1
|
Islam F, Mishra PP. Molecular Insight into the Structural Dynamics of Holliday Junctions Modulated by Integration Host Factor. J Phys Chem B 2024; 128:5642-5657. [PMID: 38812070 DOI: 10.1021/acs.jpcb.4c02997] [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: 05/31/2024]
Abstract
The integration host factor (IHF) in Escherichia coli is a nucleoid-associated protein with multifaceted roles that encompass DNA packaging, viral DNA integration, and recombination. IHF binds to double-stranded DNA featuring a 13-base pair (bp) consensus sequence with high affinity, causing a substantial bend of approximately 160° upon binding. Although wild-type IHF (WtIHF) is principally involved in DNA bending to facilitate foreign DNA integration into the host genome, its engineered counterpart, single-chain IHF (ScIHF), was specifically designed for genetic engineering and biotechnological applications. Our study delves into the interactions of both IHF variants with Holliday junctions (HJs), pivotal intermediates in DNA repair, and homologous recombination. HJs are dynamic structures capable of adopting open or stacked conformations, with the open conformation facilitating processes such as branch migration and strand exchange. Using microscale thermophoresis, we quantitatively assessed the binding of IHF to four-way DNA junctions that harbor specific binding sequences H' and H1. Our findings demonstrate that both IHF variants exhibit a strong affinity for HJs, signifying a structure-based recognition mechanism. Circular dichroism (CD) experiments unveiled the impact of the protein on the junction's conformation. Furthermore, single-molecule Förster resonance energy transfer (smFRET) confirmed the influence of IHF on the junction's dynamicity. Intriguingly, our results revealed that WtIHF and ScIHF binding shifts the population toward the open conformation of the junction and stabilizes it in that state. In summary, our findings underscore the robust affinity of the IHF for HJs and its capacity to stabilize the open conformation of these junctions.
Collapse
Affiliation(s)
- Farhana Islam
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhabha National Institute, Mumbai 400094, India
| | - Padmaja Prasad Mishra
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhabha National Institute, Mumbai 400094, India
| |
Collapse
|
2
|
Lombardo Z, Mukerji I. Site-Specific Investigation of DNA Holliday Junction Dynamics and Structure with 6-Methylisoxanthopterin, a Fluorescent Guanine Analog. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590264. [PMID: 38659790 PMCID: PMC11042373 DOI: 10.1101/2024.04.19.590264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
DNA Holliday Junction (HJ) formation and resolution is requisite for maintaining genomic stability in processes such as replication fork reversal and double-strand break repair. If HJs are not resolved, chromosome disjunction and aneuploidy result, hallmarks of tumor cells. To understand the structural features that lead to processing of these four-stranded joint molecule structures, we seek to identify structural and dynamic features unique to the central junction core. We incorporate the fluorescent guanine analog 6-methylisoxanthopterin (6-MI) at ten different locations throughout a model HJ structure to obtain site-specific information regarding the structure and dynamics of bases relative to those in a comparable sequence context in duplex DNA. These comparisons were accomplished through measuring fluorescence lifetime, relative brightness, fluorescence anisotropy, and thermodynamic stability, along with fluorescence quenching assays. These time-resolved and steady-state fluorescence measurements demonstrate that the structural distortions imposed by strand crossing result in increased solvent exposure, less stacking of bases and greater extrahelical nature of bases within the junction core. The 6-MI base analogs in the junction reflect these structural changes through an increase in intensity relative to those in the duplex. Molecular dynamics simulations performed using a model HJ indicate the primary sources of deformation are in the shift and twist parameters of the bases at the central junction step. These results suggest that junction-binding proteins may use the unique structure and dynamics of the bases at the core for recognition.
Collapse
Affiliation(s)
- Zane Lombardo
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | - Ishita Mukerji
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| |
Collapse
|
3
|
Wald J, Marlovits TC. Holliday junction branch migration driven by AAA+ ATPase motors. Curr Opin Struct Biol 2023; 82:102650. [PMID: 37604043 DOI: 10.1016/j.sbi.2023.102650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/09/2023] [Accepted: 06/11/2023] [Indexed: 08/23/2023]
Abstract
Holliday junctions are key intermediate DNA structures during genetic recombination. One of the first Holliday junction-processing protein complexes to be discovered was the well conserved RuvAB branch migration complex present in bacteria that mediates an ATP-dependent movement of the Holliday junction (branch migration). Although the RuvAB complex served as a paradigm for the processing of the Holliday junction, due to technical limitations the detailed structure and underlying mechanism of the RuvAB branch migration complex has until now remained unclear. Recently, structures of a reconstituted RuvAB complex actively-processing a Holliday junction were resolved using time-resolved cryo-electron microscopy. These structures showed distinct conformational states at different stages of the migration process. These structures made it possible to propose an integrated model for RuvAB Holliday junction branch migration. Furthermore, they revealed unexpected insights into the highly coordinated and regulated mechanisms of the nucleotide cycle powering substrate translocation in the hexameric AAA+ RuvB ATPase. Here, we review these latest advances and describe areas for future research.
Collapse
Affiliation(s)
- Jiri Wald
- Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany; Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf, Notkestraße 85, 22607 Hamburg, Germany; Deutsches Elektronen Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Thomas C Marlovits
- Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany; Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf, Notkestraße 85, 22607 Hamburg, Germany; Deutsches Elektronen Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany.
| |
Collapse
|
4
|
Gambietz S, Stenke LJ, Saccà B. Sequence-dependent folding of monolayered DNA origami domains. NANOSCALE 2023; 15:13120-13132. [PMID: 37503690 DOI: 10.1039/d3nr02537c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Current models of DNA origami folding can explain the yield of the assembly process and the isomerization of the structure upon the application of mechanical forces. Nevertheless, the role of the sequence in this conformational transformation is still unclear. In this work, we address this question by performing a systematic thermodynamic study of three origami domains that have an identical design but different sequence contents. By comparing the thermal stability of the domains in various settings and measuring the extent of isomerization at equilibrium (both at the global and single-molecule levels), we extract the contribution to folding given by the sequence and propose thermal criton maps of the isomers to rationalize our findings. Our data contribute to a deeper understanding of DNA origami assembly by considering both the topological- and thermal-dependent properties of the sites of initial folding. While the former are responsible for the mechanical aspects of the process, the latter justify the observed sequence-dependent conformational preferences, which appear evident in simple origami structures but remain typically undisclosed in large and more intricate architectures.
Collapse
Affiliation(s)
- Sabrina Gambietz
- Center of Medical Biotechnology (ZMB) and Center for Nanointegration Duisburg Essen (CENIDE), University Duisburg-Essen, 45141 Essen, Germany.
| | - Lena J Stenke
- Center of Medical Biotechnology (ZMB) and Center for Nanointegration Duisburg Essen (CENIDE), University Duisburg-Essen, 45141 Essen, Germany.
| | - Barbara Saccà
- Center of Medical Biotechnology (ZMB) and Center for Nanointegration Duisburg Essen (CENIDE), University Duisburg-Essen, 45141 Essen, Germany.
| |
Collapse
|
5
|
Integration Host Factor Binds DNA Holliday Junctions. Int J Mol Sci 2022; 24:ijms24010580. [PMID: 36614023 PMCID: PMC9820253 DOI: 10.3390/ijms24010580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 12/31/2022] Open
Abstract
Integration host factor (IHF) is a nucleoid-associated protein involved in DNA packaging, integration of viral DNA and recombination. IHF binds with nanomolar affinity to duplex DNA containing a 13 bp consensus sequence, inducing a bend of ~160° upon binding. We determined that IHF binds to DNA Four-way or Holliday junctions (HJ) with high affinity regardless of the presence of the consensus sequence, signifying a structure-based mechanism of recognition. Junctions, important intermediates in DNA repair and homologous recombination, are dynamic and can adopt either an open or stacked conformation, where the open conformation facilitates branch migration and strand exchange. Using ensemble and single molecule Förster resonance energy transfer (FRET) methods, we investigated IHF-induced changes in the population distribution of junction conformations and determined that IHF binding shifts the population to the open conformation. Further analysis of smFRET dynamics revealed that even in the presence of protein, the junctions remain dynamic as fast transitions are observed for the protein-bound open state. Protein binding alters junction conformational dynamics, as cross correlation analyses reveal the protein slows the transition rate at 1 mM Mg2+ but accelerates the transition rate at 10 mM Mg2+. Stopped flow kinetic experiments provide evidence for two binding steps, a rapid, initial binding step followed by a slower step potentially associated with a conformational change. These measurements also confirm that the protein remains bound to the junction during the conformer transitions and further suggest that the protein forms a partially dissociated state that allows junction arms to be dynamic. These findings, which demonstrate that IHF binds HJs with high affinity and stabilizes junctions in the open conformation, suggest that IHF may play multiple roles in the processes of integration and recombination in addition to stabilizing bacterial biofilms.
