilibrium distributions for populations of identical topoisomers. This model is used to examine how these distributions change with superhelicity and other factors, and applied to analyze several situations of biological interest.
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Affiliation(s)
- Craig J Benham
- UC Davis Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA
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5
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An H, Pires JC, Conant GC. Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression. PLoS Comput Biol 2024; 20:e1011803. [PMID: 38227592 PMCID: PMC10817154 DOI: 10.1371/journal.pcbi.1011803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/26/2024] [Accepted: 01/06/2024] [Indexed: 01/18/2024] Open
Abstract
Hybridization coupled to polyploidy, or allopolyploidy, has dramatically shaped the evolution of flowering plants, teleost fishes, and other lineages. Studies of recently formed allopolyploid plants have shown that the two subgenomes that merged to form that new allopolyploid do not generally express their genes equally. Instead, one of the two subgenomes expresses its paralogs more highly on average. Meanwhile, older allopolyploidy events tend to show biases in duplicate losses, with one of the two subgenomes retaining more genes than the other. Since reduced expression is a pathway to duplicate loss, understanding the origins of expression biases may help explain the origins of biased losses. Because we expect gene expression levels to experience stabilizing selection, our conceptual frameworks for how allopolyploid organisms form tend to assume that the new allopolyploid will show balanced expression between its subgenomes. It is then necessary to invoke phenomena such as differences in the suppression of repetitive elements to explain the observed expression imbalances. Here we show that, even for phenotypically identical diploid progenitors, the inherent kinetics of gene expression give rise to biases between the expression levels of the progenitor genes in the hybrid. Some of these biases are expected to be gene-specific and not give rise to global differences in progenitor gene expression. However, particularly in the case of allopolyploids formed from progenitors with different genome sizes, global expression biases favoring one subgenome are expected immediately on formation. Hence, expression biases are arguably the expectation upon allopolyploid formation rather than a phenomenon needing explanation. In the future, a deeper understanding of the kinetics of allopolyploidy may allow us to better understand both biases in duplicate losses and hybrid vigor.
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Affiliation(s)
- Hong An
- MU Bioinformatics and Analytics Core, University of Missouri, Columbia, Missouri, United States of America
| | - J. Chris Pires
- Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado, United States of America
| | - Gavin C. Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, United States of America
- Program in Genetics, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
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6
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Largy E, Ranz M, Gabelica V. A General Framework to Interpret Hydrogen-Deuterium Exchange Native Mass Spectrometry of G-Quadruplex DNA. J Am Chem Soc 2023; 145:26843-26857. [PMID: 38044563 DOI: 10.1021/jacs.3c09365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
G-quadruplexes (G4s) are secondary structures formed by guanine-rich oligonucleotides involved in various biological processes. However, characterizing G4s is challenging, because of their structural polymorphism. Here, we establish how hydrogen-deuterium exchange native mass spectrometry (HDX/MS) can help to characterize the G4 structures and dynamics in solution. We correlated the time range of G4 exchange to the number of guanines involved in the inner and outer tetrads. We also established relationships among exchange rates, numbers of tetrads and bound cations, and stability. The use of HDX/native MS allows for the determination of tetrads formed and assessment of G4 stability at a constant temperature. A key finding is that stable G4s exchange through local fluctuations (EX2 exchange), whereas less stable G4s also undergo exchange through partial or complete unfolding (EX1 exchange). Deconvolution of the bimodal isotope distributions resulting from EX1 exchange provides valuable insight into the kinetics of folding and unfolding processes and allows one to detect and characterize transiently unfolded intermediates, even if scarcely populated. HDX/native MS thus represents a powerful tool for a more comprehensive exploration of the folding landscapes of G4s.
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Affiliation(s)
- Eric Largy
- Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Matthieu Ranz
- Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Valérie Gabelica
- Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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7
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Smirnov E, Molínová P, Chmúrčiaková N, Vacík T, Cmarko D. Non-canonical DNA structures in the human ribosomal DNA. Histochem Cell Biol 2023; 160:499-515. [PMID: 37750997 DOI: 10.1007/s00418-023-02233-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 09/27/2023]
Abstract
Non-canonical structures (NCS) refer to the various forms of DNA that differ from the B-conformation described by Watson and Crick. It has been found that these structures are usual components of the genome, actively participating in its essential functions. The present review is focused on the nine kinds of NCS appearing or likely to appear in human ribosomal DNA (rDNA): supercoiling structures, R-loops, G-quadruplexes, i-motifs, DNA triplexes, cruciform structures, DNA bubbles, and A and Z DNA conformations. We discuss the conditions of their generation, including their sequence specificity, distribution within the locus, dynamics, and beneficial and detrimental role in the cell.
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Affiliation(s)
- Evgeny Smirnov
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic.
| | - Pavla Molínová
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Nikola Chmúrčiaková
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Tomáš Vacík
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Dušan Cmarko
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
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8
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Mathur D, Díaz SA, Hildebrandt N, Pensack RD, Yurke B, Biaggne A, Li L, Melinger JS, Ancona MG, Knowlton WB, Medintz IL. Pursuing excitonic energy transfer with programmable DNA-based optical breadboards. Chem Soc Rev 2023; 52:7848-7948. [PMID: 37872857 PMCID: PMC10642627 DOI: 10.1039/d0cs00936a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 10/25/2023]
Abstract
DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.
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Affiliation(s)
- Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland OH 44106, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
| | - Niko Hildebrandt
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
- Department of Engineering Physics, McMaster University, Hamilton, L8S 4L7, Canada
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Austin Biaggne
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Lan Li
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Mario G Ancona
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
- Department of Electrical and Computer Engineering, Florida State University, Tallahassee, FL 32310, USA
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
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9
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Marcus AH, Heussman D, Maurer J, Albrecht CS, Herbert P, von Hippel PH. Studies of Local DNA Backbone Conformation and Conformational Disorder Using Site-Specific Exciton-Coupled Dimer Probe Spectroscopy. Annu Rev Phys Chem 2023; 74:245-265. [PMID: 36696590 PMCID: PMC10590263 DOI: 10.1146/annurev-physchem-090419-041204] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The processes of genome expression, regulation, and repair require direct interactions between proteins and DNA at specific sites located at and near single-stranded-double-stranded DNA (ssDNA-dsDNA) junctions. Here, we review the application of recently developed spectroscopic methods and analyses that combine linear absorbance and circular dichroism spectroscopy with nonlinear 2D fluorescence spectroscopy to study the local conformations and conformational disorder of the sugar-phosphate backbones of ssDNA-dsDNA fork constructs that have been internally labeled with exciton-coupled cyanine (iCy3)2 dimer probes. With the application of these methods, the (iCy3)2 dimer can serve as a reliable probe of the mean local conformations and conformational distributions of the sugar-phosphate backbones of dsDNA at various critical positions. The results of our studies suggest a possible structural framework for understanding the roles of DNA breathing in driving the processes of protein-DNA complex assembly and function.
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Affiliation(s)
- Andrew H Marcus
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon, USA;
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA
- Department of Physics, University of Oregon, Eugene, Oregon, USA
| | - Dylan Heussman
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon, USA;
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA
| | - Jack Maurer
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon, USA;
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA
| | - Claire S Albrecht
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon, USA;
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
- Department of Physics, University of Oregon, Eugene, Oregon, USA
| | - Patrick Herbert
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon, USA;
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA
| | - Peter H von Hippel
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA
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10
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Ovcherenko SS, Shernyukov AV, Nasonov DM, Endutkin AV, Zharkov DO, Bagryanskaya EG. Dynamics of 8-Oxoguanine in DNA: Decisive Effects of Base Pairing and Nucleotide Context. J Am Chem Soc 2023; 145:5613-5617. [PMID: 36867834 DOI: 10.1021/jacs.2c11230] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
8-Oxo-7,8-dihydroguanine (oxoG), an abundant DNA lesion, can mispair with adenine and induce mutations. To prevent this, cells possess DNA repair glycosylases that excise either oxoG from oxoG:C pairs (bacterial Fpg, human OGG1) or A from oxoG:A mispairs (bacterial MutY, human MUTYH). Early lesion recognition steps remain murky and may include enforced base pair opening or capture of a spontaneously opened pair. We adapted the CLEANEX-PM NMR protocol to detect DNA imino proton exchange and analyzed the dynamics of oxoG:C, oxoG:A, and their undamaged counterparts in nucleotide contexts with different stacking energy. Even in a poorly stacking context, the oxoG:C pair did not open easier than G:C, arguing against extrahelical base capture by Fpg/OGG1. On the contrary, oxoG opposite A significantly populated the extrahelical state, which may assist recognition by MutY/MUTYH.
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Affiliation(s)
- Sergey S Ovcherenko
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Andrey V Shernyukov
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Dmitry M Nasonov
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anton V Endutkin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
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11
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Barclay MS, Chowdhury AU, Biaggne A, Huff JS, Wright ND, Davis PH, Li L, Knowlton WB, Yurke B, Pensack RD, Turner DB. Probing DNA structural heterogeneity by identifying conformational subensembles of a bicovalently bound cyanine dye. J Chem Phys 2023; 158:035101. [PMID: 36681650 DOI: 10.1063/5.0131795] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
DNA is a re-configurable, biological information-storage unit, and much remains to be learned about its heterogeneous structural dynamics. For example, while it is known that molecular dyes templated onto DNA exhibit increased photostability, the mechanism by which the structural dynamics of DNA affect the dye photophysics remains unknown. Here, we use femtosecond, two-dimensional electronic spectroscopy measurements of a cyanine dye, Cy5, to probe local conformations in samples of single-stranded DNA (ssDNA-Cy5), double-stranded DNA (dsDNA-Cy5), and Holliday junction DNA (HJ-DNA-Cy5). A line shape analysis of the 2D spectra reveals a strong excitation-emission correlation present in only the dsDNA-Cy5 complex, which is a signature of inhomogeneous broadening. Molecular dynamics simulations support the conclusion that this inhomogeneous broadening arises from a nearly degenerate conformer found only in the dsDNA-Cy5 complex. These insights will support future studies on DNA's structural heterogeneity.
