1
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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.
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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
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2
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Zhang Z, Šponer J, Bussi G, Mlýnský V, Šulc P, Simmons CR, Stephanopoulos N, Krepl M. Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. J Chem Inf Model 2023; 63:2794-2809. [PMID: 37126365 PMCID: PMC10170514 DOI: 10.1021/acs.jcim.3c00358] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Holliday junction (HJ) is a noncanonical four-way DNA structure with a prominent role in DNA repair, recombination, and DNA nanotechnology. By rearranging its four arms, HJ can adopt either closed or open state. With enzymes typically recognizing only a single state, acquiring detailed knowledge of the rearrangement process is an important step toward fully understanding the biological function of HJs. Here, we carried out standard all-atom molecular dynamics (MD) simulations of the spontaneous opening-closing transitions, which revealed complex conformational transitions of HJs with an involvement of previously unconsidered "half-closed" intermediates. Detailed free-energy landscapes of the transitions were obtained by sophisticated enhanced sampling simulations. Because the force field overstabilizes the closed conformation of HJs, we developed a system-specific modification which for the first time allows the observation of spontaneous opening-closing HJ transitions in unbiased MD simulations and opens the possibilities for more accurate HJ computational studies of biological processes and nanomaterials.
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Affiliation(s)
- Zhengyue Zhang
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
- CEITEC─Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Petr Šulc
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, 1001 S. McAllister Ave, Tempe, 85287 Arizona, United States
| | - Chad R Simmons
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, 1001 S. McAllister Ave, Tempe, 85287 Arizona, United States
| | - Nicholas Stephanopoulos
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, 1001 S. McAllister Ave, Tempe, 85287 Arizona, United States
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Slechtitelu 241/27, 783 71 Olomouc, Czech Republic
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3
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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.
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4
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Mass OA, Basu S, Patten LK, Terpetschnig EA, Krivoshey AI, Tatarets AL, Pensack RD, Yurke B, Knowlton WB, Lee J. Exciton Chirality Inversion in Dye Dimers Templated by DNA Holliday Junction. J Phys Chem Lett 2022; 13:10688-10696. [PMID: 36355575 PMCID: PMC9706552 DOI: 10.1021/acs.jpclett.2c02721] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
While only one enantiomer of chiral biomolecules performs a biological function, access to both enantiomers (or enantiomorphs) proved to be advantageous for technology. Using dye covalent attachment to a DNA Holliday junction (HJ), we created two pairs of dimers of bis(chloroindolenine)squaraine dye that enabled strongly coupled molecular excitons of opposite chirality in solution. The exciton chirality inversion was achieved by interchanging single covalent linkers of unequal length tethering the dyes of each dimer to the HJ core. Dimers in each pair exhibited profound exciton-coupled circular dichroism (CD) couplets of opposite signs. Dimer geometries, modeled by simultaneous fitting absorption and CD spectra, were related in each pair as nonsuperimposable and nearly exact mirror images. The origin of observed exciton chirality inversion was explained in the view of isomerization of the stacked Holliday junction. This study will open new opportunities for creating excitonic DNA-based materials that rely on programmable system chirality.
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Affiliation(s)
- Olga A. Mass
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Shibani Basu
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Lance K. Patten
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Ewald A. Terpetschnig
- SETA
BioMedicals, LLC, 2014
Silver Court East, Urbana, Illinois 61801, United
States
| | - Alexander I. Krivoshey
- SSI
“Institute for Single Crystals” of the National Academy
of Sciences of Ukraine, 60 Nauky Ave., 61072 Kharkiv, Ukraine
| | - Anatoliy L. Tatarets
- SSI
“Institute for Single Crystals” of the National Academy
of Sciences of Ukraine, 60 Nauky Ave., 61072 Kharkiv, Ukraine
| | - Ryan D. Pensack
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - William B. Knowlton
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Jeunghoon Lee
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
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5
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Nuclease resistance and protein recognition properties of DNA and hybrid PNA-DNA four-way junctions. Biophys Chem 2022; 289:106863. [DOI: 10.1016/j.bpc.2022.106863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/18/2022]
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6
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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.
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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
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7
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Wang W, Chen C, Vecchioni S, Zhang T, Wu C, Ohayon YP, Sha R, Seeman NC, Wei B. Reconfigurable Two‐Dimensional DNA Lattices: Static and Dynamic Angle Control. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202112487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Wen Wang
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
| | - Chunyu Chen
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
| | - Simon Vecchioni
- Department of Chemistry New York University New York New York 10003 USA
| | - Tianqing Zhang
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
| | - Chengxian Wu
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
| | - Yoel P. Ohayon
- Department of Chemistry New York University New York New York 10003 USA
| | - Ruojie Sha
- Department of Chemistry New York University New York New York 10003 USA
| | - Nadrian C. Seeman
- Department of Chemistry New York University New York New York 10003 USA
| | - Bryan Wei
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
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8
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Wang W, Chen C, Vecchioni S, Zhang T, Wu C, Ohayon YP, Sha R, Seeman NC, Wei B. Reconfigurable Two-Dimensional DNA Lattices: Static and Dynamic Angle Control. Angew Chem Int Ed Engl 2021; 60:25781-25786. [PMID: 34596325 DOI: 10.1002/anie.202112487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Indexed: 11/11/2022]
Abstract
Branched DNA motifs serve as the basic construction elements for all synthetic DNA nanostructures. However, precise control of branching orientation remains a key challenge to further heighten the overall structural order. In this study, we use two strategies to control the branching orientation. The first one is based on immobile Holliday junctions which employ specific nucleotide sequences at the branch points which dictate their orientation. The second strategy is to use angle-enforcing struts to fix the branching orientation with flexible spacers at the branch points. We have also demonstrated that the branching orientation control can be achieved dynamically, either by canonical Watson-Crick base pairing or non-canonical nucleobase interactions (e.g., i-motif and G-quadruplex). With precise angle control and feedback from the chemical environment, these results will enable novel DNA nanomechanical sensing devices, and precisely-ordered three-dimensional architectures.