Collapse
|
6
|
McQuaid K, Pipier A, Cardin C, Monchaud D. Interactions of small molecules with DNA junctions. Nucleic Acids Res 2022; 50:12636-12656. [PMID: 36382400 PMCID: PMC9825177 DOI: 10.1093/nar/gkac1043] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/13/2022] [Accepted: 10/23/2022] [Indexed: 11/17/2022] Open
Abstract
The four natural DNA bases (A, T, G and C) associate in base pairs (A=T and G≡C), allowing the attached DNA strands to assemble into the canonical double helix of DNA (or duplex-DNA, also known as B-DNA). The intrinsic supramolecular properties of nucleobases make other associations possible (such as base triplets or quartets), which thus translates into a diversity of DNA structures beyond B-DNA. To date, the alphabet of DNA structures is ripe with approximately 20 letters (from A- to Z-DNA); however, only a few of them are being considered as key players in cell biology and, by extension, valuable targets for chemical biology intervention. In the present review, we summarise what is known about alternative DNA structures (what are they? When, where and how do they fold?) and proceed to discuss further about those considered nowadays as valuable therapeutic targets. We discuss in more detail the molecular tools (ligands) that have been recently developed to target these structures, particularly the three- and four-way DNA junctions, in order to intervene in the biological processes where they are involved. This new and stimulating chemical biology playground allows for devising innovative strategies to fight against genetic diseases.
Collapse
Affiliation(s)
- Kane T McQuaid
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Angélique Pipier
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Christine J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - David Monchaud
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| |
Collapse
|
7
|
Adendorff MR, Tang GQ, Millar D, Bathe M, Bricker W. Computational investigation of the impact of core sequence on immobile DNA four-way junction structure and dynamics. Nucleic Acids Res 2022; 50:717-730. [PMID: 34935970 PMCID: PMC8789063 DOI: 10.1093/nar/gkab1246] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 11/28/2021] [Accepted: 12/06/2021] [Indexed: 12/19/2022] Open
Abstract
Immobile four-way junctions (4WJs) are core structural motifs employed in the design of programmed DNA assemblies. Understanding the impact of sequence on their equilibrium structure and flexibility is important to informing the design of complex DNA architectures. While core junction sequence is known to impact the preferences for the two possible isomeric states that junctions reside in, previous investigations have not quantified these preferences based on molecular-level interactions. Here, we use all-atom molecular dynamics simulations to investigate base-pair level structure and dynamics of four-way junctions, using the canonical Seeman J1 junction as a reference. Comparison of J1 with equivalent single-crossover topologies and isolated nicked duplexes reveal conformational impact of the double-crossover motif. We additionally contrast J1 with a second junction core sequence termed J24, with equal thermodynamic preference for each isomeric configuration. Analyses of the base-pair degrees of freedom for each system, free energy calculations, and reduced-coordinate sampling of the 4WJ isomers reveal the significant impact base sequence has on local structure, isomer bias, and global junction dynamics.
Collapse
Affiliation(s)
- Matthew R Adendorff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Guo Qing Tang
- Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - David P Millar
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - William P Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131, USA
| |
Collapse
|
8
|
Zagotta WN, Sim BS, Nhim AK, Raza MM, Evans EG, Venkatesh Y, Jones CM, Mehl RA, Petersson EJ, Gordon SE. An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET. eLife 2021; 10:e70236. [PMID: 34623258 PMCID: PMC8500717 DOI: 10.7554/elife.70236] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/09/2021] [Indexed: 11/30/2022] Open
Abstract
With the recent explosion in high-resolution protein structures, one of the next frontiers in biology is elucidating the mechanisms by which conformational rearrangements in proteins are regulated to meet the needs of cells under changing conditions. Rigorously measuring protein energetics and dynamics requires the development of new methods that can resolve structural heterogeneity and conformational distributions. We have previously developed steady-state transition metal ion fluorescence resonance energy transfer (tmFRET) approaches using a fluorescent noncanonical amino acid donor (Anap) and transition metal ion acceptor to probe conformational rearrangements in soluble and membrane proteins. Here, we show that the fluorescent noncanonical amino acid Acd has superior photophysical properties that extend its utility as a donor for tmFRET. Using maltose-binding protein (MBP) expressed in mammalian cells as a model system, we show that Acd is comparable to Anap in steady-state tmFRET experiments and that its long, single-exponential lifetime is better suited for probing conformational distributions using time-resolved FRET. These experiments reveal differences in heterogeneity in the apo and holo conformational states of MBP and produce accurate quantification of the distributions among apo and holo conformational states at subsaturating maltose concentrations. Our new approach using Acd for time-resolved tmFRET sets the stage for measuring the energetics of conformational rearrangements in soluble and membrane proteins in near-native conditions.
Collapse
Affiliation(s)
- William N Zagotta
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Brandon S Sim
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Anthony K Nhim
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Marium M Raza
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Eric Gb Evans
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Yarra Venkatesh
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
| | - Chloe M Jones
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
| | - Sharona E Gordon
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| |
Collapse
|
9
|
Bandyopadhyay D, Mishra PP. Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy. Front Mol Biosci 2021; 8:725541. [PMID: 34540899 PMCID: PMC8446445 DOI: 10.3389/fmolb.2021.725541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/30/2021] [Indexed: 12/02/2022] Open
Abstract
In addition to the canonical double helix form, DNA is known to be extrapolated into several other secondary structural patterns involving themselves in inter- and intramolecular type hydrogen bonding. The secondary structures of nucleic acids go through several stages of multiple, complex, and interconvertible heterogeneous conformations. The journey of DNA through these conformers has significant importance and has been monitored thoroughly to establish qualitative and quantitative information about the transition between the unfolded, folded, misfolded, and partially folded states. During this structural interconversion, there always exist specific populations of intermediates, which are short-lived or sometimes even do not accumulate within a heterogeneous population and are challenging to characterize using conventional ensemble techniques. The single-molecule FRET(sm-FRET) microspectroscopic method has the advantages to overcome these limitations and monitors biological phenomena transpiring at a measurable high rate and balanced stochastically over time. Thus, tracing the time trajectory of a particular molecule enables direct measurement of the rate constant of each transition step, including the intermediates that are hidden in the ensemble level due to their low concentrations. This review is focused on the advantages of the employment of single-molecule Forster's resonance energy transfer (sm-FRET), which is worthwhile to access the dynamic architecture and structural transition of various secondary structures that DNA adopts, without letting the donor of one molecule to cross-talk with the acceptor of any other. We have emphasized the studies performed to explore the states of folding and unfolding of several nucleic acid secondary structures, for example, the DNA hairpin, Holliday junction, G-quadruplex, and i-motif.
Collapse
Affiliation(s)
- Debolina Bandyopadhyay
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India
- HBNI, Mumbai, India
| | - Padmaja P. Mishra
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India
- HBNI, Mumbai, India
| |
Collapse
|
10
|
Mondal S, Mishra PP. Direct observation of effect of crowding induced macromolecular hydration on molecular breathing in the stem of Fork-DNA by single-molecule FRET microspectroscopy. Int J Biol Macromol 2020; 167:559-569. [PMID: 33278436 DOI: 10.1016/j.ijbiomac.2020.11.197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 11/15/2022]
Abstract
The perpetually changing cellular conditions, nucleotide sequence, and environmental effects including osmotic stress have multiple effects on DNA, leading to several conformational alternations and subsequently influencing their activity, too. In this work, single-molecule FRET microspectroscopy has been employed to monitor the breathing dynamics as an effect of molecular crowding in the stem region of Fork-DNA. The structural integrity greatly alters with the presence or absence of nucleotide overhangs and on the nature and concentration of the crowding agent, thus affecting the stability of the stem region and hence the forked DNA. The multiple hydrogen bonds and hydrophobic interactions between the polynucleotide strands appear to be altered with osmotic crowding. This induces increased flexibility in the double helix and allows DNA to breath. The conformational alternation of the DNA happens in nanometer resolution, that is been monitored by the change in the FRET efficiency between the dyes attached to two different strands of the DNA. The nature and molecular weight of crowding agents control the degree of spatial breathing in the stem of Fork-DNA. These constant fluctuations between the entropically favorable partially folded structures to an enthalpically favorable folded structure are not only valuable for elucidating nucleic acid structure but might play an important role in enzyme kinetics.
Collapse
Affiliation(s)
- Soma Mondal
- 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.
| |
Collapse
|
11
|
Insights into the Structure and Energy of DNA Nanoassemblies. Molecules 2020; 25:molecules25235466. [PMID: 33255286 PMCID: PMC7727707 DOI: 10.3390/molecules25235466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022] Open
Abstract
Since the pioneering work of Ned Seeman in the early 1980s, the use of the DNA molecule as a construction material experienced a rapid growth and led to the establishment of a new field of science, nowadays called structural DNA nanotechnology. Here, the self-recognition properties of DNA are employed to build micrometer-large molecular objects with nanometer-sized features, thus bridging the nano- to the microscopic world in a programmable fashion. Distinct design strategies and experimental procedures have been developed over the years, enabling the realization of extremely sophisticated structures with a level of control that approaches that of natural macromolecular assemblies. Nevertheless, our understanding of the building process, i.e., what defines the route that goes from the initial mixture of DNA strands to the final intertwined superstructure, is, in some cases, still limited. In this review, we describe the main structural and energetic features of DNA nanoconstructs, from the simple Holliday junction to more complicated DNA architectures, and present the theoretical frameworks that have been formulated until now to explain their self-assembly. Deeper insights into the underlying principles of DNA self-assembly may certainly help us to overcome current experimental challenges and foster the development of original strategies inspired to dissipative and evolutive assembly processes occurring in nature.