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Affiliation(s)
- Matthew S Barclay
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Azhad U Chowdhury
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Austin Biaggne
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Jonathan S Huff
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Nicholas D Wright
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Paul H Davis
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Lan Li
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - William B Knowlton
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Bernard Yurke
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Ryan D Pensack
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Daniel B Turner
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
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12
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Shirshikov FV, Bespyatykh JA. Loop-Mediated Isothermal Amplification: From Theory to Practice. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022; 48:1159-1174. [PMID: 36590469 PMCID: PMC9788664 DOI: 10.1134/s106816202206022x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/01/2022] [Accepted: 06/17/2022] [Indexed: 12/24/2022]
Abstract
Increasing the accuracy of pathogen identification and reducing the duration of analysis remain relevant for modern molecular diagnostics up to this day. In laboratory and clinical practice, detection of pathogens mostly relies on methods of nucleic acid amplification, among which the polymerase chain reaction (PCR) is considered the "gold standard." Nevertheless, in some cases, isothermal amplification methods act as an alternative to PCR diagnostics. Upon more than thirty years of the development of isothermal DNA synthesis, the appearance of loop-mediated isothermal amplification (LAMP) has enabled new directions of in-field diagnostics of bacterial and viral infections. This review examines the key characteristics of the LAMP method and corresponding features in practice. We discuss the structure of LAMP amplicons with single-stranded loops, which have the sites for primer annealing under isothermal conditions. The latest achievements in the modification of the LAMP method are analyzed, which allow considering it as a unique platform for creating the next-generation diagnostic assays.
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Affiliation(s)
- F. V. Shirshikov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - J. A. Bespyatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
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13
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Pokhrel P, Ren K, Shen H, Mao H. Mechanical Stability of DNA Corona Phase on Gold Nanospheres. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:13569-13576. [PMID: 36305083 PMCID: PMC10318588 DOI: 10.1021/acs.langmuir.2c02251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Noncovalent adsorption of biopolymers on the surface of gold nanoparticles (AuNPs) forms a corona phase that drastically diversify AuNP functions. However, mechanical stabilities of such corona phase are still obscure, hindering the application of biopolymer-coated AuNPs. Here, using optical tweezers, we have observed, for the first time, that DNA corona phase adsorbed on a 5 nm AuNP via two (dA)21 strands in proximity can withstand an average desorption force of 40 pN, which is higher than the stall force of DNA/RNA polymerases. This suggests a new role for AuNPs to modulate replications or transcriptions after binding to prevalent poly(dA) segments in eukaryotic genomes. We have also revealed that with increasing AuNP size (1.8-10 nm), DNA corona becomes harder to remove, likely due to the larger surfaces and flatter facets on bigger AuNPs. These findings provide guidance to design AuNP corona that can withstand harsh environments for biological and materials applications.
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Affiliation(s)
- Pravin Pokhrel
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Kehao Ren
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Hao Shen
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
- Advanced materials and liquid crystal institute, Kent State University, Kent, OH 44242, USA
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14
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Huff J, Díaz S, Barclay MS, Chowdhury AU, Chiriboga M, Ellis GA, Mathur D, Patten LK, Roy SK, Sup A, Biaggne A, Rolczynski BS, Cunningham PD, Li L, Lee J, Davis PH, Yurke B, Knowlton WB, Medintz IL, Turner DB, Melinger JS, Pensack RD. Tunable Electronic Structure via DNA-Templated Heteroaggregates of Two Distinct Cyanine Dyes. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2022; 126:17164-17175. [PMID: 36268205 PMCID: PMC9575151 DOI: 10.1021/acs.jpcc.2c04336] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/08/2022] [Indexed: 06/01/2023]
Abstract
Molecular excitons are useful for applications in light harvesting, organic optoelectronics, and nanoscale computing. Electronic energy transfer (EET) is a process central to the function of devices based on molecular excitons. Achieving EET with a high quantum efficiency is a common obstacle to excitonic devices, often owing to the lack of donor and acceptor molecules that exhibit favorable spectral overlap. EET quantum efficiencies may be substantially improved through the use of heteroaggregates-aggregates of chemically distinct dyes-rather than individual dyes as energy relay units. However, controlling the assembly of heteroaggregates remains a significant challenge. Here, we use DNA Holliday junctions to assemble homo- and heterotetramer aggregates of the prototypical cyanine dyes Cy5 and Cy5.5. In addition to permitting control over the number of dyes within an aggregate, DNA-templated assembly confers control over aggregate composition, i.e., the ratio of constituent Cy5 and Cy5.5 dyes. By varying the ratio of Cy5 and Cy5.5, we show that the most intense absorption feature of the resulting tetramer can be shifted in energy over a range of almost 200 meV (1600 cm-1). All tetramers pack in the form of H-aggregates and exhibit quenched emission and drastically reduced excited-state lifetimes compared to the monomeric dyes. We apply a purely electronic exciton theory model to describe the observed progression of the absorption spectra. This model agrees with both the measured data and a more sophisticated vibronic model of the absorption and circular dichroism spectra, indicating that Cy5 and Cy5.5 heteroaggregates are largely described by molecular exciton theory. Finally, we extend the purely electronic exciton model to describe an idealized J-aggregate based on Förster resonance energy transfer (FRET) and discuss the potential advantages of such a device over traditional FRET relays.
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Affiliation(s)
- Jonathan
S. Huff
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Sebastián
A. Díaz
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Matthew S. Barclay
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Azhad U. Chowdhury
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Matthew Chiriboga
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
- Volgenau
School of Engineering, George Mason University, Fairfax, Virginia 22030, United States
| | - Gregory A. Ellis
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Divita Mathur
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Lance K. Patten
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Simon K. Roy
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Aaron Sup
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Austin Biaggne
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Brian S. Rolczynski
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Paul D. Cunningham
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Lan Li
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
- Center
for Advanced Energy Studies, Idaho
Falls, Idaho 83401, United States
| | - Jeunghoon Lee
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Paul H. Davis
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
- Center
for Advanced Energy Studies, Idaho
Falls, Idaho 83401, United States
| | - Bernard Yurke
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - William B. Knowlton
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Daniel B. Turner
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Joseph S. Melinger
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Ryan D. Pensack
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
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15
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Cervantes-Salguero K, Biaggne A, Youngsman JM, Ward BM, Kim YC, Li L, Hall JA, Knowlton WB, Graugnard E, Kuang W. Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching. Int J Mol Sci 2022; 23:ijms23147690. [PMID: 35887059 PMCID: PMC9323263 DOI: 10.3390/ijms23147690] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/08/2022] [Accepted: 07/10/2022] [Indexed: 11/18/2022] Open
Abstract
Nanoarchitectural control of matter is crucial for next-generation technologies. DNA origami templates are harnessed to accurately position single molecules; however, direct single molecule evidence is lacking regarding how well DNA origami can control the orientation of such molecules in three-dimensional space, as well as the factors affecting control. Here, we present two strategies for controlling the polar (θ) and in-plane azimuthal (ϕ) angular orientations of cyanine Cy5 single molecules tethered on rationally-designed DNA origami templates that are physically adsorbed (physisorbed) on glass substrates. By using dipolar imaging to evaluate Cy5′s orientation and super-resolution microscopy, the absolute spatial orientation of Cy5 is calculated relative to the DNA template. The sequence-dependent partial intercalation of Cy5 is discovered and supported theoretically using density functional theory and molecular dynamics simulations, and it is harnessed as our first strategy to achieve θ control for a full revolution with dispersion as small as ±4.5°. In our second strategy, ϕ control is achieved by mechanically stretching the Cy5 from its two tethers, being the dispersion ±10.3° for full stretching. These results can in principle be applied to any single molecule, expanding in this way the capabilities of DNA as a functional templating material for single-molecule orientation control. The experimental and modeling insights provided herein will help engineer similar self-assembling molecular systems based on polymers, such as RNA and proteins.
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Affiliation(s)
- Keitel Cervantes-Salguero
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
- Correspondence: (K.C.-S.); (W.K.)
| | - Austin Biaggne
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
| | - John M. Youngsman
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
| | - Brett M. Ward
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
| | - Young C. Kim
- Materials Science and Technology Division, U.S. Naval Research Laboratory, Code 6300, Washington, DC 20375, USA;
| | - Lan Li
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - John A. Hall
- Division of Research and Economic Development, Boise State University, Boise, ID 83725, USA;
| | - William B. Knowlton
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
| | - Elton Graugnard
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - Wan Kuang
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
- Correspondence: (K.C.-S.); (W.K.)
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16
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Mathur D, Rogers KE, Díaz SA, Muroski ME, Klein WP, Nag OK, Lee K, Field LD, Delehanty JB, Medintz IL. Determining the Cytosolic Stability of Small DNA Nanostructures In Cellula. NANO LETTERS 2022; 22:5037-5045. [PMID: 35580267 PMCID: PMC9233082 DOI: 10.1021/acs.nanolett.2c00917] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
DNA nanostructures have proven potential in biomedicine. However, their intracellular interactions─especially cytosolic stability─remain mostly unknown and attempts to discern this are confounded by the complexities of endocytic uptake and entrapment. Here, we bypass the endocytic uptake and evaluate the DNA structural stability directly in live cells. Commonly used DNA structures─crosshairs and a tetrahedron─were labeled with a multistep Förster resonance energy transfer dye cascade and microinjected into the cytosol of transformed and primary cells. Energy transfer loss, as monitored by fluorescence microscopy, reported the structure's direct time-resolved breakdown in cellula. The results showed rapid degradation of the DNA crosshair within 20 min, while the tetrahedron remained consistently intact for at least 1 h postinjection. Nuclease assays in conjunction with a current understanding of the tetrahedron's torsional rigidity confirmed its higher stability. Such studies can inform design parameters for future DNA nanostructures where programmable degradation rates may be required.