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Affiliation(s)
- Wen Wang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Chunyu Chen
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, New York, 10003, USA
| | - Tianqing Zhang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Chengxian Wu
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York, 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York, 10003, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York, 10003, USA
| | - Bryan Wei
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
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9
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Ray S, Pal N, Walter NG. Single bacterial resolvases first exploit, then constrain intrinsic dynamics of the Holliday junction to direct recombination. Nucleic Acids Res 2021; 49:2803-2815. [PMID: 33619520 PMCID: PMC7969024 DOI: 10.1093/nar/gkab096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 01/30/2021] [Accepted: 02/06/2021] [Indexed: 11/13/2022] Open
Abstract
Homologous recombination forms and resolves an entangled DNA Holliday Junction (HJ) crucial for achieving genetic reshuffling and genome repair. To maintain genomic integrity, specialized resolvase enzymes cleave the entangled DNA into two discrete DNA molecules. However, it is unclear how two similar stacking isomers are distinguished, and how a cognate sequence is found and recognized to achieve accurate recombination. We here use single-molecule fluorescence observation and cluster analysis to examine how prototypic bacterial resolvase RuvC singles out two of the four HJ strands and achieves sequence-specific cleavage. We find that RuvC first exploits, then constrains the dynamics of intrinsic HJ isomer exchange at a sampled branch position to direct cleavage toward the catalytically competent HJ conformation and sequence, thus controlling recombination output at minimal energetic cost. Our model of rapid DNA scanning followed by ‘snap-locking’ of a cognate sequence is strikingly consistent with the conformational proofreading of other DNA-modifying enzymes.
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Affiliation(s)
- Sujay Ray
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan Ann Arbor, MI 48109, USA
| | - Nibedita Pal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan Ann Arbor, MI 48109, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan Ann Arbor, MI 48109, USA
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10
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Troisi M, Klein M, Smith AC, Moorhead G, Kebede Y, Huang R, Parker E, Herrada H, Wade E, Smith S, Broome P, Halsell J, Estevez L, Bell AJ. Conformation and protein interactions of intramolecular DNA and phosphorothioate four-way junctions. Exp Biol Med (Maywood) 2020; 246:707-717. [PMID: 33342281 DOI: 10.1177/1535370220973970] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The objectives of this study are to evaluate the structure and protein recognition features of branched DNA four-way junctions in an effort to explore the therapeutic potential of these molecules. The classic immobile DNA 4WJ, J1, is used as a matrix to design novel intramolecular junctions including natural and phosphorothioate bonds. Here we have inserted H2-type mini-hairpins into the helical termini of the arms of J1 to generate four novel intramolecular four-way junctions. Hairpins are inserted to reduce end fraying and effectively eliminate potential nuclease binding sites. We compare the structure and protein recognition features of J1 with four intramolecular four-way junctions: i-J1, i-J1(PS1), i-J1(PS2) and i-J1(PS3). Circular dichroism studies suggest that the secondary structure of each intramolecular 4WJ is composed predominantly of B-form helices. Thermal unfolding studies indicate that intramolecular four-way junctions are significantly more stable than J1. The Tm values of the hairpin four-way junctions are 25.2° to 32.2°C higher than the control, J1. With respect to protein recognition, gel shift assays reveal that the DNA-binding proteins HMGBb1 and HMGB1 bind the hairpin four-way junctions with affinity levels similar to control, J1. To evaluate nuclease resistance, four-way junctions are incubated with DNase I, exonuclease III (Exo III) and T5 exonuclease (T5 Exo). The enzymes probe nucleic acid cleavage that occurs non-specifically (DNase I) and in a 5'→3' (T5 Exo) and 3'→5' direction (Exo III). The nuclease digestion assays clearly show that the intramolecular four-way junctions possess significantly higher nuclease resistance than the control, J1.
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Affiliation(s)
- Maria Troisi
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Mitchell Klein
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Andrew C Smith
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Gaston Moorhead
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Yonatan Kebede
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Raymond Huang
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Elliott Parker
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Hector Herrada
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Elizabeth Wade
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Samara Smith
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Payson Broome
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Jonah Halsell
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Louis Estevez
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
| | - Anthony J Bell
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
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11
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Nagendran M, Andruska AM, Harbury PB, Desai TJ. Advances in Proximity Ligation in situ Hybridization (PLISH). Bio Protoc 2020; 10:e3808. [PMID: 33659462 PMCID: PMC7842654 DOI: 10.21769/bioprotoc.3808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/25/2020] [Accepted: 09/22/2020] [Indexed: 11/02/2022] Open
Abstract
Understanding tissues in the context of development, maintenance and disease requires determining the molecular profiles of individual cells within their native in vivo spatial context. We developed a Proximity Ligation in situ Hybridization technology (PLISH) that enables quantitative measurement of single cell gene expression in intact tissues, which we have now updated. By recording spatial information for every profiled cell, PLISH enables retrospective mapping of distinct cell classes and inference of their in vivo interactions. PLISH has high sensitivity, specificity and signal to noise ratio. It is also rapid, scalable, and does not require expertise in molecular biology so it can be easily adopted by basic and clinical researchers.
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Affiliation(s)
- Monica Nagendran
- Department of Internal Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Adam M Andruska
- Department of Internal Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Pehr B Harbury
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Tushar J Desai
- Department of Internal Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University School of Medicine, Stanford, California, USA
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12
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Bera SC, Paul T, Iyengar ANS, Mishra PP. Direct observation of the external force mediated conformational dynamics of an IHF bound Holliday junction. Faraday Discuss 2019; 207:251-265. [PMID: 29383368 DOI: 10.1039/c7fd00184c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have investigated the isomerization dynamics and plausible energy landscape of 4-way Holliday junctions (4WHJs) bound to integration host factor (IHF, a DNA binding protein), considering the effect of applied external force, by single-molecule FRET methods. A slowing down of the forward as well as the backward rates of the isomerization process of the protein bound 4WHJ has been observed under the influence of an external force, which indicates an imposed restriction on the conformational switching. This has also been reflected by an increase in rigidity, as observed from the increase in the single-molecule FRET (smFRET)-anisotropy values (0.270 ± 0.012 to 0.360 ± 0.008). The application of an external force has assisted the conformational transitions to share the unstacked open structure intermediate, with different rate-limiting steps and a huge induced variation in the energy landscape. Furthermore, the associated landscape of the 4WHJ is visualized in terms of rarely interconverting states embedded into the two isoforms by using nonlinear dynamics analysis, which shows that the chaoticity of the system increases at intermediate force (0.4 to 1.6 pN). The identification of chaos in our investigation provides useful information for a comprehensive explanation of the origin of the complex behavior of the system, which effectively helps us to perceive the dynamics of IHF bound 4WHJs under the influence of external force, and also demonstrates the applicability of nonlinear dynamics analysis in the field of biology.
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Affiliation(s)
- Subhas C Bera
- Chemical Sciences Division, Saha Institute of Nuclear Physics, HBNI Mumbai, 1/AF Bidhannagar, Kolkata 700064, India.