Collapse
|
12
|
Rout J, Swain BC, Biswas S, Das AK, Tripathy U. A simulation study on the influence of energy migration and relative interaction strengths of homo- and hetero-FRET on the net FRET efficiency. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 226:117599. [PMID: 31751800 DOI: 10.1016/j.saa.2019.117599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
Förster resonance energy transfer (FRET) is a powerful method for probing biomolecular conformations and dynamics in bulk as well as at a single-molecule level. FRET utilizes non-radiative mechanisms to transfer energy between fluorophores, donor and acceptor when placed in close proximity. The FRET efficiency has a strong distance dependence and serves as a direct read-out for molecular interaction. In case of a significant overlap of donor emission and absorption spectra, the excited state energy can be exchanged between the identical donors in close proximity, which eventually migrates back and forth until it gets dissipated. This form of energy transfer is called energy migration or homo-FRET. Here, we have simulated FRET efficiency by considering the donor-donor interaction strength (ξDD) and donor-acceptor interaction strength (ξDA) under conditions of non-uniform distribution of molecules. Our earlier studies indicate that energy migration modulate the FRET efficiency for various values of ξDD and ξDA. We, therefore, determined the limiting values of acceptor concentration (CLA) that will allow the determination of FRET efficiency in the absence and presence of energy migration. Taken together, our study optimizes the conditions for meaningful FRET efficiency for a given FRET pair for better reporting of molecular interactions.
Collapse
Affiliation(s)
- Janmejaya Rout
- Department of Applied Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad, 826004, Jharkhand, India
| | - Bikash Chandra Swain
- Department of Applied Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad, 826004, Jharkhand, India
| | - Shrutidhara Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781029, India
| | - Anand Kant Das
- Department of Applied Physics, Vienna University of Technology, Getreidemarkt-9, Vienna, 1060, Austria
| | - Umakanta Tripathy
- Department of Applied Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad, 826004, Jharkhand, India.
| |
Collapse
|
13
|
Snodin BEK, Schreck JS, Romano F, Louis AA, Doye JPK. Coarse-grained modelling of the structural properties of DNA origami. Nucleic Acids Res 2019; 47:1585-1597. [PMID: 30605514 PMCID: PMC6379721 DOI: 10.1093/nar/gky1304] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/17/2018] [Accepted: 12/20/2018] [Indexed: 01/12/2023] Open
Abstract
We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origami, focussing on archetypal 2D and 3D origami. The model reproduces well the characteristic pattern of helix bending in a 2D origami, showing that it stems from the intrinsic tendency of anti-parallel four-way junctions to splay apart, a tendency that is enhanced both by less screened electrostatic interactions and by increased thermal motion. We also compare to the structure of a 3D origami whose structure has been determined by cryo-electron microscopy. The oxDNA average structure has a root-mean-square deviation from the experimental structure of 8.4 Å, which is of the order of the experimental resolution. These results illustrate that the oxDNA model is capable of providing detailed and accurate insights into the structure of DNA origami, and has the potential to be used to routinely pre-screen putative origami designs and to investigate the molecular mechanisms that regulate the properties of DNA origami.
Collapse
Affiliation(s)
- Benedict E K Snodin
- Physical, and Theoretical Chemistry Laboratory, Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
| | - John S Schreck
- Department of Chemical Engineering, Columbia University, 500 W 120th Street, New York, NY 10027, USA
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi, Universit Ca' Foscari, Via Torino 155, 30172 Venezia Mestre, Italy
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, UK
| | - Jonathan P K Doye
- Physical, and Theoretical Chemistry Laboratory, Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
| |
Collapse
|
14
|
Whiteside MD, Werner GDA, Caldas VEA, Van't Padje A, Dupin SE, Elbers B, Bakker M, Wyatt GAK, Klein M, Hink MA, Postma M, Vaitla B, Noë R, Shimizu TS, West SA, Kiers ET. Mycorrhizal Fungi Respond to Resource Inequality by Moving Phosphorus from Rich to Poor Patches across Networks. Curr Biol 2019; 29:2043-2050.e8. [PMID: 31178314 PMCID: PMC6584331 DOI: 10.1016/j.cub.2019.04.061] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/04/2019] [Accepted: 04/23/2019] [Indexed: 01/01/2023]
Abstract
The world's ecosystems are characterized by an unequal distribution of resources [1]. Trade partnerships between organisms of different species-mutualisms-can help individuals cope with such resource inequality [2-4]. Trade allows individuals to exchange commodities they can provide at low cost for resources that are otherwise impossible or more difficult to access [5, 6]. However, as resources become increasingly patchy in time or space, it is unknown how organisms alter their trading strategies [7, 8]. Here, we show how a symbiotic fungus mediates trade with a host root in response to different levels of resource inequality across its network. We developed a quantum-dot-tracking technique to quantify phosphorus-trading strategies of arbuscular mycorrhizal fungi simultaneously exposed to rich and poor resource patches. By following fluorescent nanoparticles of different colors across fungal networks, we determined where phosphorus was hoarded, relocated, and transferred to plant hosts. We found that increasing exposure to inequality stimulated trade. Fungi responded to high resource variation by (1) increasing the total amount of phosphorus distributed to host roots, (2) decreasing allocation to storage, and (3) differentially moving resources within the network from rich to poor patches. Using single-particle tracking and high-resolution video, we show how dynamic resource movement may help the fungus capitalize on value differences across the trade network, physically moving resources to areas of high demand to gain better returns. Such translocation strategies can help symbiotic organisms cope with exposure to resource inequality.
Collapse
Affiliation(s)
- Matthew D Whiteside
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 108, 1081 HV Amsterdam, the Netherlands
| | - Gijsbert D A Werner
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Balliol College, University of Oxford, Oxford OX1 3BJ, UK
| | - Victor E A Caldas
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 108, 1081 HV Amsterdam, the Netherlands; AMOLF Institute, Science Park 104, 1098 XG Amsterdam, the Netherlands
| | - Anouk Van't Padje
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 108, 1081 HV Amsterdam, the Netherlands
| | - Simon E Dupin
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 108, 1081 HV Amsterdam, the Netherlands
| | - Bram Elbers
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 108, 1081 HV Amsterdam, the Netherlands
| | - Milenka Bakker
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 108, 1081 HV Amsterdam, the Netherlands
| | - Gregory A K Wyatt
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Malin Klein
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 108, 1081 HV Amsterdam, the Netherlands
| | - Mark A Hink
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
| | - Marten Postma
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
| | - Bapu Vaitla
- Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Ronald Noë
- Faculté Psychologie, Université de Strasbourg, 12 Rue Goethe, 67000 Strasbourg, France
| | - Thomas S Shimizu
- AMOLF Institute, Science Park 104, 1098 XG Amsterdam, the Netherlands
| | - Stuart A West
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - E Toby Kiers
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 108, 1081 HV Amsterdam, the Netherlands.
| |
Collapse
|
15
|
Sites of high local frustration in DNA origami. Nat Commun 2019; 10:1061. [PMID: 30837459 PMCID: PMC6400978 DOI: 10.1038/s41467-019-09002-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/07/2019] [Indexed: 12/30/2022] Open
Abstract
The self-assembly of a DNA origami structure, although mostly feasible, represents indeed a rather complex folding problem. Entropy-driven folding and nucleation seeds formation may provide possible solutions; however, until now, a unified view of the energetic factors in play is missing. Here, by analyzing the self-assembly of origami domains with identical structure but different nucleobase composition, in function of variable design and experimental parameters, we identify the role played by sequence-dependent forces at the edges of the structure, where topological constraint is higher. Our data show that the degree of mechanical stress experienced by these regions during initial folding reshapes the energy landscape profile, defining the ratio between two possible global conformations. We thus propose a dynamic model of DNA origami assembly that relies on the capability of the system to escape high structural frustration at nucleation sites, eventually resulting in the emergence of a more favorable but previously hidden state. Self-assembly of DNA origami is a complex folding problem without a unified view of the energetic factors involved. Here the authors analyse identical structures that differ by nucleotide sequence and identify how mechanical stress at nucleation sites shapes the energy landscape.
Collapse
|
16
|
Lu Y, Yu S, Lin F, Lin F, Zhao X, Wu L, Miao Y, Li H, Deng Y, Geng L. Simultaneous label-free screening of G-quadruplex active ligands from natural medicine via a microfluidic chip electrophoresis-based energy transfer multi-biosensor strategy. Analyst 2018; 142:4257-4264. [PMID: 28835953 DOI: 10.1039/c7an00692f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Rapid screening of active compounds plays a crucial role in the research and application of complex natural medicines. Herein, a new method of simultaneous label-free multi-drug screening based on a selective aptamer-carboxyfluorescein/graphene oxide energy transfer optical sensor combined with microfluidic chip electrophoretic separation is reported. In this study, seven traditional Chinese medicinal monomers were chosen as targets for the screening of G-quadruplex ligands. The screening results of the G-quadruplex active ligands, including daidzein, berberine hydrochloride, jatrorrhizine hydrochloride, and fangchinoline, and non-active ligands, including geniposide and oxymatrine, were consistent with those reported in literature. Moreover, one new potential G4DNA active drug, jujuboside A, was identified. Molecular simulation of the interaction between G4DNA and drugs was also carried out using HyperChem and AutoDock to verify the results of the experimental screening. It further demonstrated the reliability of our strategy. This novel separation and concentration based multi-sensing strategy provides a simple, rapid, and sensitive tool for simultaneous multi-drug screening, which is very meaningful for drug screening and bio-interaction analysis.