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Affiliation(s)
- Divita Mathur
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
| | - Katherine E Rogers
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
| | - Megan E Muroski
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
- American Society of Engineering Education, Washington, DC 20036, United States
| | - William P Klein
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
- National Research Council, Washington, DC 20001, United States
| | - Okhil K Nag
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
| | - Kwahun Lee
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
- American Society of Engineering Education, Washington, DC 20036, United States
| | - Lauren D Field
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
- National Research Council, Washington, DC 20001, United States
| | - James B Delehanty
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
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17
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Heussman D, Kittell J, von Hippel PH, Marcus AH. Temperature-dependent local conformations and conformational distributions of cyanine dimer labeled single-stranded-double-stranded DNA junctions by 2D fluorescence spectroscopy. J Chem Phys 2022; 156:045101. [PMID: 35105081 PMCID: PMC9448411 DOI: 10.1063/5.0076261] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
DNA replication and the related processes of genome expression require binding, assembly, and function of protein complexes at and near single-stranded (ss)-double-stranded (ds) DNA junctions. These central protein-DNA interactions are likely influenced by thermally induced conformational fluctuations of the DNA scaffold across an unknown distribution of functionally relevant states to provide regulatory proteins access to properly conformed DNA binding sites. Thus, characterizing the nature of conformational fluctuations and the associated structural disorder at ss-dsDNA junctions is critical for understanding the molecular mechanisms of these central biological processes. Here, we describe spectroscopic studies of model ss-dsDNA fork constructs that contain dimers of "internally labeled" cyanine (iCy3) chromophore probes that have been rigidly inserted within the sugar-phosphate backbones of the DNA strands. Our combined analyses of absorbance, circular dichroism, and two-dimensional fluorescence spectroscopy permit us to characterize the local conformational parameters and conformational distributions. We find that the DNA sugar-phosphate backbones undergo abrupt successive changes in their local conformations-initially from a right-handed and ordered DNA state to a disordered splayed-open structure and then to a disordered left-handed conformation-as the dimer probes are moved across the ss-dsDNA junction. Our results suggest that the sugar-phosphate backbones at and near ss-dsDNA junctions adopt specific position-dependent local conformations and exhibit varying extents of conformational disorder that deviate widely from the Watson-Crick structure. We suggest that some of these conformations can function as secondary-structure motifs for interaction with protein complexes that bind to and assemble at these sites.
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Affiliation(s)
| | - Justin Kittell
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, USA
| | - Peter H. von Hippel
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
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18
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Roy S, Mass OA, Kellis DL, Wilson CK, Hall JA, Yurke B, Knowlton WB. Exciton Delocalization and Scaffold Stability in Bridged Nucleotide-Substituted, DNA Duplex-Templated Cyanine Aggregates. J Phys Chem B 2021; 125:13670-13684. [PMID: 34894675 PMCID: PMC8713290 DOI: 10.1021/acs.jpcb.1c07602] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/04/2021] [Indexed: 11/28/2022]
Abstract
Molecular excitons play a foundational role in chromophore aggregates found in light-harvesting systems and offer potential applications in engineered excitonic systems. Controlled aggregation of chromophores to promote exciton delocalization has been achieved by covalently tethering chromophores to deoxyribonucleic acid (DNA) scaffolds. Although many studies have documented changes in the optical properties of chromophores upon aggregation using DNA scaffolds, more limited work has investigated how structural modifications of DNA via bridged nucleotides and chromophore covalent attachment impact scaffold stability as well as the configuration and optical behavior of attached aggregates. Here we investigated the impact of two types of bridged nucleotides, LNA and BNA, as a structural modification of duplex DNA-templated cyanine (Cy5) aggregates. The bridged nucleotides were incorporated in the domain of one to four Cy5 chromophores attached between adjacent bases of a DNA duplex. We found that bridged nucleotides increase the stability of DNA scaffolds carrying Cy5 aggregates in comparison with natural nucleotides in analogous constructs. Exciton coupling strength and delocalization in Cy5 aggregates were evaluated via steady-state absorption, circular dichroism, and theoretical modeling. Replacing natural nucleotides with bridged nucleotides resulted in a noticeable increase in the coupling strength (≥10 meV) between chromophores and increased H-like stacking behavior (i.e., more face-to-face stacking). Our results suggest that bridged nucleotides may be useful for increasing scaffold stability and coupling between DNA templated chromophores.
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Affiliation(s)
- Simon
K. Roy
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Olga A. Mass
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Donald L. Kellis
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Christopher K. Wilson
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - John A. Hall
- Division
of Research and Economic Development, Boise
State University, Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - William B. Knowlton
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
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19
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Khamis H, Rudnizky S, Melamed P, Kaplan A. Single molecule characterization of the binding kinetics of a transcription factor and its modulation by DNA sequence and methylation. Nucleic Acids Res 2021; 49:10975-10987. [PMID: 34606618 PMCID: PMC8565314 DOI: 10.1093/nar/gkab843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/04/2021] [Accepted: 09/24/2021] [Indexed: 12/14/2022] Open
Abstract
The interaction of transcription factors with their response elements in DNA is emerging as a highly complex process, whose characterization requires measuring the full distribution of binding and dissociation times in a well-controlled assay. Here, we present a single-molecule assay that exploits the thermal fluctuations of a DNA hairpin to detect the association and dissociation of individual, unlabeled transcription factors. We demonstrate this new approach by following the binding of Egr1 to its consensus motif and the three binding sites found in the promoter of the Lhb gene, and find that both association and dissociation are modulated by the 9 bp core motif and the sequences around it. In addition, CpG methylation modulates the dissociation kinetics in a sequence and position-dependent manner, which can both stabilize or destabilize the complex. Together, our findings show how variations in sequence and methylation patterns synergistically extend the spectrum of a protein's binding properties, and demonstrate how the proposed approach can provide new insights on the function of transcription factors.
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Affiliation(s)
- Hadeel Khamis
- Faculty of Biology, Technion – Israel Institute of Technology, Haifa 32000, Israel
- Faculty of Physics, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Sergei Rudnizky
- Faculty of Biology, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Philippa Melamed
- Faculty of Biology, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Ariel Kaplan
- Faculty of Biology, Technion – Israel Institute of Technology, Haifa 32000, Israel
- Faculty of Biomedical Engineering, Technion – Israel Institute of Technology, Haifa 32000, Israel
- Russell Berrie Nanotechnology Institute, Technion – Israel Institute of Technology, Haifa 32000, Israel
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20
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Huff JS, Turner DB, Mass OA, Patten LK, Wilson CK, Roy SK, Barclay MS, Yurke B, Knowlton WB, Davis PH, Pensack RD. Excited-State Lifetimes of DNA-Templated Cyanine Dimer, Trimer, and Tetramer Aggregates: The Role of Exciton Delocalization, Dye Separation, and DNA Heterogeneity. J Phys Chem B 2021; 125:10240-10259. [PMID: 34473494 PMCID: PMC8450906 DOI: 10.1021/acs.jpcb.1c04517] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
DNA-templated molecular
(dye) aggregates are a novel class of materials
that have garnered attention in a broad range of areas including light
harvesting, sensing, and computing. Using DNA to template dye aggregation
is attractive due to the relative ease with which DNA nanostructures
can be assembled in solution, the diverse array of nanostructures
that can be assembled, and the ability to precisely position dyes
to within a few Angstroms of one another. These factors, combined
with the programmability of DNA, raise the prospect of designer materials
custom tailored for specific applications. Although considerable progress
has been made in characterizing the optical properties and associated
electronic structures of these materials, less is known about their
excited-state dynamics. For example, little is known about how the
excited-state lifetime, a parameter essential to many applications,
is influenced by structural factors, such as the number of dyes within
the aggregate and their spatial arrangement. In this work, we use
a combination of transient absorption spectroscopy and global target
analysis to measure excited-state lifetimes in a series of DNA-templated
cyanine dye aggregates. Specifically, we investigate six distinct
dimer, trimer, and tetramer aggregates—based on the ubiquitous
cyanine dye Cy5—templated using both duplex and Holliday junction
DNA nanostructures. We find that these DNA-templated Cy5 aggregates
all exhibit significantly reduced excited-state lifetimes, some by
more than 2 orders of magnitude, and observe considerable variation
among the lifetimes. We attribute the reduced excited-state lifetimes
to enhanced nonradiative decay and proceed to discuss various structural
factors, including exciton delocalization, dye separation, and DNA
heterogeneity, that may contribute to the observed reduction and variability
of excited-state lifetimes. Guided by insights from structural modeling,
we find that the reduced lifetimes and enhanced nonradiative decay
are most strongly correlated with the distance between the dyes. These
results inform potential tradeoffs between dye separation, excitonic
coupling strength, and excited-state lifetime that motivate deeper
mechanistic understanding, potentially via further dye and dye template
design.
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Affiliation(s)
- Jonathan S Huff
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Daniel B Turner
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Olga A Mass
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Lance K Patten
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Christopher K Wilson
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Simon K Roy
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Matthew S Barclay
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States.,Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States.,Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Paul H Davis
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
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21
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Israels B, Albrecht CS, Dang A, Barney M, von Hippel PH, Marcus AH. Submillisecond Conformational Transitions of Short Single-Stranded DNA Lattices by Photon Correlation Single-Molecule Förster Resonance Energy Transfer. J Phys Chem B 2021; 125:9426-9440. [PMID: 34379430 DOI: 10.1021/acs.jpcb.1c04119] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Thermally driven conformational fluctuations (or "breathing") of DNA play important roles in the function and regulation of the "macromolecular machinery of genome expression." Fluctuations in double-stranded (ds) DNA are involved in the transient exposure of pathways to protein binding sites within the DNA framework, leading to the binding of regulatory proteins to single-stranded (ss) DNA templates. These interactions often require that the ssDNA sequences, as well as the proteins involved, assume transient conformations critical for successful binding. Here, we use microsecond-resolved single-molecule Förster resonance energy transfer (smFRET) experiments to investigate the backbone fluctuations of short [oligo(dT)n] templates within DNA constructs that also serve as models for ss-dsDNA junctions. Such junctions, together with the attached ssDNA sequences, are involved in interactions with the ssDNA binding (ssb) proteins that control and integrate the functions of DNA replication complexes. We analyze these data using a chemical network model based on multiorder time-correlation functions and probability distribution functions that characterize the kinetic and thermodynamic behavior of the system. We find that the oligo(dT)n tails of ss-dsDNA constructs interconvert, on submillisecond time scales, between three macrostates with distinctly different end-to-end distances. These are (i) a "compact" macrostate that represents the dominant species at equilibrium; (ii) a "partially extended" macrostate that exists as minority species; and (iii) a "highly extended" macrostate that is present in trace amounts. We propose a model for ssDNA secondary structure that advances our understanding of how spontaneously formed nucleic acid conformations may facilitate the activities of ssDNA-associating proteins.