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13
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Sobhy MA, Bralić A, Raducanu VS, Takahashi M, Tehseen M, Rashid F, Zaher MS, Hamdan SM. Resolution of the Holliday junction recombination intermediate by human GEN1 at the single-molecule level. Nucleic Acids Res 2019; 47:1935-1949. [PMID: 30590761 PMCID: PMC6393306 DOI: 10.1093/nar/gky1280] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/19/2018] [Accepted: 12/13/2018] [Indexed: 01/18/2023] Open
Abstract
Human GEN1 is a cytosolic homologous recombination protein that resolves persisting four-way Holliday junctions (HJ) after the dissolution of the nuclear membrane. GEN1 dimerization has been suggested to play key role in the resolution of the HJ, but the kinetic details of its reaction remained elusive. Here, single-molecule FRET shows how human GEN1 binds the HJ and always ensures its resolution within the lifetime of the GEN1-HJ complex. GEN1 monomer generally follows the isomer bias of the HJ in its initial binding and subsequently distorts it for catalysis. GEN1 monomer remains tightly bound with no apparent dissociation until GEN1 dimer is formed and the HJ is fully resolved. Fast on- and slow off-rates of GEN1 dimer and its increased affinity to the singly-cleaved HJ enforce the forward reaction. Furthermore, GEN1 monomer binds singly-cleaved HJ tighter than intact HJ providing a fail-safe mechanism if GEN1 dimer or one of its monomers dissociates after the first cleavage. The tight binding of GEN1 monomer to intact- and singly-cleaved HJ empowers it as the last resort to process HJs that escape the primary mechanisms.
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Affiliation(s)
- Mohamed A Sobhy
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Amer Bralić
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Vlad-Stefan Raducanu
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Masateru Takahashi
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Muhammad Tehseen
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Fahad Rashid
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Manal S Zaher
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Samir M Hamdan
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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14
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Jiang S, Hong F, Hu H, Yan H, Liu Y. Understanding the Elementary Steps in DNA Tile-Based Self-Assembly. ACS NANO 2017; 11:9370-9381. [PMID: 28813590 DOI: 10.1021/acsnano.7b04845] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Although many models have been developed to guide the design and implementation of DNA tile-based self-assembly systems with increasing complexity, the fundamental assumptions of the models have not been thoroughly tested. To expand the quantitative understanding of DNA tile-based self-assembly and to test the fundamental assumptions of self-assembly models, we investigated DNA tile attachment to preformed "multi-tile" arrays in real time and obtained the thermodynamic and kinetic parameters of single tile attachment in various sticky end association scenarios. With more sticky ends, tile attachment becomes more thermostable with an approximately linear decrease in the free energy change (more negative). The total binding free energy of sticky ends is partially compromised by a sequence-independent energy penalty when tile attachment forms a constrained configuration: "loop". The minimal loop is a 2 × 2 tetramer (Loop4). The energy penalty of loops of 4, 6, and 8 tiles was analyzed with the independent loop model assuming no interloop tension, which is generalizable to arbitrary tile configurations. More sticky ends also contribute to a faster on-rate under isothermal conditions when nucleation is the rate-limiting step. Incorrect sticky end contributes to neither the thermostability nor the kinetics. The thermodynamic and kinetic parameters of DNA tile attachment elucidated here will contribute to the future improvement and optimization of tile assembly modeling, precise control of experimental conditions, and structural design for error-free self-assembly.
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Affiliation(s)
- Shuoxing Jiang
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Fan Hong
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Huiyu Hu
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Hao Yan
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Yan Liu
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
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15
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Song J, Li Z, Wang P, Meyer T, Mao C, Ke Y. Reconfiguration of DNA molecular arrays driven by information relay. Science 2017. [DOI: 10.1126/science.aan3377] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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16
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Abstract
Self-assembling nucleic acid molecules have shown merit as versatile materials for organizing and constructing nanoscale structures with both 2D and 3D geometries. This chapter focuses on strategies in designing DNA gridiron nanostructures based on four-arm junction. This design strategies aims at controlling DNA self-assembly with a higher degree of spatial precision by depicting arbitrary 3D geometries with their wireframe outlines using DNA helices (for edges) and four-arm junctions (for vertices).
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Affiliation(s)
- Dongran Han
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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17
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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.
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18
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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.
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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.
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19
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Dhakal S, Adendorff MR, Liu M, Yan H, Bathe M, Walter NG. Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis. NANOSCALE 2016; 8:3125-3137. [PMID: 26788713 DOI: 10.1039/c5nr07263h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The control of enzymatic reactions using nanoscale DNA devices offers a powerful application of DNA nanotechnology uniquely derived from actuation. However, previous characterization of enzymatic reaction rates using bulk biochemical assays reported suboptimal function of DNA devices such as tweezers. To gain mechanistic insight into this deficiency and to identify design rules to improve their function, here we exploit the synergy of single molecule imaging and computational modeling to characterize the three-dimensional structures and catalytic functions of DNA tweezer-actuated nanoreactors. Our analysis revealed two important deficiencies--incomplete closure upon actuation and conformational heterogeneity. Upon rational redesign of the Holliday junctions located at their hinge and arms, we found that the DNA tweezers could be more completely and uniformly closed. A novel single molecule enzyme assay was developed to demonstrate that our design improvements yield significant, independent enhancements in the fraction of active enzyme nanoreactors and their individual substrate turnover frequencies. The sequence-level design strategies explored here may aid more broadly in improving the performance of DNA-based nanodevices including biological and chemical sensors.
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Affiliation(s)
- Soma Dhakal
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Matthew R Adendorff
- Department of Biological Engineering, Laboratory for Computational Biology & Biophysics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Minghui Liu
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Hao Yan
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Mark Bathe
- Department of Biological Engineering, Laboratory for Computational Biology & Biophysics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Nils G Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA.
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20
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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.
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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
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21
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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.
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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.
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22
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Shoura MJ, Ranatunga RJKU, Harris SA, Nielsen SO, Levene SD. Contribution of fluorophore dynamics and solvation to resonant energy transfer in protein-DNA complexes: a molecular-dynamics study. Biophys J 2015; 107:700-710. [PMID: 25099809 DOI: 10.1016/j.bpj.2014.06.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 06/09/2014] [Accepted: 06/10/2014] [Indexed: 01/23/2023] Open
Abstract
In Förster resonance energy transfer (FRET) experiments, extracting accurate structural information about macromolecules depends on knowing the positions and orientations of donor and acceptor fluorophores. Several approaches have been employed to reduce uncertainties in quantitative FRET distance measurements. Fluorophore-position distributions can be estimated by surface accessibility (SA) calculations, which compute the region of space explored by the fluorophore within a static macromolecular structure. However, SA models generally do not take fluorophore shape, dye transition-moment orientation, or dye-specific chemical interactions into account. We present a detailed molecular-dynamics (MD) treatment of fluorophore dynamics for an ATTO donor/acceptor dye pair and specifically consider as case studies dye-labeled protein-DNA intermediates in Cre site-specific recombination. We carried out MD simulations in both an aqueous solution and glycerol/water mixtures to assess the effects of experimental solvent systems on dye dynamics. Our results unequivocally show that MD simulations capture solvent effects and dye-dye interactions that can dramatically affect energy transfer efficiency. We also show that results from SA models and MD simulations strongly diverge in cases where donor and acceptor fluorophores are in close proximity. Although atomistic simulations are computationally more expensive than SA models, explicit MD studies are likely to give more realistic results in both homogeneous and mixed solvents. Our study underscores the model-dependent nature of FRET analyses, but also provides a starting point to develop more realistic in silico approaches for obtaining experimental ensemble and single-molecule FRET data.