Collapse
Affiliation(s)
- Yi Lu
- School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, P.R. China.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Lahiri S, Li Y, Hingorani MM, Mukerji I. MutSγ-Induced DNA Conformational Changes Provide Insights into Its Role in Meiotic Recombination. Biophys J 2018; 115:2087-2101. [PMID: 30467025 DOI: 10.1016/j.bpj.2018.10.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/16/2018] [Accepted: 10/22/2018] [Indexed: 01/11/2023] Open
Abstract
In many organisms, MutSγ plays a role in meiotic recombination, facilitating crossover formation between homologous chromosomes. Failure to form crossovers leads to improper segregation of chromosomes and aneuploidy, which in humans result in infertility and birth defects. To improve current understanding of MutSγ function, this study investigates the binding affinities and structures of MutSγ in complex with DNA substrates that model homologous recombination intermediates. For these studies, we overexpressed and isolated from Escherichia coli the yeast MutSγ protein Saccharomyces cerevisiae (Sc) Msh4-Msh5. Sc Msh4-Msh5 binds Holliday junction (HJ)-like substrates, 3' overhangs, single-stranded (ss) forks, and the displacement loop with nanomolar affinity. The weakest binding affinities are detected for an intact duplex and open-junction construct. Similar to the human protein, Sc Msh4-Msh5 exhibits the highest affinity for the HJ with a Kd < 0.4 nM in solution. Energy-transfer experiments further demonstrate that DNA structure is modulated by the binding interaction with the largest changes associated with substrates containing an ss end. Upon binding, Sc Msh4-Msh5 displaces the ss away from the duplex in most of the ss-containing intermediates, potentially enabling the binding of RPA and other proteins. In the case of the junction-like intermediates, Msh4-Msh5 binding either stabilizes the existing stacked structure or induces formation of the stacked X conformation. Significantly, we find that upon binding, Msh4-Msh5 stacks an open-junction construct to the same extent as the standard junction. Stabilization of the junction in the stacked conformation is generally refractory to branch migration, which is consistent with a potential role for MutSγ to stabilize HJs and prevent branch migration until resolution by MutLγ. The different binding modalities observed suggest that Msh4-Msh5 not only binds to and stabilizes stacked junctions but also participates in meiotic recombination before junction formation through the stabilization of single-end invasion intermediates.
Collapse
Affiliation(s)
- Sudipta Lahiri
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut
| | - Yan Li
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut
| | - Manju M Hingorani
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut
| | - Ishita Mukerji
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut.
| |
Collapse
|
18
|
Han JH, Park S, Hashiya F, Sugiyama H. Approach to the Investigation of Nucleosome Structure by Using the Highly Emissive Nucleobase
th
dG–tC FRET Pair. Chemistry 2018; 24:17091-17095. [DOI: 10.1002/chem.201803382] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/07/2018] [Indexed: 01/27/2023]
Affiliation(s)
- Ji Hoon Han
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho Sakyo-ku Kyoto 606–8502 Japan
| | - Soyoung Park
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho Sakyo-ku Kyoto 606–8502 Japan
| | - Fumitaka Hashiya
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho Sakyo-ku Kyoto 606–8502 Japan
| | - Hiroshi Sugiyama
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho Sakyo-ku Kyoto 606–8502 Japan
- Institute for Integrated Cell-Material Sciences (iCeMS)Kyoto University Yoshida-ushinomiyacho Sakyo-ku Kyoto 606–8501 Japan
| |
Collapse
|
19
|
Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study. Nat Methods 2018; 15:669-676. [PMID: 30171252 PMCID: PMC6121742 DOI: 10.1038/s41592-018-0085-0] [Citation(s) in RCA: 269] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 05/25/2018] [Indexed: 12/12/2022]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods. A multi-laboratory study finds that single-molecule FRET is a reproducible and reliable approach for determining accurate distances in dye-labeled DNA duplexes.
Collapse
|
20
|
Dey SK, Pettersson JR, Topacio AZ, Das SR, Peteanu LA. Eliminating Spurious Zero-Efficiency FRET States in Diffusion-Based Single-Molecule Confocal Microscopy. J Phys Chem Lett 2018; 9:2259-2265. [PMID: 29570297 DOI: 10.1021/acs.jpclett.8b00362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) of freely diffusing biomolecules using confocal microscopy is a simple and powerful technique for measuring conformation and dynamics. However, a spurious zero-FRET population can significantly distort the measured histograms and lead to incorrect results, particularly in measurements of intrinsically low-FRET systems. Using a model system consisting of duplex DNAs, we show that there are two important contributions to the zero-FRET state: (1) formation of a dark triplet state of the acceptor dye and (2) the presence of donor-only strands due to incomplete hybridization between donor- and acceptor-labeled strands. The combined strategy of using Trolox as a triplet-state quencher and labeling the same DNA strand with donor and acceptor dyes effectively eliminates the zero-FRET population, even for constructs with intrinsically low FRET efficiencies. This strategy allows us to perform smFRET experiments using a simple confocal microscope with improved accuracy.
Collapse
Affiliation(s)
- Sourav K Dey
- Department of Chemistry and Center for Nucleic Acids Science & Technology , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
| | - John R Pettersson
- Department of Chemistry and Center for Nucleic Acids Science & Technology , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
| | - Andrea Z Topacio
- Department of Chemistry and Center for Nucleic Acids Science & Technology , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
| | - Subha R Das
- Department of Chemistry and Center for Nucleic Acids Science & Technology , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
| | - Linda A Peteanu
- Department of Chemistry and Center for Nucleic Acids Science & Technology , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
| |
Collapse
|
21
|
Yoo J, Aksimentiev A. New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions. Phys Chem Chem Phys 2018; 20:8432-8449. [PMID: 29547221 DOI: 10.1039/c7cp08185e] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly ordered three-dimensional structures that define their functions. The key to folding of a biopolymer into a unique 3D structure or to an assembly of several biopolymers into a functional unit is a delicate balance between the attractive and repulsive forces that also makes such self-assembly reversible under physiological conditions. The all-atom molecular dynamics (MD) method has emerged as a powerful tool for studies of individual biomolecules and their functional assemblies, encompassing systems of ever increasing complexity. However, advances in parallel computing technology have outpaced the development of the underlying theoretical models-the molecular force fields, pushing the MD method into an untested territory. Recent tests of the MD method have found the most commonly used molecular force fields to be out of balance, overestimating attractive interactions between charged and hydrophobic groups, which can promote artificial aggregation in MD simulations of multi-component protein, nucleic acid, and lipid systems. One route towards improving the force fields is through the NBFIX corrections method, in which the intermolecular forces are calibrated against experimentally measured quantities such as osmotic pressure by making atom pair-specific adjustments to the non-bonded interactions. In this article, we review development of the NBFIX (Non-Bonded FIX) corrections to the AMBER and CHARMM force fields and discuss their implications for MD simulations of electrolyte solutions, dense DNA systems, Holliday junctions, protein folding, and lipid bilayer membranes.
Collapse
Affiliation(s)
- Jejoong Yoo
- Center for the Physics of Living Cells, Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA. and Center for Self-assembly and Complexity, Institute for Basic Science, Pohang, 37363, Republic of Korea
| | - Aleksei Aksimentiev
- Center for the Physics of Living Cells, Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA.
| |
Collapse
|
22
|
Liu Y, Freeman A, Déclais AC, Gartner A, Lilley DMJ. Biochemical and Structural Properties of Fungal Holliday Junction-Resolving Enzymes. Methods Enzymol 2018; 600:543-568. [PMID: 29458774 DOI: 10.1016/bs.mie.2017.11.021] [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] [Indexed: 02/01/2023]
Abstract
Four-way Holliday junctions in DNA are the central intermediates of genetic recombination and must be processed into regular duplex species. One mechanism for achieving this is called resolution, brought about by structure-selective nucleases. GEN1 is an important junction-resolving enzyme in eukaryotic cells, a member of the FEN1/EXO1 superfamily of nucleases. While human GEN1 is difficult to work with because of aggregation, orthologs from thermophilic fungi have been identified using bioinformatics and have proved to have excellent properties. Here, the expression and purification of this enzyme from Chaetomium thermophilum is described, together with the means of investigating its biochemical properties. The enzyme is quite similar to junction-resolving enzymes from lower organisms, binding to junctions in dimeric form, introducing symmetrical bilateral cleavages, the second of which is accelerated to promote productive resolution. Crystallization of C. thermophilum GEN1 is described, and the structure of a DNA-product complex. Juxtaposition of complexes in the crystal lattice suggests how the structure of a dimeric enzyme with an intact junction is organized.