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Affiliation(s)
- Brett Israels
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States.,Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403, United States
| | - Claire S Albrecht
- Department of Physics, Center for Optical, Molecular and Quantum Science, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Anson Dang
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Megan Barney
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Peter H von Hippel
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Andrew H Marcus
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States.,Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403, United States.,Department of Physics, Center for Optical, Molecular and Quantum Science, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
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22
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Helicase-like functions in phosphate loop containing beta-alpha polypeptides. Proc Natl Acad Sci U S A 2021; 118:2016131118. [PMID: 33846247 DOI: 10.1073/pnas.2016131118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The P-loop Walker A motif underlies hundreds of essential enzyme families that bind nucleotide triphosphates (NTPs) and mediate phosphoryl transfer (P-loop NTPases), including the earliest DNA/RNA helicases, translocases, and recombinases. What were the primordial precursors of these enzymes? Could these large and complex proteins emerge from simple polypeptides? Previously, we showed that P-loops embedded in simple βα repeat proteins bind NTPs but also, unexpectedly so, ssDNA and RNA. Here, we extend beyond the purely biophysical function of ligand binding to demonstrate rudimentary helicase-like activities. We further constructed simple 40-residue polypeptides comprising just one β-(P-loop)-α element. Despite their simplicity, these P-loop prototypes confer functions such as strand separation and exchange. Foremost, these polypeptides unwind dsDNA, and upon addition of NTPs, or inorganic polyphosphates, release the bound ssDNA strands to allow reformation of dsDNA. Binding kinetics and low-resolution structural analyses indicate that activity is mediated by oligomeric forms spanning from dimers to high-order assemblies. The latter are reminiscent of extant P-loop recombinases such as RecA. Overall, these P-loop prototypes compose a plausible description of the sequence, structure, and function of the earliest P-loop NTPases. They also indicate that multifunctionality and dynamic assembly were key in endowing short polypeptides with elaborate, evolutionarily relevant functions.
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23
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Beyerle ER, Dinpajooh M, Ji H, von Hippel PH, Marcus AH, Guenza MG. Dinucleotides as simple models of the base stacking-unstacking component of DNA 'breathing' mechanisms. Nucleic Acids Res 2021; 49:1872-1885. [PMID: 33503257 PMCID: PMC7913701 DOI: 10.1093/nar/gkab015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/22/2020] [Accepted: 01/07/2021] [Indexed: 01/11/2023] Open
Abstract
Regulatory protein access to the DNA duplex ‘interior’ depends on local DNA ‘breathing’ fluctuations, and the most fundamental of these are thermally-driven base stacking-unstacking interactions. The smallest DNA unit that can undergo such transitions is the dinucleotide, whose structural and dynamic properties are dominated by stacking, while the ion condensation, cooperative stacking and inter-base hydrogen-bonding present in duplex DNA are not involved. We use dApdA to study stacking-unstacking at the dinucleotide level because the fluctuations observed are likely to resemble those of larger DNA molecules, but in the absence of constraints introduced by cooperativity are likely to be more pronounced, and thus more accessible to measurement. We study these fluctuations with a combination of Molecular Dynamics simulations on the microsecond timescale and Markov State Model analyses, and validate our results by calculations of circular dichroism (CD) spectra, with results that agree well with the experimental spectra. Our analyses show that the CD spectrum of dApdA is defined by two distinct chiral conformations that correspond, respectively, to a Watson–Crick form and a hybrid form with one base in a Hoogsteen configuration. We find also that ionic structure and water orientation around dApdA play important roles in controlling its breathing fluctuations.
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Affiliation(s)
- Eric R Beyerle
- Institute for Fundamental Science and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Mohammadhasan Dinpajooh
- Institute for Fundamental Science and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Huiying Ji
- Center for Optical, Molecular and Quantum Science and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA.,Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Peter H von Hippel
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Andrew H Marcus
- Center for Optical, Molecular and Quantum Science and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA.,Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Marina G Guenza
- Institute for Fundamental Science and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA.,Center for Optical, Molecular and Quantum Science and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA.,Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
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24
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Menssen RJ, Kimmel GJ, Tokmakoff A. Investigation into the mechanism and dynamics of DNA association and dissociation utilizing kinetic Monte Carlo simulations. J Chem Phys 2021; 154:045101. [PMID: 33514113 DOI: 10.1063/5.0035187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In this work, we present a kinetic Markov state Monte Carlo model designed to complement temperature-jump (T-jump) infrared spectroscopy experiments probing the kinetics and dynamics of short DNA oligonucleotides. The model is designed to be accessible to experimental researchers in terms of both computational simplicity and expense while providing detailed insights beyond those provided by experimental methods. The model is an extension of a thermodynamic lattice model for DNA hybridization utilizing the formalism of the nucleation-zipper mechanism. Association and dissociation trajectories were generated utilizing the Gillespie algorithm and parameters determined via fitting the association and dissociation timescales to previously published experimental data. Terminal end fraying, experimentally observed following a rapid T-jump, in the sequence 5'-ATATGCATAT-3' was replicated by the model that also demonstrated that experimentally observed fast dynamics in the sequences 5'-C(AT)nG-3', where n = 2-6, were also due to terminal end fraying. The dominant association pathways, isolated by transition pathway theory, showed two primary motifs: initiating at or next to a G:C base pair, which is enthalpically favorable and related to the increased strength of G:C base pairs, and initiating in the center of the sequence, which is entropically favorable and related to minimizing the penalty associated with the decrease in configurational entropy due to hybridization.
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Affiliation(s)
- Ryan J Menssen
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Gregory J Kimmel
- Moffitt Cancer Center, 12902 USF Magnolia Drive, Tampa, Florida 33612, USA
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
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25
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Glazier R, Shinde P, Ogasawara H, Salaita K. Spectroscopic Analysis of a Library of DNA Tension Probes for Mapping Cellular Forces at Fluid Interfaces. ACS APPLIED MATERIALS & INTERFACES 2021; 13:2145-2164. [PMID: 33417432 DOI: 10.1021/acsami.0c09774] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Oligonucleotide-based probes offer the highest spatial resolution, force sensitivity, and molecular specificity for cellular tension sensing and have been developed to measure a variety of molecular forces mediated by individual receptors in T cells, platelets, fibroblasts, B-cells, and immortalized cancer cell lines. These fluorophore-oligonucleotide conjugate probes are designed with a stem-loop structure that engages cell receptors and reversibly unfolds due to mechanical strain. With the growth of recent work bridging molecular mechanobiology and biomaterials, there is a need for a detailed spectroscopic analysis of DNA tension probes that are used for cellular imaging. In this manuscript, we conducted an analysis of 19 DNA hairpin-based tension probe variants using molecular dynamics simulations, absorption spectroscopy, and fluorescence imaging (epifluorescence and fluorescence lifetime imaging microscopy). We find that tension probes are highly sensitive to their molecular design, including donor and acceptor proximity and pairing, DNA stem-loop structure, and conjugation chemistry. We demonstrate the impact of these design features using a supported lipid bilayer model of podosome-like adhesions. Finally, we discuss the requirements for tension imaging in various biophysical contexts and offer a series of experimental recommendations, thus providing a guide for the design and application of DNA hairpin-based molecular tension probes.
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Affiliation(s)
- Roxanne Glazier
- Wallace H. Coulter Department of Biomedical Engineering at Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Pushkar Shinde
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Hiroaki Ogasawara
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Khalid Salaita
- Wallace H. Coulter Department of Biomedical Engineering at Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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26
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Ghosh S, Casto J, Bogetti X, Arora C, Wang J, Saxena S. Orientation and dynamics of Cu 2+ based DNA labels from force field parameterized MD elucidates the relationship between EPR distance constraints and DNA backbone distances. Phys Chem Chem Phys 2020; 22:26707-26719. [PMID: 33159779 PMCID: PMC10521111 DOI: 10.1039/d0cp05016d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Pulsed electron paramagnetic resonance (EPR) based distance measurements using the recently developed Cu2+-DPA label present a promising strategy for measuring DNA backbone distance constraints. Herein we develop force field parameters for Cu2+-DPA in order to understand the features of this label at an atomic level. We perform molecular dynamics (MD) simulations using the force field parameters of Cu2+-DPA on four different DNA duplexes. The distance between the Cu2+ centers, extracted from the 2 μs MD trajectories, agrees well with the experimental distance for all the duplexes. Further analyses of the trajectory provide insight into the orientation of the Cu2+-DPA inside the duplex that leads to such agreement with experiments. The MD results also illustrate the ability of the Cu2+-DPA to report on the DNA backbone distance constraints. Furthermore, measurement of fluctuations of individual residues showed that the flexibility of Cu2+-DPA in a DNA depends on the position of the label in the duplex, and a 2 μs MD simulation is not sufficient to fully capture the experimental distribution in some cases. Finally, the MD trajectories were utilized to understand the key aspects of the double electron electron resonance (DEER) results. The lack of orientational selectivity effects of the Cu2+-DPA at Q-band frequency is rationalized in terms of fluctuations in the Cu2+ coordination environment and rotameric fluctuations of the label linker. Overall, a combination of EPR and MD simulations based on the Cu2+-DPA labelling strategy can contribute towards understanding changes in DNA backbone conformations during protein-DNA interactions.
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Affiliation(s)
- Shreya Ghosh
- Department of Chemistry, University of Pittsburgh, PA 15260, USA.