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Affiliation(s)
- Massa J Shoura
- Department of Bioengineering, University of Texas at Dallas, Richardson, Texas; Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas
| | | | - Sarah A Harris
- Department of Physics and Astronomy, University of Leeds, Leeds, UK
| | - Steven O Nielsen
- Department of Chemistry, University of Texas at Dallas, Richardson, Texas
| | - Stephen D Levene
- Department of Bioengineering, University of Texas at Dallas, Richardson, Texas; Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas; Department of Physics, University of Texas at Dallas, Richardson, Texas.
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23
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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.
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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
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24
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Han D, Pal S, Yang Y, Jiang S, Nangreave J, Liu Y, Yan H. DNA gridiron nanostructures based on four-arm junctions. Science 2013; 339:1412-5. [PMID: 23520107 DOI: 10.1126/science.1232252] [Citation(s) in RCA: 188] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Engineering wireframe architectures and scaffolds of increasing complexity is one of the important challenges in nanotechnology. We present a design strategy to create gridiron-like DNA structures. A series of four-arm junctions are used as vertices within a network of double-helical DNA fragments. Deliberate distortion of the junctions from their most relaxed conformations ensures that a scaffold strand can traverse through individual vertices in multiple directions. DNA gridirons were assembled, ranging from two-dimensional arrays with reconfigurability to multilayer and three-dimensional structures and curved objects.
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Affiliation(s)
- Dongran Han
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
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25
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Vitoc CI, Mukerji I. HU binding to a DNA four-way junction probed by Förster resonance energy transfer. Biochemistry 2011; 50:1432-41. [PMID: 21230005 PMCID: PMC4724199 DOI: 10.1021/bi1007589] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The Escherichia coli protein HU is a non-sequence-specific DNA-binding protein that interacts with DNA primarily through electrostatic interactions. In addition to nonspecific binding to linear DNA, HU has been shown to bind with nanomolar affinity to discontinuous DNA substrates, such as repair and recombination intermediates. This work specifically examines the HU-four-way junction (4WJ) interaction using fluorescence spectroscopic methods. The conformation of the junction in the presence of different counterions was investigated by Förster resonance energy transfer (FRET) measurements, which revealed an ion-type conformational dependence, where Na(+) yields the most stacked conformation followed by K(+) and Mg(2+). HU binding induces a greater degree of stacking in the Na(+)-stabilized and Mg(2+)-stabilized junctions but not the K(+)-stabilized junction, which is attributed to differences in the size of the ionic radii and potential differences in ion binding sites. Interestingly, junction conformation modulates binding affinity, where HU exhibits the lowest affinity for the Mg(2+)-stabilized form (24 μM(-1)), which is the least stacked conformation. Protein binding to a mixed population of open and stacked forms of the junction leads to nearly complete formation of a protein-stabilized stacked-X junction. These results strongly support a model in which HU binds to and stabilizes the stacked-X conformation.
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Affiliation(s)
- Codruta Iulia Vitoc
- Molecular Biology and Biochemistry Department, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459-0175
| | - Ishita Mukerji
- Molecular Biology and Biochemistry Department, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459-0175
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26
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Nangreave J, Yan H, Liu Y. DNA nanostructures as models for evaluating the role of enthalpy and entropy in polyvalent binding. J Am Chem Soc 2011; 133:4490-7. [PMID: 21381740 DOI: 10.1021/ja1103298] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA nanotechnology allows the design and construction of nanoscale objects that have finely tuned dimensions, orientation, and structure with remarkable ease and convenience. Synthetic DNA nanostructures can be precisely engineered to model a variety of molecules and systems, providing the opportunity to probe very subtle biophysical phenomena. In this study, several such synthetic DNA nanostructures were designed to serve as models to study the binding behavior of polyvalent molecules and gain insight into how small changes to the ligand/receptor scaffolds, intended to vary their conformational flexibility, will affect their association equilibrium. This approach has yielded a quantitative identification of the roles of enthalpy and entropy in the affinity of polyvalent DNA nanostructure interactions, which exhibit an intriguing compensating effect.
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Affiliation(s)
- Jeanette Nangreave
- Department of Chemistry and Biochemistry and Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
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27
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Rindermann JJ, Akhtman Y, Richardson J, Brown T, Lagoudakis PG. Gauging the Flexibility of Fluorescent Markers for the Interpretation of Fluorescence Resonance Energy Transfer. J Am Chem Soc 2010; 133:279-85. [DOI: 10.1021/ja105720j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jan J. Rindermann
- School of Physics and Astronomy and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom, and Department of Computer Science, Maths and Physics, The University of the West Indies, Cave Hill, Bridgetown BB11000, Barbados
| | - Yosef Akhtman
- School of Physics and Astronomy and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom, and Department of Computer Science, Maths and Physics, The University of the West Indies, Cave Hill, Bridgetown BB11000, Barbados
| | - James Richardson
- School of Physics and Astronomy and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom, and Department of Computer Science, Maths and Physics, The University of the West Indies, Cave Hill, Bridgetown BB11000, Barbados
| | - Tom Brown
- School of Physics and Astronomy and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom, and Department of Computer Science, Maths and Physics, The University of the West Indies, Cave Hill, Bridgetown BB11000, Barbados
| | - Pavlos G. Lagoudakis
- School of Physics and Astronomy and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom, and Department of Computer Science, Maths and Physics, The University of the West Indies, Cave Hill, Bridgetown BB11000, Barbados
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28
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Papadakis G, Tsortos A, Gizeli E. Acoustic characterization of nanoswitch structures: application to the DNA Holliday Junction. NANO LETTERS 2010; 10:5093-5097. [PMID: 21038866 DOI: 10.1021/nl103491v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A novel biophysical approach in combination with an acoustic device is demonstrated as a sensitive, rapid, and label-free technique for characterizing various structures of the DNA Holliday Junction (J1) nanoswitch. We were successful in discriminating the "closed" from the "open" state, as well as confirming that the digestion of the J1 junction resulted in the two, anticipated, rod-shaped, 20 bp long fragments. Furthermore, we propose a possible structure for the ∼10 nm long (DNA58) component participating in the J1 assembly. This work reveals the potential of acoustic devices as a powerful tool for molecular conformation studies.