Collapse
Affiliation(s)
- Yijin Liu
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - Alasdair Freeman
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - Anne-Cécile Déclais
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - Anton Gartner
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom.
| |
Collapse
|
23
|
Vámosi G, Rueda D. DNA Bends the Knee to Transcription Factors. Biophys J 2017; 114:2253-2254. [PMID: 29229184 DOI: 10.1016/j.bpj.2017.10.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 10/11/2017] [Indexed: 11/25/2022] Open
Affiliation(s)
- György Vámosi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
| | - David Rueda
- Single Molecule Imaging Group, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| |
Collapse
|
24
|
Peulen TO, Opanasyuk O, Seidel CAM. Combining Graphical and Analytical Methods with Molecular Simulations To Analyze Time-Resolved FRET Measurements of Labeled Macromolecules Accurately. J Phys Chem B 2017; 121:8211-8241. [PMID: 28709377 PMCID: PMC5592652 DOI: 10.1021/acs.jpcb.7b03441] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Förster resonance energy transfer
(FRET) measurements from
a donor, D, to an acceptor, A, fluorophore are frequently used in vitro and in live cells to reveal information on the
structure and dynamics of DA labeled macromolecules. Accurate descriptions
of FRET measurements by molecular models are complicated because the
fluorophores are usually coupled to the macromolecule via flexible
long linkers allowing for diffusional exchange between multiple states
with different fluorescence properties caused by distinct environmental
quenching, dye mobilities, and variable DA distances. It is often
assumed for the analysis of fluorescence intensity decays that DA
distances and D quenching are uncorrelated (homogeneous quenching
by FRET) and that the exchange between distinct fluorophore states
is slow (quasistatic). This allows us to introduce the FRET-induced
donor decay, εD(t), a function solely
depending on the species fraction distribution of the rate constants
of energy transfer by FRET, for a convenient joint analysis of fluorescence
decays of FRET and reference samples by integrated graphical and analytical
procedures. Additionally, we developed a simulation toolkit to model
dye diffusion, fluorescence quenching by the protein surface, and
FRET. A benchmark study with simulated fluorescence decays of 500
protein structures demonstrates that the quasistatic homogeneous model
works very well and recovers for single conformations the average
DA distances with an accuracy of < 2%. For more complex
cases, where proteins adopt multiple conformations with significantly
different dye environments (heterogeneous case), we introduce a general
analysis framework and evaluate its power in resolving heterogeneities
in DA distances. The developed fast simulation methods, relying on
Brownian dynamics of a coarse-grained dye in its sterically accessible
volume, allow us to incorporate structural information in the decay
analysis for heterogeneous cases by relating dye states with protein
conformations to pave the way for fluorescence and FRET-based dynamic
structural biology. Finally, we present theories and simulations to
assess the accuracy and precision of steady-state and time-resolved
FRET measurements in resolving DA distances on the single-molecule
and ensemble level and provide a rigorous framework for estimating
approximation, systematic, and statistical errors.
Collapse
Affiliation(s)
- Thomas-Otavio Peulen
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität , Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Oleg Opanasyuk
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität , Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität , Universitätsstraße 1, 40225 Düsseldorf, Germany
| |
Collapse
|
25
|
Zheng YN, Liang WB, Xiong CY, Zhuo Y, Chai YQ, Yuan R. Universal Ratiometric Photoelectrochemical Bioassay with Target-Nucleotide Transduction-Amplification and Electron-Transfer Tunneling Distance Regulation Strategies for Ultrasensitive Determination of microRNA in Cells. Anal Chem 2017; 89:9445-9451. [DOI: 10.1021/acs.analchem.7b02270] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Ying-Ning Zheng
- Key
Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest
University), Ministry of Education, College of Chemistry and Chemical
Engineering, Southwest University, Chongqing 400715, PR China
| | - Wen-Bin Liang
- Key
Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest
University), Ministry of Education, College of Chemistry and Chemical
Engineering, Southwest University, Chongqing 400715, PR China
- Department
of Clinical Biochemistry, Laboratory Sciences, Southwest Hospital, Third Military Medical University, 30 Gaotanyan Street, Shapingba
District, Chongqing 400038, PR China
| | - Cheng-Yi Xiong
- Key
Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest
University), Ministry of Education, College of Chemistry and Chemical
Engineering, Southwest University, Chongqing 400715, PR China
| | - Ying Zhuo
- Key
Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest
University), Ministry of Education, College of Chemistry and Chemical
Engineering, Southwest University, Chongqing 400715, PR China
| | - Ya-Qin Chai
- Key
Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest
University), Ministry of Education, College of Chemistry and Chemical
Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key
Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest
University), Ministry of Education, College of Chemistry and Chemical
Engineering, Southwest University, Chongqing 400715, PR China
| |
Collapse
|
26
|
Han JH, Yamamoto S, Park S, Sugiyama H. Development of a Vivid FRET System Based on a Highly Emissive dG-dC Analogue Pair. Chemistry 2017; 23:7607-7613. [PMID: 28411372 DOI: 10.1002/chem.201701118] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Indexed: 12/12/2022]
Abstract
A new type of Förster Resonance Energy Transfer (FRET) system using highly emissive isomorphic nucleobase analogues is reported. The FRET pair consists of 2-aminothieno[3,4-d]pyrimidine G-mimic deoxyribonucleoside (th dG) as an energy donor and 1,3-diaza-2-oxophenothiazine (tC) as an energy acceptor. The distance and orientation between donor and acceptor was controlled by systematic incorporation of th dG and tC into DNA sequences to investigate the FRET efficiencies. This is the first Watson-Crick base-pairable FRET pair to produce vivid colors. In addition, this nucleic acid-based FRET pair was used to monitor DNA conformation and achieved visualization of the B-Z transition.
Collapse
Affiliation(s)
- Ji Hoon Han
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Seigi Yamamoto
- Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505, Japan
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University,Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| |
Collapse
|
27
|
Lilley DMJ. Holliday junction-resolving enzymes-structures and mechanisms. FEBS Lett 2017; 591:1073-1082. [PMID: 27990631 DOI: 10.1002/1873-3468.12529] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 12/12/2016] [Accepted: 12/13/2016] [Indexed: 12/15/2022]
Abstract
Holliday junction-resolving enzymes are nucleases that are highly specific for the structure of the junction, to which they bind in dimeric form. Two symmetrically disposed cleavages are made. These are not simultaneous, but the second cleavage is accelerated relative to the first, so ensuring that bilateral cleavage occurs during the lifetime of the DNA-protein complex. In eukaryotic cells there are two known junction-resolving activities. GEN1 is similar to enzymes from lower organisms. A crystallographic structure of a fungal GEN1 bound to the product of resolution has been determined. These complexes are dimerized within the crystal lattice such that the strands of the products may be simply reconnected to form a junction. These structures suggest a trajectory for the resolution process.
Collapse
Affiliation(s)
- David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, UK
| |
Collapse
|
28
|
Dimura M, Peulen TO, Hanke CA, Prakash A, Gohlke H, Seidel CA. Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems. Curr Opin Struct Biol 2016; 40:163-185. [PMID: 27939973 DOI: 10.1016/j.sbi.2016.11.012] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 11/11/2016] [Accepted: 11/11/2016] [Indexed: 01/11/2023]
Abstract
Förster Resonance Energy Transfer (FRET) combined with single-molecule spectroscopy probes macromolecular structure and dynamics and identifies coexisting conformational states. We review recent methodological developments in integrative structural modeling by satisfying spatial restraints on networks of FRET pairs (hybrid-FRET). We discuss procedures to incorporate prior structural knowledge and to obtain optimal distance networks. Finally, a workflow for hybrid-FRET is presented that automates integrative structural modeling and experiment planning to put hybrid-FRET on rails. To test this workflow, we simulate realistic single-molecule experiments and resolve three protein conformers, exchanging at 30μs and 10ms, with accuracies of 1-3Å RMSD versus the target structure. Incorporation of data from other spectroscopies and imaging is also discussed.
Collapse
Affiliation(s)
- Mykola Dimura
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Thomas O Peulen
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Christian A Hanke
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Aiswaria Prakash
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Claus Am Seidel
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
| |
Collapse
|
29
|
Ong HS, Syafiq-Rahim M, Kasim NHA, Firdaus-Raih M, Ramlan EI. Self-assembly programming of DNA polyominoes. J Biotechnol 2016; 236:141-51. [PMID: 27569553 DOI: 10.1016/j.jbiotec.2016.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 08/04/2016] [Accepted: 08/24/2016] [Indexed: 10/21/2022]
Abstract
Fabrication of functional DNA nanostructures operating at a cellular level has been accomplished through molecular programming techniques such as DNA origami and single-stranded tiles (SST). During implementation, restrictive and constraint dependent designs are enforced to ensure conformity is attainable. We propose a concept of DNA polyominoes that promotes flexibility in molecular programming. The fabrication of complex structures is achieved through self-assembly of distinct heterogeneous shapes (i.e., self-organised optimisation among competing DNA basic shapes) with total flexibility during the design and assembly phases. In this study, the plausibility of the approach is validated using the formation of multiple 3×4 DNA network fabricated from five basic DNA shapes with distinct configurations (monomino, tromino and tetrominoes). Computational tools to aid the design of compatible DNA shapes and the structure assembly assessment are presented. The formations of the desired structures were validated using Atomic Force Microscopy (AFM) imagery. Five 3×4 DNA networks were successfully constructed using combinatorics of these five distinct DNA heterogeneous shapes. Our findings revealed that the construction of DNA supra-structures could be achieved using a more natural-like orchestration as compared to the rigid and restrictive conventional approaches adopted previously.
Collapse
Affiliation(s)
- Hui San Ong
- Natural Computing Laboratory, Department of Artificial Intelligence, Faculty of Computer Science and Information Technology, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Mohd Syafiq-Rahim
- School of Biosciences and Biotechnology, Faculty of Science and Technology and Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Malaysia
| | - Noor Hayaty Abu Kasim
- Department of Restorative Dentistry, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohd Firdaus-Raih
- School of Biosciences and Biotechnology, Faculty of Science and Technology and Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Malaysia
| | - Effirul Ikhwan Ramlan
- Natural Computing Laboratory, Department of Artificial Intelligence, Faculty of Computer Science and Information Technology, University of Malaya, 50603, Kuala Lumpur, Malaysia; Centre of Research for Computational Sciences and Informatics for Biology, Bioindustry, Environment, Agriculture, and Healthcare (CRYSTAL), University of Malaya, 50603 Kuala Lumpur, Malaysia.
| |
Collapse
|
30
|
Smith-Peter E, Lamontagne AM, Lafontaine DA. Role of lysine binding residues in the global folding of the lysC riboswitch. RNA Biol 2016; 12:1372-82. [PMID: 26403229 DOI: 10.1080/15476286.2015.1094603] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Riboswitches regulate gene expression by rearranging their structure upon metabolite binding. The lysine-sensing lysC riboswitch is a rare example of an RNA aptamer organized around a 5-way helical junction in which ligand binding is performed exclusively through nucleotides located at the junction core. We have probed whether the nucleotides involved in ligand binding play any role in the global folding of the riboswitch. As predicted, our findings indicate that ligand-binding residues are critical for the lysine-dependent gene regulation mechanism. We also find that these residues are not important for the establishment of key magnesium-dependent tertiary interactions, suggesting that folding and ligand recognition are uncoupled in this riboswitch for the formation of specific interactions. However, FRET assays show that lysine binding results in an additional conformational change, indicating that lysine binding may also participate in a specific folding transition. Thus, in contrast to helical junctions being primary determinants in ribozymes and rRNA folding, we speculate that the helical junction of the lysine-sensing lysC riboswitch is not employed as structural a scaffold to direct global folding, but rather has a different role in establishing RNA-ligand interactions required for riboswitch regulation. Our work suggests that helical junctions may adopt different functions such as the coordination of global architecture or the formation of specific ligand binding site.