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27
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Bandyopadhyay D, Mishra PP. Real-Time Monitoring of the Multistate Conformational Dynamics of Polypurine Reverse Hoogsteen Hairpin To Capture Their Triplex-Affinity for Gene Silencing by smFRET Microspectroscopy. J Phys Chem B 2020; 124:8230-8239. [DOI: 10.1021/acs.jpcb.0c05493] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Debolina Bandyopadhyay
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, HBNI Mumbai, 1/AF Bidhannagar, Kolkata 700064, India
| | - Padmaja P. Mishra
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, HBNI Mumbai, 1/AF Bidhannagar, Kolkata 700064, India
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28
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Li S, Li P, Ge M, Wang H, Cheng Y, Li G, Huang Q, He H, Cao C, Lin D, Yang L. Elucidation of leak-resistance DNA hybridization chain reaction with universality and extensibility. Nucleic Acids Res 2020; 48:2220-2231. [PMID: 32020194 PMCID: PMC7049695 DOI: 10.1093/nar/gkaa016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/30/2019] [Accepted: 01/23/2020] [Indexed: 12/14/2022] Open
Abstract
Hybridization chain reaction (HCR) was a significant discovery for the development of nanoscale materials and devices. One key challenge for HCR is the vulnerability to background leakage in the absence of the initiator. Here, we systematically analyze the sources of leakage and refine leak-resistant rule by using molecular thermodynamics and dynamics, biochemical and biophysical methods. Transient melting of DNA hairpin is revealed to be the underlying cause of leakage and that this can be mitigated through careful consideration of the sequence thermodynamics. The transition threshold of the energy barrier is proposed as a testing benchmark of leak-resistance DNA hairpins. The universal design of DNA hairpins is illustrated by the analysis of hsa-miR-21-5p as biomarker when used in conjunction with surface-enhanced Raman spectroscopy. We further extend the strategy for specific signal amplification of miRNA homologs. Significantly, it possibly provides a practical route to improve the accuracy of DNA self-assembly for signal amplification, and that could facilitate the development of sensors for the sensitive detection of interest molecules in biotechnology and clinical medicine.
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Affiliation(s)
- Shaofei Li
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China.,School of Life Science, Anhui University, Hefei, Anhui 230601, China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Pan Li
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Meihong Ge
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Hongzhi Wang
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China.,Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Yizhuang Cheng
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Gan Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Huan He
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Chentai Cao
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Dongyue Lin
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Liangbao Yang
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China.,Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui 230031, China
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29
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Langeberg CJ, Welch WRW, McGuire JV, Ashby A, Jackson AD, Chapman EG. Biochemical Characterization of Yeast Xrn1. Biochemistry 2020; 59:1493-1507. [PMID: 32251580 DOI: 10.1021/acs.biochem.9b01035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Messenger RNA degradation is an important component of overall gene expression. During the final step of eukaryotic mRNA degradation, exoribonuclease 1 (Xrn1) carries out 5' → 3' processive, hydrolytic degradation of RNA molecules using divalent metal ion catalysis. To initiate studies of the 5' → 3' RNA decay machinery in our lab, we expressed a C-terminally truncated version of Saccharomyces cerevisiae Xrn1 and explored its enzymology using a second-generation, time-resolved fluorescence RNA degradation assay. Using this system, we quantitatively explored Xrn1's preference for 5'-monophosphorylated RNA substrates, its pH dependence, and the importance of active site mutations in the molecule's conserved catalytic core. Furthermore, we explore Xrn1's preference for RNAs containing a 5' single-stranded region both in an intermolecular hairpin structure and in an RNA-DNA hybrid duplex system. These results both expand and solidify our understanding of Xrn1, a centrally important enzyme whose biochemical properties have implications in numerous RNA degradation and processing pathways.
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Affiliation(s)
- Conner J Langeberg
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - William R W Welch
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - John V McGuire
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Alison Ashby
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Alexander D Jackson
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Erich G Chapman
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
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30
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Lysne D, Jones K, Stosius A, Hachigian T, Lee J, Graugnard E. Availability-Driven Design of Hairpin Fuels and Small Interfering Strands for Leakage Reduction in Autocatalytic Networks. J Phys Chem B 2020; 124:3326-3335. [PMID: 32223244 DOI: 10.1021/acs.jpcb.0c01229] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA-based circuits and computational tools offer great potential for advanced biomedical and technological applications. However, leakage, which is the production of an output in the absence of an input, widely exists in DNA network. As a new approach to leakage reduction, this study utilizes availability to reduce leakage in an entropy-driven autocatalytic DNA reaction networks. Here, we report the performance improvements resulting from direct tailoring of fuel strand availability through two novel approaches: (1) the addition of interfering domains to fuel strands, and (2) the introduction of separate small interfering strands. The best performing fuel designs resulted in increased performance ratios of up to 22%. Employing small interfering strands (5-12 nucleotides (nt)) improved the performance ratios by up to 21%. Furthermore, the stability of the network using either leakage reduction method matched well with computed availability and experimental results showing Spearman correlation coefficients of -0.84 for modified fuel strands and -0.92 for small interfering strands.
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Affiliation(s)
- Drew Lysne
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Drive, Boise, Idaho 83725, United States
| | - Kailee Jones
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Drive, Boise, Idaho 83725, United States
| | - Alma Stosius
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Drive, Boise, Idaho 83725, United States
| | - Tim Hachigian
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Drive, Boise, Idaho 83725, United States
| | - Jeunghoon Lee
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Drive, Boise, Idaho 83725, United States.,Department of Chemistry and Biochemistry, Boise State University, 1910 University Drive, Boise, Idaho 83725, United States
| | - Elton Graugnard
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Drive, Boise, Idaho 83725, United States
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31
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Savva R. The Essential Co-Option of Uracil-DNA Glycosylases by Herpesviruses Invites Novel Antiviral Design. Microorganisms 2020; 8:microorganisms8030461. [PMID: 32214054 PMCID: PMC7143999 DOI: 10.3390/microorganisms8030461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/20/2020] [Accepted: 03/21/2020] [Indexed: 01/10/2023] Open
Abstract
Vast evolutionary distances separate the known herpesviruses, adapted to colonise specialised cells in predominantly vertebrate hosts. Nevertheless, the distinct herpesvirus families share recognisably related genomic attributes. The taxonomic Family Herpesviridae includes many important human and animal pathogens. Successful antiviral drugs targeting Herpesviridae are available, but the need for reduced toxicity and improved efficacy in critical healthcare interventions invites novel solutions: immunocompromised patients presenting particular challenges. A conserved enzyme required for viral fitness is Ung, a uracil-DNA glycosylase, which is encoded ubiquitously in Herpesviridae genomes and also host cells. Research investigating Ung in Herpesviridae dynamics has uncovered an unexpected combination of viral co-option of host Ung, along with remarkable Subfamily-specific exaptation of the virus-encoded Ung. These enzymes apparently play essential roles, both in the maintenance of viral latency and during initiation of lytic replication. The ubiquitously conserved Ung active site has previously been explored as a therapeutic target. However, exquisite selectivity and better drug-like characteristics might instead be obtained via targeting structural variations within another motif of catalytic importance in Ung. The motif structure is unique within each Subfamily and essential for viral survival. This unique signature in highly conserved Ung constitutes an attractive exploratory target for the development of novel beneficial therapeutics.
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Affiliation(s)
- Renos Savva
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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32
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Largy E, Gabelica V. Native Hydrogen/Deuterium Exchange Mass Spectrometry of Structured DNA Oligonucleotides. Anal Chem 2020; 92:4402-4410. [PMID: 32039580 DOI: 10.1021/acs.analchem.9b05298] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although solution hydrogen-deuterium exchange mass spectrometry (HDX/MS) is well-established for the analysis of the structure and dynamics of proteins, it is currently not exploited for nucleic acids. Here we used DNA G-quadruplex structures as model systems to demonstrate that DNA oligonucleotides are amenable to in-solution HDX/MS in native conditions. In trimethylammonium acetate solutions and in soft source conditions, the protonated phosphate groups are fully back-exchanged in the source, while the exchanged nucleobases remain labeled without detectable back-exchange. As a result, the exchange rates depend strongly on the secondary structure (hydrogen bonding status) of the oligonucleotides, but neither on their charge state nor on the presence of nonspecific adducts. We show that native mass spectrometry methods can measure these exchange rates on the second to the day time scale with high precision. Such combination of HDX with native MS opens promising avenues for the analysis of the structural and biophysical properties of oligonucleotides and their complexes.
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Affiliation(s)
- Eric Largy
- University of Bordeaux, INSERM and CNRS, Laboratoires Acides Nucléiques: Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33600 Pessac, France
| | - Valérie Gabelica
- University of Bordeaux, INSERM and CNRS, Laboratoires Acides Nucléiques: Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33600 Pessac, France
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33
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McDaniel YZ, Wang D, Love RP, Adolph MB, Mohammadzadeh N, Chelico L, Mansky LM. Deamination hotspots among APOBEC3 family members are defined by both target site sequence context and ssDNA secondary structure. Nucleic Acids Res 2020; 48:1353-1371. [PMID: 31943071 PMCID: PMC7026630 DOI: 10.1093/nar/gkz1164] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 12/26/2022] Open
Abstract
The human apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3 (APOBEC3, A3) family member proteins can deaminate cytosines in single-strand (ss) DNA, which restricts human immunodeficiency virus type 1 (HIV-1), retrotransposons, and other viruses such as hepatitis B virus, but can cause a mutator phenotype in many cancers. While structural information exists for several A3 proteins, the precise details regarding deamination target selection are not fully understood. Here, we report the first parallel, comparative analysis of site selection of A3 deamination using six of the seven purified A3 member enzymes, oligonucleotides having 5'TC3' or 5'CT3' dinucleotide target sites, and different flanking bases within diverse DNA secondary structures. A3A, A3F and A3H were observed to have strong preferences toward the TC target flanked by A or T, while all examined A3 proteins did not show a preference for a TC target flanked by a G. We observed that the TC target was strongly preferred in ssDNA regions rather than dsDNA, loop or bulge regions, with flanking bases influencing the degree of preference. CT was also shown to be a potential deamination target. Taken together, our observations provide new insights into A3 enzyme target site selection and how A3 mutagenesis impacts mutation rates.