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Affiliation(s)
- George Papadakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 100 N. Plastira, Vassilika Vouton, 70013 Heraklion, Greece
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29
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Campbell CJ, Mountford CP, Stoquert HC, Buck AH, Dickinson P, Ferapontova E, Terry JG, Beattie JS, Walton AJ, Crain J, Ghazal P, Mount AR. A DNA nanoswitch incorporating the fluorescent base analogue 2-aminopurine detects single nucleotide mismatches in unlabelled targets. Analyst 2009; 134:1873-9. [PMID: 19684913 DOI: 10.1039/b900325h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
DNA nanoswitches can be designed to detect unlabelled nucleic acid targets and have been shown to discriminate between targets which differ in the identity of only one base. This paper demonstrates that the fluorescent base analogue 2-aminopurine (AP) can be used to discriminate between nanoswitches with and without targets and to discriminate between matched and mismatched targets. In particular, we have used both steady-state and time-resolved fluorescence spectroscopy to determine differences in AP environment at the branchpoint of nanoswitches assembled using complementary targets and targets which incorporate single base mismatches.
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Affiliation(s)
- Colin J Campbell
- Division of Pathway Medicine, University of Edinburgh, Edinburgh, UK EH16 4SB.
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30
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Karymov MA, Chinnaraj M, Bogdanov A, Srinivasan AR, Zheng G, Olson WK, Lyubchenko YL. Structure, dynamics, and branch migration of a DNA Holliday junction: a single-molecule fluorescence and modeling study. Biophys J 2008; 95:4372-83. [PMID: 18658216 PMCID: PMC2567953 DOI: 10.1529/biophysj.108.135103] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Accepted: 07/18/2008] [Indexed: 11/18/2022] Open
Abstract
The Holliday junction (HJ) is a central intermediate of various genetic processes, including homologous and site-specific DNA recombination and DNA replication. Elucidating the structure and dynamics of HJs provides the basis for understanding the molecular mechanisms of these genetic processes. Our previous single-molecule fluorescence studies led to a model according to which branch migration is a stepwise process consisting of consecutive migration and folding steps. These data led us to the conclusion that one hop can be more than 1 basepair (bp); moreover, we hypothesized that continuous runs over the entire sequence homology (5 bp) can occur. Direct measurements of the dependence of the fluorescence resonance energy transfer (FRET) value on the donor-acceptor (D-A) distance are required to justify this model and are the major goal of this article. To accomplish this goal, we performed single-molecule FRET experiments with a set of six immobile HJ molecules with varying numbers of bps between fluorescent dyes placed on opposite arms. The designs were made in such a way that the distances between the donor and acceptor were equal to the distances between the dyes formed upon 1-bp migration hops of a HJ having 10-bp homology. Using these designs, we confirmed our previous hypothesis that the migration of the junction can be measured with bp accuracy. Moreover, the FRET values determined for each acceptor-donor separation corresponded very well to the values for the steps on the FRET time trajectories, suggesting that each step corresponds to the migration of the branch at a defined depth. We used the dependence of the FRET value on the D-A distance to measure directly the size for each step on the FRET time trajectories. These data showed that one hop is not necessarily 1 bp. The junction is able to migrate over several bps, detected as one hop and confirming our model. The D-A distances extracted from the FRET properties of the immobile junctions formed the basis for modeling the HJ structures. The composite data fit a partially opened, side-by-side model with adjacent double-helical arms slightly kinked at the four-way junction and the junction as a whole adopting a global X-shaped form that mimics the coaxially stacked-X structure implicated in previous solution studies.
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Affiliation(s)
- Mikhail A Karymov
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, USA
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Abstract
Electrophoresis in polyacrylamide gels provides a simple yet powerful means of analyzing the relative disposition of helical arms in branched nucleic acids. The electrophoretic mobility of DNA or RNA with a central discontinuity is determined by the angle subtended between the arms radiating from the branchpoint. In a multi-helical branchpoint, comparative gel electrophoresis can provide a relative measure of all the inter-helical angles and thus the shape and symmetry of the molecule. Using the long-short arm approach, the electrophoretic mobility of all the species with two helical arms that are longer than all others is compared. This can be done as a function of conditions, allowing the analysis of ion-dependent folding of branched DNA and RNA species. Notable successes for the technique include the four-way (Holliday) junction in DNA and helical junctions in functionally significant RNA species such as ribozymes. Many of these structures have subsequently been proved correct by crystallography or other methods, up to 10 years later in the case of the Holliday junction. Just as important, the technique has not failed to date. Comparative gel electrophoresis can provide a window on both fast and slow conformational equilibria such as conformer exchange in four-way DNA junctions. But perhaps the biggest test of the approach has been to deduce the structures of complexes of four-way DNA junctions with proteins. Two recent crystallographic structures show that the global structures were correctly deduced by electrophoresis, proving the worth of the method even in these rather complex systems. Comparative gel electrophoresis is a robust method for the analysis of branched nucleic acids and their complexes.
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32
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Vámosi G, Clegg RM. Helix−Coil Transition of a Four-Way DNA Junction Observed by Multiple Fluorescence Parameters. J Phys Chem B 2008; 112:13136-48. [DOI: 10.1021/jp8034055] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- György Vámosi
- Cell Biology and Signaling Research Group of the Hungarian Academy of Sciences, Department of Biophysics and Cell Biology, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary HU H-4012, and Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801-3080
| | - Robert M. Clegg
- Cell Biology and Signaling Research Group of the Hungarian Academy of Sciences, Department of Biophysics and Cell Biology, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary HU H-4012, and Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801-3080
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Mountford CP, Buck AH, Campbell CJ, Dickinson P, Ferapontova EE, Terry JG, Beattie JS, Walton AJ, Ghazal P, Mount AR, Crain J. Molecular Recognition with DNA Nanoswitches: Effects of Single Base Mutations on Structure. J Phys Chem B 2008; 112:2439-44. [DOI: 10.1021/jp073817o] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- C. P. Mountford
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - A. H. Buck
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - C. J. Campbell
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - P. Dickinson
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - E. E. Ferapontova
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - J. G. Terry
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - J. S. Beattie
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - A. J. Walton
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - P. Ghazal
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - A. R. Mount
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - J. Crain
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
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34
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Buck AH, Campbell CJ, Dickinson P, Mountford CP, Stoquert HC, Terry JG, Evans SAG, Keane LM, Su TJ, Mount AR, Walton AJ, Beattie JS, Crain J, Ghazal P. DNA nanoswitch as a biosensor. Anal Chem 2007; 79:4724-8. [PMID: 17508719 DOI: 10.1021/ac070251r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a new type of DNA switch, based on the Holliday junction, that uses a combination of binding and conformational switching to enable specific label-free detection of DNA and RNA. We show that a single RNA oligonucleotide species can be detected in a complex mixture of extracted cellular RNA and demonstrate that by exploiting different aspects of the switch characteristics we can achieve 30-fold discrimination between single-nucleotide mismatches in a DNA oligonucleotide.