Collapse
Affiliation(s)
- Erich Smith-Peter
- a Department of Biology ; Faculty of Science, RNA Group, Université de Sherbrooke , Sherbrooke ; Quebec , Canada
| | - Anne-Marie Lamontagne
- a Department of Biology ; Faculty of Science, RNA Group, Université de Sherbrooke , Sherbrooke ; Quebec , Canada
| | - Daniel A Lafontaine
- a Department of Biology ; Faculty of Science, RNA Group, Université de Sherbrooke , Sherbrooke ; Quebec , Canada
| |
Collapse
|
31
|
Benson E, Mohammed A, Bosco A, Teixeira AI, Orponen P, Högberg B. Computer-Aided Production of Scaffolded DNA Nanostructures from Flat Sheet Meshes. Angew Chem Int Ed Engl 2016; 55:8869-72. [PMID: 27304204 PMCID: PMC6680348 DOI: 10.1002/anie.201602446] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Indexed: 01/19/2023]
Abstract
The use of DNA as a nanoscale construction material has been a rapidly developing field since the 1980s, in particular since the introduction of scaffolded DNA origami in 2006. Although software is available for DNA origami design, the user is generally limited to architectures where finding the scaffold path through the object is trivial. Herein, we demonstrate the automated conversion of arbitrary two-dimensional sheets in the form of digital meshes into scaffolded DNA nanostructures. We investigate the properties of DNA meshes based on three different internal frameworks in standard folding buffer and physiological salt buffers. We then employ the triangulated internal framework and produce four 2D structures with complex outlines and internal features. We demonstrate that this highly automated technique is capable of producing complex DNA nanostructures that fold with high yield to their programmed configurations, covering around 70 % more surface area than classic origami flat sheets.
Collapse
Affiliation(s)
- Erik Benson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | | | - Alessandro Bosco
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Ana I Teixeira
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Pekka Orponen
- Department of Computer Science, Aalto University, 00076, Aalto, Finland
| | - Björn Högberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden.
| |
Collapse
|
32
|
Benson E, Mohammed A, Bosco A, Teixeira AI, Orponen P, Högberg B. Computer-Aided Production of Scaffolded DNA Nanostructures from Flat Sheet Meshes. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Erik Benson
- Department of Medical Biochemistry and Biophysics; Karolinska Institutet; 17177 Stockholm Sweden
| | | | - Alessandro Bosco
- Department of Medical Biochemistry and Biophysics; Karolinska Institutet; 17177 Stockholm Sweden
| | - Ana I. Teixeira
- Department of Medical Biochemistry and Biophysics; Karolinska Institutet; 17177 Stockholm Sweden
| | - Pekka Orponen
- Department of Computer Science; Aalto University; 00076 Aalto Finland
| | - Björn Högberg
- Department of Medical Biochemistry and Biophysics; Karolinska Institutet; 17177 Stockholm Sweden
| |
Collapse
|
33
|
Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments. Sci Rep 2016; 6:22863. [PMID: 26971574 PMCID: PMC4789735 DOI: 10.1038/srep22863] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/22/2016] [Indexed: 02/08/2023] Open
Abstract
Holliday junctions play a central role in genetic recombination, DNA repair and other cellular processes. We combine simulations and experiments to evaluate the ability of the 3SPN.2 model, a coarse-grained representation designed to mimic B-DNA, to predict the properties of DNA Holliday junctions. The model reproduces many experimentally determined aspects of junction structure and stability, including the temperature dependence of melting on salt concentration, the bias between open and stacked conformations, the relative populations of conformers at high salt concentration, and the inter-duplex angle (IDA) between arms. We also obtain a close correspondence between the junction structure evaluated by all-atom and coarse-grained simulations. We predict that, for salt concentrations at physiological and higher levels, the populations of the stacked conformers are independent of salt concentration, and directly observe proposed tetrahedral intermediate sub-states implicated in conformational transitions. Our findings demonstrate that the 3SPN.2 model captures junction properties that are inaccessible to all-atom studies, opening the possibility to simulate complex aspects of junction behavior.
Collapse
|
34
|
Litke JL, Li Y, Nocka LM, Mukerji I. Probing the Ion Binding Site in a DNA Holliday Junction Using Förster Resonance Energy Transfer (FRET). Int J Mol Sci 2016; 17:366. [PMID: 26978349 PMCID: PMC4813226 DOI: 10.3390/ijms17030366] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/21/2016] [Accepted: 02/26/2016] [Indexed: 11/17/2022] Open
Abstract
Holliday Junctions are critical DNA intermediates central to double strand break repair and homologous recombination. The junctions can adopt two general forms: open and stacked-X, which are induced by protein or ion binding. In this work, fluorescence spectroscopy, metal ion luminescence and thermodynamic measurements are used to elucidate the ion binding site and the mechanism of junction conformational change. Förster resonance energy transfer measurements of end-labeled junctions monitored junction conformation and ion binding affinity, and reported higher affinities for multi-valent ions. Thermodynamic measurements provided evidence for two classes of binding sites. The higher affinity ion-binding interaction is an enthalpy driven process with an apparent stoichiometry of 2.1 ± 0.2. As revealed by Eu(3+) luminescence, this binding class is homogeneous, and results in slight dehydration of the ion with one direct coordination site to the junction. Luminescence resonance energy transfer experiments confirmed the presence of two ions and indicated they are 6-7 Å apart. These findings are in good agreement with previous molecular dynamics simulations, which identified two symmetrical regions of high ion density in the center of stacked junctions. These results support a model in which site-specific binding of two ions in close proximity is required for folding of DNA Holliday junctions into the stacked-X conformation.
Collapse
Affiliation(s)
- Jacob L Litke
- Department of Molecular Biology and Biochemistry and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459-0175, USA.
| | - Yan Li
- Department of Molecular Biology and Biochemistry and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459-0175, USA.
| | - Laura M Nocka
- Department of Molecular Biology and Biochemistry and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459-0175, USA.
| | - Ishita Mukerji
- Department of Molecular Biology and Biochemistry and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459-0175, USA.
| |
Collapse
|
35
|
Spillmann CM, Stewart MH, Susumu K, Medintz IL. Combining semiconductor quantum dots and bioscaffolds into nanoscale energy transfer devices. APPLIED OPTICS 2015; 54:F85-F95. [PMID: 26560627 DOI: 10.1364/ao.54.000f85] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Significant advances have been made in the development of nanoscale devices capable of exciton transport via Förster resonance energy transfer. Several requirements must be met for effective operation, including a reliable energy-harvesting source along with highly organized, precisely placed energy relay elements. For the latter, biological scaffolds such as DNA provide a customizable, symmetric, and stable structure that can be site-specifically modified with organic fluorophores. Here, advancements in nanoscale energy transfer devices incorporating semiconductor nanocrystals and bioscaffolds are reviewed with discussion of biofunctionalization, linker chemistries, design considerations, and concluding with applications in light harvesting, multiplexed biosensing, and optical logic.
Collapse
|
36
|
Zhao Q, Saro D, Sachpatzidis A, Singh TR, Schlingman D, Zheng XF, Mack A, Tsai MS, Mochrie S, Regan L, Meetei AR, Sung P, Xiong Y. The MHF complex senses branched DNA by binding a pair of crossover DNA duplexes. Nat Commun 2015; 5:2987. [PMID: 24390579 DOI: 10.1038/ncomms3987] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 11/21/2013] [Indexed: 01/07/2023] Open
Abstract
The conserved MHF1-MHF2 (MHF) complex functions in the activation of the Fanconi anaemia pathway of the DNA damage response, in regulating homologous recombination, and in DNA replication fork maintenance. MHF facilitates the processing of multiple types of branched DNAs by the DNA translocase FANCM. Here we report the crystal structure of a human MHF-DNA complex that reveals the DNA-binding mode of MHF. The structure suggests that MHF prefers branched DNA over double-stranded DNA because it engages two duplex arms. Biochemical analyses verify that MHF preferentially engages DNA forks or various four-way junctions independent of the junction-site structure. Furthermore, genetic experiments provide evidence that the observed DNA-binding interface of MHF is important for cellular resistance to DNA damage. These results offer insights into how the MHF complex recognizes branched DNA and stimulates FANCM activity at such a structure to promote genome maintenance.