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Affiliation(s)
- Yumeng Z McDaniel
- Veterinary Medicine Graduate Program, University of Minnesota, Minneapolis, MN 55455 USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455 USA
| | - Dake Wang
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455 USA
- Pharmacology Graduate Program, University of Minnesota, Minneapolis, MN 55455 USA
| | - Robin P Love
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Madison B Adolph
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Nazanin Mohammadzadeh
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Linda Chelico
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Louis M Mansky
- Veterinary Medicine Graduate Program, University of Minnesota, Minneapolis, MN 55455 USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455 USA
- Pharmacology Graduate Program, University of Minnesota, Minneapolis, MN 55455 USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455 USA
- Department of Microbiology & Immunology, University of Minnesota, Minneapolis, MN 55455 USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455 USA
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Abstract
Graphene liquid-cell electron microscopy reveals intermediate states of self-assembly—in this example, DNA when single strands form double helices. Molecules are observed for up to minutes at a time without apparent beam damage when electron energy and electron dose are low. Simultaneous in situ single-molecule imaging of conformational adaptations and motion gives more comprehensive understanding of self-assembly successes, failures, and error-producing mechanisms, confirming some earlier predictions and also presenting surprises. Loop intermediates were observed to facilitate error correction. Hybridization events accompany enhanced translational mobility and mechanistically specific persistent rotation. The information obtained goes beyond that from other single-molecule methods. Traditional single-molecule methods do not report whole-molecule kinetic conformations, and their adaptive shape changes during the process of self-assembly. Here, using graphene liquid-cell electron microscopy with electrons of low energy at low dose, we show that this approach resolves the time dependence of conformational adaptations of macromolecules for times up to minutes, the resolution determined by motion blurring, with DNA as the test case. Single-stranded DNA molecules are observed in real time as they hybridize near the solid surface to form double-stranded helices; we contrast molecules the same length but differing in base-pair microstructure (random, blocky, and palindromic hairpin) whose key difference is that random sequences possess only one stable final state, but the others offer metastable intermediate structures. Hybridization is observed to couple with enhanced translational mobility and torsion-induced rotation of the molecule. Prevalent transient loops are observed in error-correction processes. Transient melting and other failed encounters are observed in the competitive binding of multiple single-stranded molecules. Among the intermediate states reported here, some were predicted but not observed previously, and the high incidence of looping and enhanced mobility come as surprises. The error-producing mechanisms, failed encounters, and transient intermediate states would not be easily resolved by traditional single-molecule methods. The methods generalize to visualize motions and interactions of other organic macromolecules.
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Sicard F, Destainville N, Rousseau P, Tardin C, Manghi M. Dynamical control of denaturation bubble nucleation in supercoiled DNA minicircles. Phys Rev E 2020; 101:012403. [PMID: 32069623 DOI: 10.1103/physreve.101.012403] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Indexed: 06/10/2023]
Abstract
We examine the behavior of supercoiled DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, in which supercoiling favors thermally assisted DNA denaturation bubbles of nanometer size and controls their lifetime. Mesoscopic modeling and accelerated dynamics simulations allow us to overcome the limitations of atomistic simulations encountered in such systems, and offer detailed insight into the thermodynamic and dynamical properties associated with the nucleation and closure mechanisms of long-lived thermally assisted denaturation bubbles which do not stem from bending- or torque-driven stress. Suitable tuning of the degree of supercoiling and size of specifically designed microDNA is observed to lead to the control of opening characteristic times in the millisecond range, and closure characteristic times ranging over well distinct timescales, from microseconds to several minutes. We discuss how our results can be seen as a dynamical bandwidth which might enhance selectivity for specific DNA binding proteins.
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Affiliation(s)
- François Sicard
- Department of Chemistry, King's College London, SE1 1DB London, United Kingdom
| | - Nicolas Destainville
- Laboratoire de Physique Théorique, IRSAMC, Université de Toulouse, CNRS, UPS, France
| | - Philippe Rousseau
- Laboratoire de Microbiologie et Génetique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Catherine Tardin
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, UPS, France
| | - Manoel Manghi
- Laboratoire de Physique Théorique, IRSAMC, Université de Toulouse, CNRS, UPS, France
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36
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Abstract
The opening of a Watson-Crick double helix is required for crucial cellular processes, including replication, repair, and transcription. It has long been assumed that RNA or DNA base pairs are broken by the concerted symmetric movement of complementary nucleobases. By analyzing thousands of base-pair opening and closing events from molecular simulations, here, we uncover a systematic stepwise process driven by the asymmetric flipping-out probability of paired nucleobases. We demonstrate experimentally that such asymmetry strongly biases the unwinding efficiency of DNA helicases toward substrates that bear highly dynamic nucleobases, such as pyrimidines, on the displaced strand. Duplex substrates with identical thermodynamic stability are thus shown to be more easily unwound from one side than the other, in a quantifiable and predictable manner. Our results indicate a possible layer of gene regulation coded in the direction-dependent unwindability of the double helix.
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Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects. Proc Natl Acad Sci U S A 2019; 116:17169-17174. [PMID: 31413203 PMCID: PMC6717297 DOI: 10.1073/pnas.1909122116] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The main stabilizer of the DNA double helix is not the base-pair hydrogen bonds but coin-pile stacking of base pairs, whose hydrophobic cohesion, requiring abundant water, indirectly makes the DNA interior dry so that hydrogen bonds can exert full recognition power. We report that certain semihydrophobic agents depress the stacking energy (measurable in single-molecule experiments), leading to transiently occurring holes in the base-pair stack (monitorable via binding of threading intercalators). Similar structures observed in DNA complexes with RecA and Rad51, and previous observations of spontaneous strand exchange catalyzed in semihydrophobic model systems, make us propose that some hydrophobic protein residues may have roles in catalyzing homologous recombination. We speculate that hydrophobic catalysis is a general phenomenon in DNA enzymes. Hydrophobic base stacking is a major contributor to DNA double-helix stability. We report the discovery of specific unstacking effects in certain semihydrophobic environments. Water-miscible ethylene glycol ethers are found to modify structure, dynamics, and reactivity of DNA by mechanisms possibly related to a biologically relevant hydrophobic catalysis. Spectroscopic data and optical tweezers experiments show that base-stacking energies are reduced while base-pair hydrogen bonds are strengthened. We propose that a modulated chemical potential of water can promote “longitudinal breathing” and the formation of unstacked holes while base unpairing is suppressed. Flow linear dichroism in 20% diglyme indicates a 20 to 30% decrease in persistence length of DNA, supported by an increased flexibility in single-molecule nanochannel experiments in poly(ethylene glycol). A limited (3 to 6%) hyperchromicity but unaffected circular dichroism is consistent with transient unstacking events while maintaining an overall average B-DNA conformation. Further information about unstacking dynamics is obtained from the binding kinetics of large thread-intercalating ruthenium complexes, indicating that the hydrophobic effect provides a 10 to 100 times increased DNA unstacking frequency and an “open hole” population on the order of 10−2 compared to 10−4 in normal aqueous solution. Spontaneous DNA strand exchange catalyzed by poly(ethylene glycol) makes us propose that hydrophobic residues in the L2 loop of recombination enzymes RecA and Rad51 may assist gene recombination via modulation of water activity near the DNA helix by hydrophobic interactions, in the manner described here. We speculate that such hydrophobic interactions may have catalytic roles also in other biological contexts, such as in polymerases.
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Pannunzio NR, Lieber MR. Constitutively active Artemis nuclease recognizes structures containing single-stranded DNA configurations. DNA Repair (Amst) 2019; 83:102676. [PMID: 31377101 DOI: 10.1016/j.dnarep.2019.102676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 01/03/2023]
Abstract
The Artemis nuclease recognizes and endonucleolytically cleaves at single-stranded to double-stranded DNA (ss/dsDNA) boundaries. It is also a key enzyme in the non-homologous end joining (NHEJ) DNA double-strand break repair pathway. Previously, a truncated form, Artemis-413, was developed that is constitutively active both in vitro and in vivo. Here, we use this constitutively active form of Artemis to detect DNA structures with ss/dsDNA boundaries that arise under topological stress. Topoisomerases prevent abnormal levels of torsional stress through modulation of positive and negative supercoiling. We show that overexpression of Artemis-413 in yeast cells carrying genetic mutations that ablate topoisomerase activity have an increased frequency of DNA double-strand breaks (DSBs). Based on the biochemical activity of Artemis, this suggests an increase in ss/dsDNA-containing structures upon increased torsional stress, with DSBs arising due to Artemis cutting at these ss/dsDNA structures. Camptothecin targets topoisomerase IB (Top1), and cells treated with camptothecin show increased DSBs. We find that expression of Artemis-413 in camptothecin-treated cells leads to a reduction in DSBs, the opposite of what we find with topoisomerase genetic mutations. This contrast between outcomes not only confirms that topoisomerase mutation and topoisomerase poisoning have distinct effects on cells, but also demonstrates the usefulness of Artemis-413 to study changes in DNA structure.
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Affiliation(s)
- Nicholas R Pannunzio
- Department of Pathology, Keck School of Medicine of University of Southern California, Los Angeles, CA, 90089, USA; Norris Comprehensive Cancer Center, Keck School of Medicine of University of Southern California, Los Angeles, CA, 90089, USA.
| | - Michael R Lieber
- Department of Pathology, Keck School of Medicine of University of Southern California, Los Angeles, CA, 90089, USA; Norris Comprehensive Cancer Center, Keck School of Medicine of University of Southern California, Los Angeles, CA, 90089, USA; Department of Biological Sciences, Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90089, USA.