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35
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Voth AR, Hays FA, Ho PS. Directing macromolecular conformation through halogen bonds. Proc Natl Acad Sci U S A 2007; 104:6188-93. [PMID: 17379665 PMCID: PMC1851028 DOI: 10.1073/pnas.0610531104] [Citation(s) in RCA: 308] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Indexed: 11/18/2022] Open
Abstract
The halogen bond, a noncovalent interaction involving polarizable chlorine, bromine, or iodine molecular substituents, is now being exploited to control the assembly of small molecules in the design of supramolecular complexes and new materials. We demonstrate that a halogen bond formed between a brominated uracil and phosphate oxygen can be engineered to direct the conformation of a biological molecule, in this case to define the conformational isomer of a four-stranded DNA junction when placed in direct competition against a classic hydrogen bond. As a result, this bromine interaction is estimated to be approximately 2-5 kcal/mol stronger than the analogous hydrogen bond in this environment, depending on the geometry of the halogen bond. This study helps to establish halogen bonding as a potential tool for the rational design and construction of molecular materials with DNA and other biological macromolecules.
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Affiliation(s)
- Andrea Regier Voth
- Department of Biochemistry and Biophysics, ALS 2011, Oregon State University, Corvallis, OR 97331-7503
| | - Franklin A. Hays
- Department of Biochemistry and Biophysics, ALS 2011, Oregon State University, Corvallis, OR 97331-7503
| | - P. Shing Ho
- Department of Biochemistry and Biophysics, ALS 2011, Oregon State University, Corvallis, OR 97331-7503
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36
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Mount AR, Mountford CP, Evans SAG, Su TJ, Buck AH, Dickinson P, Campbell CJ, Keane LM, Terry JG, Beattie JS, Walton AJ, Ghazal P, Crain J. The stability and characteristics of a DNA Holliday junction switch. Biophys Chem 2006; 124:214-21. [PMID: 16716492 DOI: 10.1016/j.bpc.2006.03.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Accepted: 03/25/2006] [Indexed: 11/17/2022]
Abstract
A Holliday junction (HJ) consists of four DNA double helices, with a branch point discontinuity at the intersection of the component strands. At low ionic strength, the HJ adopts an open conformation, with four widely spaced arms, primarily due to strong electrostatic repulsion between the phosphate groups on the backbones. At high ionic strength, screening of this repulsion induces a switch to a more compact (closed) junction conformation. Fluorescent labelling with dyes placed on the HJ arms allows this conformational switch to be detected optically using fluorescence resonance energy transfer (FRET), producing a sensitive fluorescent output of the switch state. This paper presents a systematic and quantitative survey of the switch characteristics of such a labelled HJ. A short HJ (arm length 8 bp) is shown to be prone to dissociation at low switching ion concentration, whereas an HJ of arm length 12 bp is shown to be stable over all switching ion concentrations studied. The switching characteristics of this HJ have been systematically and quantitatively studied for a variety of switching ions, by measuring the required ion concentration, the sharpness of the switching transition and the fluorescent output intensity of the open and closed states. This stable HJ is shown to have favourable switch characteristics for a number of inorganic switching ions, making it a promising candidate for use in nanoscale biomolecular switch devices.
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Affiliation(s)
- A R Mount
- School of Chemistry, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JJ, UK.
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37
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Myong S, Stevens BC, Ha T. Bridging conformational dynamics and function using single-molecule spectroscopy. Structure 2006; 14:633-43. [PMID: 16615904 DOI: 10.1016/j.str.2006.02.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2005] [Revised: 01/28/2006] [Accepted: 02/06/2006] [Indexed: 11/29/2022]
Abstract
In a typical structure-function relation study, the primary structure of proteins or nucleic acids is changed by mutagenesis and its functional effect is measured via biochemical means. Single-molecule spectroscopy has begun to give a whole new meaning to the "structure-function relation" by measuring the real-time conformational changes of individual biological macromolecules while they are functioning. This review discusses a few recent examples: untangling internal chemistry and conformational dynamics of a ribozyme, branch migration landscape of a Holliday junction at a single-step resolution, tRNA selection and dynamics in a ribosome, repetitive shuttling and snapback of a helicase, and discrete rotation of an ATP synthase.
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Affiliation(s)
- Sua Myong
- Department of Physics, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
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38
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Liu J, Déclais AC, McKinney SA, Ha T, Norman DG, Lilley DMJ. Stereospecific effects determine the structure of a four-way DNA junction. ACTA ACUST UNITED AC 2005; 12:217-28. [PMID: 15734649 DOI: 10.1016/j.chembiol.2004.12.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2004] [Revised: 11/08/2004] [Accepted: 12/03/2004] [Indexed: 11/25/2022]
Abstract
Conversion of a centrally located phosphate group to an electrically neutral methyl phosphonate in a four-way DNA junction can exert a major influence on its conformation. However, the effect is strongly dependent on stereochemistry. Substitution of the proR oxygen atom by methyl leads to conformational transition to the stacking conformer that places this phosphate at the point of strand exchange. By contrast, corresponding modification of the proS oxygen destabilizes this conformation of the junction. Single-molecule analysis shows that both molecules are in a dynamic equilibrium between alternative stacking conformers, but the configuration of the methyl phosphonate determines the bias of the conformational equilibrium. It is likely that the stereochemical environment of the methyl group affects the interaction with metal ions in the center of the junction.
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Affiliation(s)
- Jia Liu
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH , United Kingdom
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39
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Potaman VN, Shlyakhtenko LS, Oussatcheva EA, Lyubchenko YL, Soldatenkov VA. Specific Binding of Poly(ADP-ribose) Polymerase-1 to Cruciform Hairpins. J Mol Biol 2005; 348:609-15. [PMID: 15826658 DOI: 10.1016/j.jmb.2005.03.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2004] [Revised: 02/27/2005] [Accepted: 03/02/2005] [Indexed: 10/25/2022]
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) participates in DNA cleavage and rejoining-dependent reactions, such as DNA replication, recombination and repair. PARP-1 is also important in transcriptional regulation, although the determinants for its binding to undamaged genomic DNA have not been defined. Previously, we have shown by low-resolution mapping that PARP-1 may bind to the cruciform-forming regions of its own promoter. Here, using DNase I and nuclease P(1) footprinting and atomic force microscopy, we show that PARP-1 binds to stem/loop boundaries of cruciform hairpins. Cleavage of the cruciform by the junction resolvase T4 endonuclease VII is independent of PARP-1, which indicates that PARP-1 does not bind to the four-arm junctions of the cruciform. Thus, PARP-1 differs from other cruciform-binding proteins by binding to hairpin tips rather than to junctions. Furthermore, our data indicate that PARP-1 can interact with the gene regulatory sequences by binding to the promoter-localized cruciforms.