Collapse
Affiliation(s)
- Qi Zhao
- 1] Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA [2]
| | - Dorina Saro
- 1] Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA [2]
| | - Aristidis Sachpatzidis
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Thiyam Ramsing Singh
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Research Foundation and University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
| | - Daniel Schlingman
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Xiao-Feng Zheng
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Andrew Mack
- Department of Applied Physics, Yale University, New Haven, Connecticut 06511, USA
| | - Miaw-Sheue Tsai
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Simon Mochrie
- 1] Department of Applied Physics, Yale University, New Haven, Connecticut 06511, USA [2] Department of Physics, Yale University, New Haven, Connecticut 06511, USA
| | - Lynne Regan
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Amom Ruhikanta Meetei
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Research Foundation and University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| |
Collapse
|
37
|
Cannon B, Kachroo AH, Jarmoskaite I, Jayaram M, Russell R. Hexapeptides that inhibit processing of branched DNA structures induce a dynamic ensemble of Holliday junction conformations. J Biol Chem 2015; 290:22734-46. [PMID: 26209636 PMCID: PMC4566245 DOI: 10.1074/jbc.m115.663930] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 07/23/2015] [Indexed: 11/06/2022] Open
Abstract
Holliday junctions are critical intermediates in DNA recombination, repair, and restart of blocked replication. Hexapeptides have been identified that bind to junctions and inhibit various junction-processing enzymes, and these peptides confer anti-microbial and anti-tumor properties. Earlier studies suggested that inhibition results from stabilization of peptide-bound Holliday junctions in the square planar conformation. Here, we use single molecule fluorescence resonance energy transfer (smFRET) and two model junctions, which are AT- or GC-rich at the branch points, to show that binding of the peptide KWWCRW induces a dynamic ensemble of junction conformations that differs from both the square planar and stacked X conformations. The specific features of the conformational distributions differ for the two peptide-bound junctions, but both junctions display greatly decreased Mg(2+) dependence and increased conformational fluctuations. The smFRET results, complemented by gel mobility shift and small angle x-ray scattering analyses, reveal structural effects of peptides and highlight the sensitivity of smFRET for analyzing complex mixtures of DNA structures. The peptide-induced conformational dynamics suggest multiple stacking arrangements of aromatic amino acids with the nucleobases at the junction core. This conformational heterogeneity may inhibit DNA processing by increasing the population of inactive junction conformations, thereby preventing the binding of processing enzymes and/or resulting in their premature dissociation.
Collapse
Affiliation(s)
- Brian Cannon
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Aashiq H Kachroo
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Inga Jarmoskaite
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Makkuni Jayaram
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Rick Russell
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| |
Collapse
|
38
|
Iverson D, Serrano C, Brahan AM, Shams A, Totsingan F, Bell AJ. Characterization of the structural and protein recognition properties of hybrid PNA-DNA four-way junctions. Arch Biochem Biophys 2015; 587:1-11. [PMID: 26348651 DOI: 10.1016/j.abb.2015.08.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/11/2015] [Accepted: 08/26/2015] [Indexed: 01/31/2023]
Abstract
The objective of this study is to evaluate the structure and protein recognition properties of hybrid four-way junctions (4WJs) composed of DNA and peptide nucleic acid (PNA) strands. We compare a classic immobile DNA junction, J1, vs. six PNA-DNA junctions, including a number with blunt DNA ends and multiple PNA strands. Circular dichroism (CD) analysis reveals that hybrid 4WJs are composed of helices that possess structures intermediate between A- and B-form DNA, the apparent level of A-form structure correlates with the PNA content. The structure of hybrids that contain one PNA strand is sensitive to Mg(+2). For these constructs, the apparent B-form structure and conformational stability (Tm) increase in high Mg(+2). The blunt-ended junction, b4WJ-PNA3, possesses the highest B-form CD signals and Tm (40.1 °C) values vs. all hybrids and J1. Protein recognition studies are carried out using the recombinant DNA-binding protein, HMGB1b. HMGB1b binds the blunt ended single-PNA hybrids, b4WJ-PNA1 and b4WJ-PNA3, with high affinity. HMGB1b binds the multi-PNA hybrids, 4WJ-PNA1,3 and b4WJ-PNA1,3, but does not form stable protein-nucleic acid complexes. Protein interactions with hybrid 4WJs are influenced by the ratio of A- to B-form helices: hybrids with helices composed of higher levels of B-form structure preferentially associate with HMGB1b.
Collapse
Affiliation(s)
- Douglas Iverson
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA
| | - Crystal Serrano
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA
| | - Ann Marie Brahan
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA
| | - Arik Shams
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA
| | | | - Anthony J Bell
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA.
| |
Collapse
|
39
|
Use of biomolecular scaffolds for assembling multistep light harvesting and energy transfer devices. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2015. [DOI: 10.1016/j.jphotochemrev.2014.12.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
40
|
Herschlag D, Allred BE, Gowrishankar S. From static to dynamic: the need for structural ensembles and a predictive model of RNA folding and function. Curr Opin Struct Biol 2015; 30:125-133. [PMID: 25744941 DOI: 10.1016/j.sbi.2015.02.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/11/2015] [Accepted: 02/11/2015] [Indexed: 12/18/2022]
Abstract
To understand RNA, it is necessary to move beyond a descriptive categorization towards quantitative predictions of its molecular conformations and functional behavior. An incisive approach to understanding the function and folding of biological RNA systems involves characterizing small, simple components that are largely responsible for the behavior of complex systems including helix-junction-helix elements and tertiary motifs. State-of-the-art methods have permitted unprecedented insight into the conformational ensembles of these elements revealing, for example, that conformations of helix-junction-helix elements are confined to a small region of the ensemble, that this region is highly dependent on the junction's topology, and that the correct alignment of tertiary motifs may be a rare conformation on the overall folding landscape. Further characterization of RNA components and continued development of experimental and computational methods with the goal of quantitatively predicting RNA folding and functional behavior will be critical to understanding biological RNA systems.
Collapse
Affiliation(s)
- Daniel Herschlag
- Department of Biochemistry, Beckman Center, B400, 279 W. Campus Dr. MC: 5307, Stanford University, Stanford, CA 94305, USA; Department of Chemistry, 333 Campus Drive, Mudd Building, Room 121, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, 443 Via Ortega, Room 129, Stanford University, Stanford, CA 94305, USA.
| | - Benjamin E Allred
- Department of Biochemistry, Beckman Center, B400, 279 W. Campus Dr. MC: 5307, Stanford University, Stanford, CA 94305, USA
| | - Seshadri Gowrishankar
- Department of Chemical Engineering, 443 Via Ortega, Room 129, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
41
|
Lattice-free prediction of three-dimensional structure of programmed DNA assemblies. Nat Commun 2014; 5:5578. [PMID: 25470497 PMCID: PMC4268701 DOI: 10.1038/ncomms6578] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 10/15/2014] [Indexed: 12/17/2022] Open
Abstract
DNA can be programmed to self-assemble into high molecular weight 3D assemblies with precise nanometer-scale structural features. Although numerous sequence design strategies exist to realize these assemblies in solution, there is currently no computational framework to predict their 3D structures on the basis of programmed underlying multi-way junction topologies constrained by DNA duplexes. Here, we introduce such an approach and apply it to assemblies designed using the canonical immobile four-way junction. The procedure is used to predict the 3D structure of high molecular weight planar and spherical ring-like origami objects, a tile-based sheet-like ribbon, and a 3D crystalline tensegrity motif, in quantitative agreement with experiments. Our framework provides a new approach to predict programmed nucleic acid 3D structure on the basis of prescribed secondary structure motifs, with possible application to the design of such assemblies for use in biomolecular and materials science. DNA may be used to fabricate functional nanostructures with various possible geometries, but first being able to predict these structures is a challenging task. Here, the authors use coarse-grained modelling to predict the shape of artificial DNA nanostructures in solution.
Collapse
|
42
|
Abstract
Four-way DNA intermediates, called Holliday junctions (HJs), can form during meiotic and mitotic recombination, and their removal is crucial for chromosome segregation. A group of ubiquitous and highly specialized structure-selective endonucleases catalyze the cleavage of HJs into two disconnected DNA duplexes in a reaction called HJ resolution. These enzymes, called HJ resolvases, have been identified in bacteria and their bacteriophages, archaea, and eukaryotes. In this review, we discuss fundamental aspects of the HJ structure and their interaction with junction-resolving enzymes. This is followed by a brief discussion of the eubacterial RuvABC enzymes, which provide the paradigm for HJ resolvases in other organisms. Finally, we review the biochemical and structural properties of some well-characterized resolvases from archaea, bacteriophage, and eukaryotes.
Collapse
Affiliation(s)
- Haley D M Wyatt
- London Research Institute, Cancer Research UK, Clare Hall Laboratories, South Mimms, Herts EN6 3LD, United Kingdom
| | - Stephen C West
- London Research Institute, Cancer Research UK, Clare Hall Laboratories, South Mimms, Herts EN6 3LD, United Kingdom
| |
Collapse
|
43
|
Mukherjee S, Wright WD, Ehmsen KT, Heyer WD. The Mus81-Mms4 structure-selective endonuclease requires nicked DNA junctions to undergo conformational changes and bend its DNA substrates for cleavage. Nucleic Acids Res 2014; 42:6511-22. [PMID: 24744239 PMCID: PMC4041439 DOI: 10.1093/nar/gku265] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Mus81-Mms4/EME1 is a DNA structure-selective endonuclease that cleaves joint DNA molecules that form during homologous recombination in mitotic and meiotic cells. Here, we demonstrate by kinetic analysis using physically tethered DNA substrates that budding yeast Mus81-Mms4 requires inherent rotational flexibility in DNA junctions for optimal catalysis. Förster Resonance Energy Transfer experiments further reveal that recognition of 3′-flap and nicked Holliday junction substrates by Mus81-Mms4 involves induction of a sharp bend with a 100° angle between two duplex DNA arms. In addition, thiol crosslinking of Mus81-Mms4 bound to DNA junctions demonstrates that the heterodimer undergoes a conformational change induced by joint DNA molecules with preferred structural properties. The results from all three approaches suggest a model for catalysis by Mus81-Mms4 in which initial DNA binding is based on minimal structural requirements followed by a rate-limiting conformational transition of the substrate and protein. This leads to a sharply kinked DNA molecule that may fray the DNA four base pairs away from the junction point to position the nuclease for cleavage between the fourth and fifth nucleotide. These data suggest that mutually compatible conformational changes of Mus81-Mms4 and its substrates tailor its incision activity to nicked junction molecules.