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39
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Brunet A, Salomé L, Rousseau P, Destainville N, Manghi M, Tardin C. How does temperature impact the conformation of single DNA molecules below melting temperature? Nucleic Acids Res 2019; 46:2074-2081. [PMID: 29294104 PMCID: PMC5829751 DOI: 10.1093/nar/gkx1285] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/19/2017] [Indexed: 01/26/2023] Open
Abstract
The double stranded DNA molecule undergoes drastic structural changes during biological processes such as transcription during which it opens locally under the action of RNA polymerases. Local spontaneous denaturation could contribute to this mechanism by promoting it. Supporting this idea, different biophysical studies have found an unexpected increase in the flexibility of DNA molecules with various sequences as a function of the temperature, which would be consistent with the formation of a growing number of locally denatured sequences. Here, we take advantage of our capacity to detect subtle changes occurring on DNA by using high throughput tethered particle motion to question the existence of bubbles in double stranded DNA under physiological salt conditions through their conformational impact on DNA molecules ranging from several hundreds to thousands of base pairs. Our results strikingly differ from previously published ones, as we do not detect any unexpected change in DNA flexibility below melting temperature. Instead, we measure a bending modulus that remains stable with temperature as expected for intact double stranded DNA.
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Affiliation(s)
- Annaël Brunet
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France.,Laboratoire de Physique Théorique (IRSAMC), Université de Toulouse, CNRS, Toulouse, France
| | - Laurence Salomé
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France
| | - Philippe Rousseau
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Nicolas Destainville
- Laboratoire de Physique Théorique (IRSAMC), Université de Toulouse, CNRS, Toulouse, France
| | - Manoel Manghi
- Laboratoire de Physique Théorique (IRSAMC), Université de Toulouse, CNRS, Toulouse, France
| | - Catherine Tardin
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France
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40
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Heussman D, Kittell J, Kringle L, Tamimi A, von Hippel PH, Marcus AH. Measuring local conformations and conformational disorder of (Cy3) 2 dimer labeled DNA fork junctions using absorbance, circular dichroism and two-dimensional fluorescence spectroscopy. Faraday Discuss 2019; 216:211-235. [PMID: 31038134 DOI: 10.1039/c8fd00245b] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The sugar-phosphate backbone of DNA near single-stranded (ss)-double-stranded (ds) junctions likely fluctuates within a broad distribution of conformations to permit the proper binding of genome regulatory proteins that function at these sites. In this work we use absorbance, circular dichroism (CD), and two-dimensional fluorescence spectroscopy (2DFS) to study the local conformations and conformational disorder within chromophore-labeled DNA constructs. These constructs employ dimers of the fluorescent chromophore Cy3 that are site-specifically incorporated into the sugar-phosphate backbones of DNA strands at ss-ds DNA fork junctions. We show that these data can be analyzed to determine the local conformations of the (Cy3)2 dimer, and the degree of conformational disorder. Our analysis employs an essential-state Holstein-Frenkel Hamiltonian model, which takes into account the internal electronic-vibrational motions within each Cy3 chromophore, and the resonant electronic interaction that couples the two chromophores together. Our results suggest that this approach may be applied generally to understand local backbone conformation and conformational disorder at ss-ds DNA fork junctions.
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Affiliation(s)
- Dylan Heussman
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, OR 97403, USA.
| | - Justin Kittell
- Department of Physics, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, OR 97403, USA
| | - Loni Kringle
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, OR 97403, USA.
| | - Amr Tamimi
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, OR 97403, USA.
| | - Peter H von Hippel
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Andrew H Marcus
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, OR 97403, USA. and Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
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41
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Mandal S, Kawamoto Y, Yue Z, Hashiya K, Cui Y, Bando T, Pandey S, Hoque ME, Hossain MA, Sugiyama H, Mao H. Submolecular dissection reveals strong and specific binding of polyamide-pyridostatin conjugates to human telomere interface. Nucleic Acids Res 2019; 47:3295-3305. [PMID: 30820532 PMCID: PMC6468309 DOI: 10.1093/nar/gkz135] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/13/2019] [Accepted: 02/26/2019] [Indexed: 01/20/2023] Open
Abstract
To modulate biological functions, G-quadruplexes in genome are often non-specifically targeted by small molecules. Here, specificity is increased by targeting both G-quadruplex and its flanking duplex DNA in a naturally occurring dsDNA-ssDNA telomere interface using polyamide (PA) and pyridostatin (PDS) conjugates (PA-PDS). We innovated a single-molecule assay in which dissociation constant (Kd) of the conjugate can be separately evaluated from the binding of either PA or PDS. We found Kd of 0.8 nM for PA-PDS, which is much lower than PDS (Kd ∼ 450 nM) or PA (Kd ∼ 35 nM). Functional assays further indicated that the PA-PDS conjugate stopped the replication of a DNA polymerase more efficiently than PA or PDS. Our results not only established a new method to dissect multivalent binding into actions of individual monovalent components, they also demonstrated a strong and specific G-quadruplex targeting strategy by conjugating highly specific duplex-binding molecules with potent quadruplex ligands.
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Affiliation(s)
- Shankar Mandal
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Zhizhou Yue
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yunxi Cui
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Shankar Pandey
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | | | | | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell–Material Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Hanbin Mao
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
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42
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Melittin Exerts Beneficial Effects on Paraquat-Induced Lung Injuries In Mice by Modifying Oxidative Stress and Apoptosis. Molecules 2019; 24:molecules24081498. [PMID: 30995821 PMCID: PMC6514788 DOI: 10.3390/molecules24081498] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/05/2019] [Accepted: 04/08/2019] [Indexed: 12/21/2022] Open
Abstract
Melittin (MEL) is a 26-amino acid peptide with numerous biological activities. Paraquat (PQ) is one of the most widely used herbicides, although it is extremely toxic to humans. To date, PQ poisoning has no effective treatment, and therefore the current study aimed to assess for the first time the possible effects of MEL on PQ-induced lung injuries in mice. Mice received a single intraperitoneal (IP) injection of PQ (30 mg/kg), followed by IP treatment with MEL (0.1 and 0.5 mg/kg) twice per week for four consecutive weeks. Histological alterations, oxidative stress, and apoptosis in the lungs were studied. Hematoxylin and eosin (H&E) staining indicated that MEL markedly reduced lung injuries induced by PQ. Furthermore, treatment with MEL increased superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) activity, and decreased malonaldehyde (MDA) and nitric oxide (NO) levels in lung tissue homogenates. Moreover, immunohistochemical staining showed that B-cell lymphoma-2 (Bcl-2) and survivin expressions were upregulated after MEL treatment, while Ki-67 expression was downregulated. The high dose of MEL was more effective than the low dose in all experiments. In summary, MEL efficiently reduced PQ-induced lung injuries in mice. Specific pharmacological examinations are required to determine the effectiveness of MEL in cases of human PQ poisoning.
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43
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Yang C, Kim E, Lim M, Pak Y. Computational Probing of Watson-Crick/Hoogsteen Breathing in a DNA Duplex Containing N1-Methylated Adenine. J Chem Theory Comput 2018; 15:751-761. [PMID: 30501194 DOI: 10.1021/acs.jctc.8b00936] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA breathing is a local conformational fluctuation spontaneously occurring in double-stranded DNAs. In particular, the possibility of individual base pairs (bps) in duplex DNA to flip between alternate bp modes, i.e., Watson-Crick (WC)-like and Hoogsteen (HG)-like, at relevant time scales has impacted DNA research fields for many years. In this study, to computationally probe effects of chemical modification on the DNA breathing, we present a free energy landscape of spontaneous thermal transitions between WC and HG bps in a free DNA duplex containing N1-methylated adenine (m1A). For the current free energy computation, a variant of well-tempered metadynamics simulation was extensively performed for a total of 40 μs to produce free energy surfaces. The free energy profile indicated that, upon the chemical modification of adenine, the HG bp (m1A·T) was located in the most favorable conformation (96.7%); however, the canonical WC bp (m1A·T) was distorted into two WC-like bps of WC* (2.8%) and WC** (0.5%). The conformational exchange between these two minor WC-like bps occurs with the first hundred nanoseconds. The transition between WC-like and HG bp features multiple transition pathways displaying various extents of base flipping in combination with glycosidic rotation. Analysis of the simulated ensemble showed that the m1A-induced changes of the backbone and sugar pucker were in a reasonable agreement with previous results inferred from NMR experiments. Also, this study revealed that the formation of the stable HG bp upon the mutation alters the characteristics of dynamic fluctuations of the neighboring WC residues of m1A. We expect this simulation approach to be a robust computational scheme to complement and guide future high-resolution experiments on many outstanding issues of duplex DNA breathing.
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Affiliation(s)
- Changwon Yang
- Department of Chemistry and Institute of Functional Materials , Pusan National University , Busan 46241 , South Korea
| | - Eunae Kim
- College of Pharmacy , Chosun University , Gwangju 61452 , South Korea
| | - Manho Lim
- Department of Chemistry and Institute of Functional Materials , Pusan National University , Busan 46241 , South Korea
| | - Youngshang Pak
- Department of Chemistry and Institute of Functional Materials , Pusan National University , Busan 46241 , South Korea
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44
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Johnson RP, Perera RT, Fleming AM, Burrows CJ, White HS. Energetics of base flipping at a DNA mismatch site confined at the latch constriction of α-hemolysin. Faraday Discuss 2018; 193:471-485. [PMID: 27711888 DOI: 10.1039/c6fd00058d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Unique, two-state modulating current signatures are observed when a cytosine-cytosine mismatch pair is confined at the 2.4 nm latch constriction of the α-hemolysin (αHL) nanopore. We have previously speculated that the modulation is due to base flipping at the mismatch site. Base flipping is a biologically significant mechanism in which a single base is rotated out of the DNA helical stack by 180°. It is the mechanism by which enzymes are able to access bases for repair operations without disturbing the global structure of the helix. Here, temperature dependent ion channel recordings of individual double-stranded DNA duplexes inside αHL are used to derive thermodynamic (ΔH, ΔS) and kinetic (EA) parameters for base flipping of a cytosine at an unstable cytosine-cytosine mismatch site. The measured activation energy for flipping a cytosine located at the latch of αHL out of the helix (18 ± 1 kcal mol-1) is comparable to that previously reported for base flipping at mismatch sites from NMR measurements and potential mean force calculations. We propose that the αHL nanopore is a useful tool for measuring conformational changes in dsDNA at the single molecule level.