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Affiliation(s)
- Vladimir N Potaman
- Institute of Biosciences and Technology, Texas A & M University System Health Science Center, 2121 W. Holcombe Blvd., Houston, TX 77030, USA.
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40
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McKinney SA, Freeman ADJ, Lilley DMJ, Ha T. Observing spontaneous branch migration of Holliday junctions one step at a time. Proc Natl Acad Sci U S A 2005; 102:5715-20. [PMID: 15824311 PMCID: PMC556122 DOI: 10.1073/pnas.0409328102] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genetic recombination occurs between homologous DNA molecules via a four-way (Holliday) junction intermediate. This ancient and ubiquitous process is important for the repair of double-stranded breaks, the restart of stalled replication forks, and the creation of genetic diversity. Once formed, the four-way junction alone can undergo the stepwise exchange of base pairs known as spontaneous branch migration. Conventional ensemble assays, useful for finding average migration rates over long sequences, have been unable to examine the affect of sequence and structure on the migration process. Here, we present a single-molecule spontaneous branch migration assay with single-base pair resolution in a study of individual DNA junctions that can undergo one step of migration. Junctions exhibit markedly different dynamics of exchange between stacking conformers depending on the point of strand exchange, allowing the moment at which branch migration occurs to be detected. The free energy landscape of spontaneous branch migration is found to be highly nonuniform and governed by two types of sequence-dependent barriers, with unmediated local migration being up to 10 times more rapid than the previously deduced average rate.
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Affiliation(s)
- Sean A McKinney
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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41
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Liu J, Déclais AC, Lilley DMJ. Electrostatic Interactions and the Folding of the Four-way DNA Junction: Analysis by Selective Methyl Phosphonate Substitution. J Mol Biol 2004; 343:851-64. [PMID: 15476805 DOI: 10.1016/j.jmb.2004.08.079] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Revised: 08/24/2004] [Accepted: 08/25/2004] [Indexed: 11/16/2022]
Abstract
The structure and dynamics of the four-way (Holliday) junction are strongly dependent on the presence of metal ions. In this study, the importance of phosphate charge in and around the point of strand exchange has been explored by selective replacement with electrically neutral methyl phosphonate groups, guided by crystal structures of the junction in the folded, stacked X conformation. Junction conformation has been analysed by comparative gel electrophoresis and fluorescence resonance energy transfer (FRET). Three of sets of phosphate groups on the exchanging strands have been analysed; those at the point of strand exchange and those to their 3' and 5' sides. The exchanging and 3' phosphate groups form a box of negatively charged groups on the minor groove face of the junction, while the 5' phosphate groups face each other on the major groove side, with their proR oxygen atoms directed at one another. The largest effects are observed on substitution of the exchanging phosphate groups; replacement of both groups leads to the loss of the requirement for addition of metal ions to allow junction folding. When the equivalent phosphate groups on the continuous strands were substituted, a proportion of the junction folded into the alternative conformer so as to bring these phosphate groups onto the exchanging strands. These species did not interconvert, and thus this is likely to result from the alternative diasteromeric forms of the methyl phosphonate group. This shows that some of the conformational effects result from more than purely electrostatic interactions. Smaller but significant effects were observed on substitution of the flanking phosphate groups. All methyl phosphonate substitutions at these positions allowed folding to proceed at a reduced concentration of magnesium ions, with double substitutions more effective than single substitutions. Substitution of 5' phosphates resulted in a greater degree of folding at a given ionic concentration compared to the corresponding 3' phosphate substitutions. These results show that the phosphate groups at the point of strand exchange exert the largest electrostatic effect on junction folding, but a number of phosphate groups in the vicinity of the exchange region contribute to the overall effects.
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Affiliation(s)
- Jia Liu
- Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, UK
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42
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Joo C, McKinney SA, Lilley DMJ, Ha T. Exploring rare conformational species and ionic effects in DNA Holliday junctions using single-molecule spectroscopy. J Mol Biol 2004; 341:739-51. [PMID: 15288783 DOI: 10.1016/j.jmb.2004.06.024] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2004] [Revised: 05/24/2004] [Accepted: 06/07/2004] [Indexed: 11/28/2022]
Abstract
The four-way DNA (Holliday) junction is an essential intermediate in DNA recombination, and its dynamic characteristics are likely to be important in its cellular processing. In our previous study we observed transitions between two antiparallel stacked conformations using a single-molecule fluorescence approach. The magnesium concentration-dependent rates of transitions between stacking conformers suggested that an unstacked open structure, which is stable in the absence of metal ions, is an intermediate. Here, we sought to detect possible rare species such as open and parallel conformations and further characterized ionic effects. The hypothesized open intermediate cannot be resolved directly due to the limited time resolution and sensitivity, but our study suggests that the open form is achieved very frequently, hundreds of times per second under physiologically relevant conditions. Therefore despite being a minority species, its frequent formation raises the probability that it could become stabilized by protein binding. By contrast, we cannot detect even a transient existence of the junctions in a parallel form, and the probability of such forms with a lifetime greater than 5 ms is less than 0.01%. Stacking conformer transitions are observable in the presence of sodium or hexammine cobalt (III) ions as well as magnesium ions, but the transition rates are higher for lower valence ions at the same concentrations. This further supports the notion that electrostatic stabilization of the stacked structures dictates the interconversion rates between different structural forms.