Collapse
Affiliation(s)
- Sucheta Mukherjee
- Department of Microbiology & Molecular Genetics, University of California, One Shields Ave., Davis, Davis CA 95616-8665, USA
| | - William Douglass Wright
- Department of Microbiology & Molecular Genetics, University of California, One Shields Ave., Davis, Davis CA 95616-8665, USA
| | - Kirk Tevebaugh Ehmsen
- Department of Microbiology & Molecular Genetics, University of California, One Shields Ave., Davis, Davis CA 95616-8665, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology & Molecular Genetics, University of California, One Shields Ave., Davis, Davis CA 95616-8665, USA Department of Molecular & Cellular Biology, University of California, One Shields Ave., Davis, Davis CA 95616-8665, USA
| |
Collapse
|
44
|
Chen SH, Plank JL, Willcox S, Griffith JD, Hsieh TS. Top3α is required during the convergent migration step of double Holliday junction dissolution. PLoS One 2014; 9:e83582. [PMID: 24392087 PMCID: PMC3879244 DOI: 10.1371/journal.pone.0083582] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 11/06/2013] [Indexed: 11/19/2022] Open
Abstract
Although Blm and Top3α are known to form a minimal dissolvasome that can uniquely undo a double Holliday junction structure, the details of the mechanism remain unknown. It was originally suggested that Blm acts first to create a hemicatenane structure from branch migration of the junctions, followed by Top3α performing strand passage to decatenate the interlocking single strands. Recent evidence suggests that Top3α may also be important for assisting in the migration of the junctions. Using a mismatch-dHJ substrate (MM-DHJS) and eukaryotic Top1 (in place of Top3α), we show that the presence of a topoisomerase is required for Blm to substantially migrate a topologically constrained Holliday junction. When investigated by electron microscopy, these migrated structures did not resemble a hemicatenane. However, when Blm is together with Top3α, the dissolution reaction is processive with no pausing at a partially migrated structure. Potential mechanisms are discussed.
Collapse
Affiliation(s)
- Stefanie Hartman Chen
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Jody L. Plank
- Department of Microbiology, University of California Davis, Davis, California, United States of America
| | - Smaranda Willcox
- Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jack D. Griffith
- Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Tao-shih Hsieh
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- * E-mail:
| |
Collapse
|
45
|
Chen SH, Plank JL, Willcox S, Griffith JD, Hsieh TS. Improved methods for creating migratable Holliday junction substrates. Nucleic Acids Res 2012; 41:e60. [PMID: 23275569 PMCID: PMC3597647 DOI: 10.1093/nar/gks1343] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Previously, we published a method for creating a novel DNA substrate, the double Holliday junction substrate. This substrate contains two Holliday junctions that are mobile, topologically constrained and separated by a distance comparable with conversion tract lengths. Although useful for studying late stage homologous recombination in vitro, construction of the substrate requires significant effort. In particular, there are three bottlenecks: (i) production of large quantities of single-stranded DNA; (ii) the loss of a significant portion of the DNA following the recombination step; and (iii) the loss of DNA owing to inefficient gel extraction. To address these limitations, we have made the following changes to the protocol: (i) use of a helper plasmid, rather than exogenous helper phage, to produce single-stranded DNA; (ii) use of the unidirectional ϕC31 integrase system in place of the bidirectional Cre recombinase reaction; and (iii) gel extraction by DNA diffusion. Here, we describe the changes made to the materials and methods and characterize the substrates that can be produced, including migratable single Holliday junctions, hemicatenanes and a quadruple Holliday junction substrate.
Collapse
|
46
|
Yu X, Wu X, Bermejo GA, Brooks BR, Taraska JW. Accurate high-throughput structure mapping and prediction with transition metal ion FRET. Structure 2012; 21:9-19. [PMID: 23273426 DOI: 10.1016/j.str.2012.11.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/15/2012] [Accepted: 11/17/2012] [Indexed: 11/28/2022]
Abstract
Mapping the landscape of a protein's conformational space is essential to understanding its functions and regulation. The limitations of many structural methods have made this process challenging for most proteins. Here, we report that transition metal ion FRET (tmFRET) can be used in a rapid, highly parallel screen, to determine distances from multiple locations within a protein at extremely low concentrations. The distances generated through this screen for the protein maltose binding protein (MBP) match distances from the crystal structure to within a few angstroms. Furthermore, energy transfer accurately detects structural changes during ligand binding. Finally, fluorescence-derived distances can be used to guide molecular simulations to find low energy states. Our results open the door to rapid, accurate mapping and prediction of protein structures at low concentrations, in large complex systems, and in living cells.
Collapse
Affiliation(s)
- Xiaozhen Yu
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiongwu Wu
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Guillermo A Bermejo
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Justin W Taraska
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
47
|
Bai XC, Martin TG, Scheres SHW, Dietz H. Cryo-EM structure of a 3D DNA-origami object. Proc Natl Acad Sci U S A 2012; 109:20012-7. [PMID: 23169645 PMCID: PMC3523823 DOI: 10.1073/pnas.1215713109] [Citation(s) in RCA: 184] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A key goal for nanotechnology is to design synthetic objects that may ultimately achieve functionalities known today only from natural macromolecular complexes. Molecular self-assembly with DNA has shown potential for creating user-defined 3D scaffolds, but the level of attainable positional accuracy has been unclear. Here we report the cryo-EM structure and a full pseudoatomic model of a discrete DNA object that is almost twice the size of a prokaryotic ribosome. The structure provides a variety of stable, previously undescribed DNA topologies for future use in nanotechnology and experimental evidence that discrete 3D DNA scaffolds allow the positioning of user-defined structural motifs with an accuracy that is similar to that observed in natural macromolecules. Thereby, our results indicate an attractive route to fabricate nanoscale devices that achieve complex functionalities by DNA-templated design steered by structural feedback.
Collapse
Affiliation(s)
- Xiao-chen Bai
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; and
| | - Thomas G. Martin
- Physics Department, Walter Schottky Institute, Technische Universität München, 85748 Garching near Munich, Germany
| | - Sjors H. W. Scheres
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; and
| | - Hendrik Dietz
- Physics Department, Walter Schottky Institute, Technische Universität München, 85748 Garching near Munich, Germany
| |
Collapse
|
48
|
Zhang X, Lee W, Fan X. Bio-switchable optofluidic lasers based on DNA Holliday junctions. LAB ON A CHIP 2012; 12:3673-3675. [PMID: 22790530 DOI: 10.1039/c2lc40183e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Bio-switchable optofluidic lasers based on DNA Holliday junctions were demonstrated. Nearly 100% wavelength switching was achieved through reversible conformational change of the Holliday junction controlled by magnesium ionic strength.
Collapse
Affiliation(s)
- Xingwang Zhang
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, Michigan 48109, USA
| | | | | |
Collapse
|
49
|
Preus S, Wilhelmsson LM. Advances in quantitative FRET-based methods for studying nucleic acids. Chembiochem 2012; 13:1990-2001. [PMID: 22936620 DOI: 10.1002/cbic.201200400] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Indexed: 01/02/2023]
Abstract
Förster resonance energy transfer (FRET) is a powerful tool for monitoring molecular distances and interactions at the nanoscale level. The strong dependence of transfer efficiency on probe separation makes FRET perfectly suited for "on/off" experiments. To use FRET to obtain quantitative distances and three-dimensional structures, however, is more challenging. This review summarises recent studies and technological advances that have improved FRET as a quantitative molecular ruler in nucleic acid systems, both at the ensemble and at the single-molecule levels.
Collapse
Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | | |
Collapse
|
50
|
Sherman WB. HolT Hunter: software for identifying and characterizing low-strain DNA Holliday Triangles. J Comput Chem 2012; 33:1393-405. [PMID: 22488413 DOI: 10.1002/jcc.22975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 02/06/2012] [Accepted: 03/05/2012] [Indexed: 11/11/2022]
Abstract
Synthetic DNA nanostructures are most commonly held together via Holliday junctions. These junctions allow for a wide variety of different angles between the double helices they connect. Nevertheless, only constructs with a very limited selection of angles have been built, to date, because of the computational complexity of identifying structures that fit together with low strain at odd angles. I have developed an algorithm that finds over 95% of the possible solutions by breaking the problem down into two portions. First, there is a problem of how smooth rods can form triangles by lying across one another. This problem is easily handled by numerical computation. Second, there is the question of how distorted DNA double helices would need to be to fit onto the rod structure. This strain is calculated directly. The algorithm has been implemented in a Mathematica 8 notebook called Holliday Triangle Hunter. A large database of solutions has been identified. Additional interface software is available to facilitate drawing and viewing models.
Collapse
Affiliation(s)
- William B Sherman
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973-5000, USA.
| |
Collapse
|