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Affiliation(s)
- Robert P Johnson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Rukshan T Perera
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Henry S White
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
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45
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Non-dissociative structural transitions of the Watson-Crick and reverse Watson-Crick А·Т DNA base pairs into the Hoogsteen and reverse Hoogsteen forms. Sci Rep 2018; 8:10371. [PMID: 29991693 PMCID: PMC6039495 DOI: 10.1038/s41598-018-28636-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/21/2018] [Indexed: 11/08/2022] Open
Abstract
In this study it was theoretically shown that discovered by us recently (Brovarets' et al., Frontiers in Chemistry, 2018, 6:8; doi: 10.3389/fchem.2018.00008) high-energetical, significantly non-planar (symmetry C1), short-lived wobbled conformers of the classical Watson-Crick А·Т(WC), reverse Watson-Crick А·Т(rWC), Hoogsteen А·Т(Н) and reverse Hoogsteen А·Т(rН) DNA base pairs are the intermediates of their pairwise А∙Т(WC)/А∙Т(rWC) ↔ А∙Т(H)/А∙Т(rH) conformational transformations. These transitions do not require for their realization the energy-consumable anisotropic rotation of the amino group of A around the exocyclic C6-N6 bond. They are controlled by the non-planar transition states with quasi-orthogonal geometry (symmetry C1) joined by the single intermolecular (Т)N3H···N6(А) H-bond (~4 kcal∙mol-1). The Gibbs free energies of activation for these non-dissociative, dipole-active conformational transitions consist 7.33 and 7.81 kcal∙mol-1, accordingly. Quantum-mechanical (QM) calculations in combination with Bader's quantum theory of "Atoms in Molecules" (QTAIM) have been performed at the MP2/aug-cc-pVDZ//B3LYP/6-311++G(d,p) level of QM theory in the continuum with ε = 4 under normal conditions.
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46
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Kringle L, Sawaya NPD, Widom J, Adams C, Raymer MG, Aspuru-Guzik A, Marcus AH. Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA. J Chem Phys 2018; 148:085101. [PMID: 29495791 DOI: 10.1063/1.5020084] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Understanding the properties of electronically interacting molecular chromophores, which involve internally coupled electronic-vibrational motions, is important to the spectroscopy of many biologically relevant systems. Here we apply linear absorption, circular dichroism, and two-dimensional fluorescence spectroscopy to study the polarized collective excitations of excitonically coupled cyanine dimers (Cy3)2 that are rigidly positioned within the opposing sugar-phosphate backbones of the double-stranded region of a double-stranded (ds)-single-stranded (ss) DNA fork construct. We show that the exciton-coupling strength of the (Cy3)2-DNA construct can be systematically varied with temperature below the ds-ss DNA denaturation transition. We interpret spectroscopic measurements in terms of the Holstein vibronic dimer model, from which we obtain information about the local conformation of the (Cy3)2 dimer, as well as the degree of static disorder experienced by the Cy3 monomer and the (Cy3)2 dimer probe locally within their respective DNA duplex environments. The properties of the (Cy3)2-DNA construct we determine suggest that it may be employed as a useful model system to test fundamental concepts of protein-DNA interactions and the role of electronic-vibrational coherence in electronic energy migration within exciton-coupled bio-molecular arrays.
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Affiliation(s)
- Loni Kringle
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403, USA
| | - Nicolas P D Sawaya
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Julia Widom
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Carson Adams
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403, USA
| | - Michael G Raymer
- Department of Physics, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403, USA
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Andrew H Marcus
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403, USA
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47
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Brovarets' OO, Tsiupa KS, Hovorun DM. Surprising Conformers of the Biologically Important A·T DNA Base Pairs: QM/QTAIM Proofs. Front Chem 2018; 6:8. [PMID: 29536003 PMCID: PMC5835050 DOI: 10.3389/fchem.2018.00008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 01/11/2018] [Indexed: 11/22/2022] Open
Abstract
For the first time novel high-energy conformers-A·T(wWC) (5.36), A·T(wrWC) (5.97), A·T(wH) (5.78), and A·T(wrH) (ΔG = 5.82 kcal·mol-1) (See Graphical Abstract) were revealed for each of the four biologically important A·T DNA base pairs - Watson-Crick A·T(WC), reverse Watson-Crick A·T(rWC), Hoogsteen A·T(H) and reverse Hoogsteen A·T(rH) at the MP2/aug-cc-pVDZ//B3LYP/6-311++G(d,p) level of quantum-mechanical theory in the continuum with ε = 4 under normal conditions. Each of these conformers possesses substantially non-planar wobble (w) structure and is stabilized by the participation of the two anti-parallel N6H/N6H'…O4/O2 and N3H…N6 H-bonds, involving the pyramidalized amino group of the A DNA base as an acceptor and a donor of the H-bonding. The transition states - TSA·T(WC)↔A·T(wWC), TSA·T(rWC)↔A·T(wrWC), TSA·T(H)↔A·T(wH), and TSA·T(rH)↔A·T(wrH), controlling the dipole-active transformations of the conformers from the main plane-symmetric state into the high-energy, significantly non-planar state and vice versa, were localized. They also possess wobble structures similarly to the high-energy conformers and are stabilized by the participation of the N6H/N6H'…O4/O2 and N3H…N6 H-bonds. Discovered conformers of the A·T DNA base pairs are dynamically stable short-lived structures [lifetime τ = (1.4-3.9) ps]. Their possible biological significance and future perspectives have been briefly discussed.
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Affiliation(s)
- Ol'ha O. Brovarets'
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Kostiantyn S. Tsiupa
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
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48
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High Impact Gene Discovery: Simple Strand-Specific mRNA Library Construction and Differential Regulatory Analysis Based on Gene Co-Expression Network. Methods Mol Biol 2018; 1830:163-189. [PMID: 30043371 DOI: 10.1007/978-1-4939-8657-6_11] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Plant transcription factors have potential to behave as hubs in gene regulatory networks through altering the expression of many downstream genes, and identification of such hub transcription factors strongly enhances our understating of biological processes. Transcriptome analysis has become a staple of gene expression analyses. In addition to current advances in Next Generation Sequencing (NGS) technology, various methods for mRNA library construction and downstream data analyses have been enthusiastically developed. Here, we describe Breath Adapter Directional sequencing (BrAD-seq), a simple strand-specific mRNA library preparation for the Illumina platform, allowing easy scaling of transcriptome experiments with low reagent and labor costs. This protocol includes our recent modifications and the detailed practical procedure for BrAD-seq. Because extracting biological meanings from large-scale transcriptome data presents a significant challenge, we also describe a new analytical method that goes beyond differential expression. Differential regulatory analysis (DRA) is based on a gene co-expression network to address which regulatory factor or factors have the ability to predict the abundance of differentially expressed genes between two groups or conditions. This protocol provides a ready-to-use informatics pipeline from raw sequence data to DRA for plant transcriptome datasets.
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49
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Benetatos P. Tensile elasticity of semiflexible polymers with hinge defects. Phys Rev E 2017; 96:042502. [PMID: 29347551 DOI: 10.1103/physreve.96.042502] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Indexed: 11/07/2022]
Abstract
It has become clear in recent years that the simple uniform wormlike chain model needs to be modified in order to account for more complex behavior which has been observed experimentally in some important biopolymers. For example, the large flexibility of short ds-DNA has been attributed to kink or hinge defects. In this paper, we calculate analytically, within the weak bending approximation, the force-extension relation of a wormlike chain with a permanent hinge defect along its contour. The defect is characterized by its bending energy (which can be zero, in the completely flexible case) and its position along the polymer contour. Besides the bending rigidity of the chain, these are the only parameters which describe our model. We show that a hinge defect causes a significant increase in the differential tensile compliance of a prestressed chain. In the small force limit, a hinge defect significantly increases the entropic elasticity. Our results apply to any pair of semiflexible segments connected by a hinge. As such, they may also be relevant to cytoskeletal filaments (F-actin, microtubules), where one may treat the cross-link connecting two filaments as a hinge defect.
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Affiliation(s)
- Panayotis Benetatos
- Department of Physics, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Korea
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50
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Alexandrov LB, Rasmussen KØ, Bishop AR, Alexandrov BS. Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization. Sci Rep 2017; 7:9731. [PMID: 28851939 PMCID: PMC5575098 DOI: 10.1038/s41598-017-09537-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 07/27/2017] [Indexed: 12/11/2022] Open
Abstract
The innate flexibility of a DNA sequence is quantified by the Jacobson-Stockmayer's J-factor, which measures the propensity for DNA loop formation. Recent studies of ultra-short DNA sequences revealed a discrepancy of up to six orders of magnitude between experimentally measured and theoretically predicted J-factors. These large differences suggest that, in addition to the elastic moduli of the double helix, other factors contribute to loop formation. Here, we develop a new theoretical model that explores how coherent delocalized phonon-like modes in DNA provide single-stranded "flexible hinges" to assist in loop formation. We combine the Czapla-Swigon-Olson structural model of DNA with our extended Peyrard-Bishop-Dauxois model and, without changing any of the parameters of the two models, apply this new computational framework to 86 experimentally characterized DNA sequences. Our results demonstrate that the new computational framework can predict J-factors within an order of magnitude of experimental measurements for most ultra-short DNA sequences, while continuing to accurately describe the J-factors of longer sequences. Further, we demonstrate that our computational framework can be used to describe the cyclization of DNA sequences that contain a base pair mismatch. Overall, our results support the conclusion that coherent delocalized phonon-like modes play an important role in DNA cyclization.
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Affiliation(s)
- Ludmil B Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545, United States of America
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, 87102, USA
| | - Kim Ø Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545, United States of America
| | - Alan R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545, United States of America
| | - Boian S Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545, United States of America.
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, 87102, USA.
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