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Affiliation(s)
- Chirlmin Joo
- Physics Department, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
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43
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Wu B, Girard F, van Buuren B, Schleucher J, Tessari M, Wijmenga S. Global structure of a DNA three-way junction by solution NMR: towards prediction of 3H fold. Nucleic Acids Res 2004; 32:3228-39. [PMID: 15199171 PMCID: PMC434450 DOI: 10.1093/nar/gkh645] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Three-way junctions (3H) are the simplest and most commonly occurring branched nucleic acids. They consist of three double helical arms (A to C), connected at the junction point, with or without a number of unpaired bases in one or more of the three different strands. Three-way junctions with two unpaired bases in one strand (3HS2) have a high tendency to adopt either of two alternative stacked conformations in which two of the three arms A, B and C are coaxially stacked, i.e. A/B-stacked or A/C-stacked. Empirical stacking rules, which successfully predict for DNA 3HS2 A/B-stacking preference from sequence, have been extended to A/C-stacked conformations. Three novel DNA 3HS2 sequences were designed to test the validity of these extended stacking rules and their conformational behavior was studied by solution NMR. All three show the predicted A/C-stacking preference even in the absence of multivalent cations. The stacking preference for both classes of DNA 3HS2 can thus be predicted from sequence. The high-resolution NMR solution structure for one of the stacked 3HS2 is also reported. It shows a well-defined local and global structure defined by an extensive set of classical NMR restraints and residual dipolar couplings. Analysis of its global conformation and that of other representatives of the 3H family, shows that the relative orientations of the stacked and non-stacked arms, are restricted to narrow regions of conformational space, which can be understood from geometric considerations. Together, these findings open up the possibility of full prediction of 3HS2 conformation (stacking and global fold) directly from sequence.
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Affiliation(s)
- Bin Wu
- Department of Physical Chemistry/Biophysical Chemistry, University of Nijmegen, Toernooiveld 1 6225 ED Nijmegen, The Netherlands
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44
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Watson J, Hays FA, Ho PS. Definitions and analysis of DNA Holliday junction geometry. Nucleic Acids Res 2004; 32:3017-27. [PMID: 15173384 PMCID: PMC434437 DOI: 10.1093/nar/gkh631] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2004] [Revised: 05/11/2004] [Accepted: 05/11/2004] [Indexed: 11/14/2022] Open
Abstract
A number of single-crystal structures have now been solved of the four-stranded antiparallel stacked-X form of the Holliday junction. These structures demonstrate how base sequence, substituents, and drug and ion interactions affect the general conformation of this recombination intermediate. The geometry of junctions had previously been described in terms of a specific set of parameters that include: (i) the angle relating the ends of DNA duplexes arms of the junction (interduplex angle); (ii) the relative rotation of the duplexes about the helix axes of the stacked duplex arms (J(roll)); and (iii) the translation of the duplexes along these helix axes (J(slide)). Here, we present a consistent set of definitions and methods to accurately calculate each of these parameters based on the helical features of the stacked duplex arms in the single-crystal structures of the stacked-X junction, and demonstrate how each of these parameters contributes to an overall conformational feature of the structure. We show that the values for these parameters derived from global rather than local helical axes through the stacked bases of the duplex arms are the most representative of the stacked-X junction conformation. In addition, a very specific parameter (J(twist)) is introduced which relates the relative orientation of the stacked duplex arms across the junction which, unlike the interduplex angle, is length independent. The results from this study provide a general means to relate the geometric features seen in the crystal structures to those determined in solution.
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Affiliation(s)
- Jeffrey Watson
- Department of Biochemistry and Biophysics, ALS 2011, Oregon State University, Corvallis, OR 97331-7305, USA
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Ghosh S, Grove A. Histone-like Protein HU from Deinococcus radiodurans Binds Preferentially to Four-way DNA Junctions. J Mol Biol 2004; 337:561-71. [PMID: 15019777 DOI: 10.1016/j.jmb.2004.02.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2003] [Revised: 01/23/2004] [Accepted: 02/05/2004] [Indexed: 01/31/2023]
Abstract
The histone-like protein HU from Escherichia coli is involved in DNA compaction and in processes such as DNA repair and recombination. Its participation in these events is reflected in its ability to bend DNA and in its preferred binding to DNA junctions and DNA with single-strand breaks. Deinococcus radiodurans is unique in its ability to reconstitute its genome from double strand breaks incurred after exposure to ionizing radiation. Using electrophoretic mobility shift assays (EMSA), we show that D.radiodurans HU (DrHU) binds preferentially only to DNA junctions, with half-maximal saturation of 18 nM. In distinct contrast to E.coli HU, DrHU does not exhibit a marked preference for DNA with nicks or gaps compared to perfect duplex DNA, nor is it able to mediate circularization of linear duplex DNA. These unexpected properties identify DrHU as the first member of the HU protein family not to serve an architectural role and point to its potential participation in DNA recombination events. Our data also point to a mechanism whereby differential target site selection by HU proteins is achieved and suggest that the substrate specificity of HU proteins should be expected to vary as a consequence of their individual capacity for inducing the required DNA bend.
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Affiliation(s)
- Sharmistha Ghosh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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Wang H, Yang Y, Schofield MJ, Du C, Fridman Y, Lee SD, Larson ED, Drummond JT, Alani E, Hsieh P, Erie DA. DNA bending and unbending by MutS govern mismatch recognition and specificity. Proc Natl Acad Sci U S A 2003; 100:14822-7. [PMID: 14634210 PMCID: PMC299810 DOI: 10.1073/pnas.2433654100] [Citation(s) in RCA: 152] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA mismatch repair is central to the maintenance of genomic stability. It is initiated by the recognition of base-base mismatches and insertion/deletion loops by the family of MutS proteins. Subsequently, ATP induces a unique conformational change in the MutS-mismatch complex but not in the MutS-homoduplex complex that sets off the cascade of events that leads to repair. To gain insight into the mechanism by which MutS discriminates between mismatch and homoduplex DNA, we have examined the conformations of specific and nonspecific MutS-DNA complexes by using atomic force microscopy. Interestingly, MutS-DNA complexes exhibit a single population of conformations, in which the DNA is bent at homoduplex sites, but two populations of conformations, bent and unbent, at mismatch sites. These results suggest that the specific recognition complex is one in which the DNA is unbent. Combining our results with existing biochemical and crystallographic data leads us to propose that MutS: (i) binds to DNA nonspecifically and bends it in search of a mismatch; (ii) on specific recognition of a mismatch, undergoes a conformational change to an initial recognition complex in which the DNA is kinked, with interactions similar to those in the published crystal structures; and (iii) finally undergoes a further conformational change to the ultimate recognition complex in which the DNA is unbent. Our results provide a structural explanation for the long-standing question of how MutS achieves mismatch repair specificity.
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Affiliation(s)
- Hong Wang
- Department of Chemistry and Curriculum in Applied and Materials Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
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Hays FA, Watson J, Ho PS. Caution! DNA crossing: crystal structures of Holliday junctions. J Biol Chem 2003; 278:49663-6. [PMID: 14563836 DOI: 10.1074/jbc.r300033200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Franklin A Hays
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305, USA
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Melcher SE, Wilson TJ, Lilley DMJ. The dynamic nature of the four-way junction of the hepatitis C virus IRES. RNA (NEW YORK, N.Y.) 2003; 9:809-20. [PMID: 12810915 PMCID: PMC1370448 DOI: 10.1261/rna.5130703] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2003] [Accepted: 03/26/2003] [Indexed: 05/19/2023]
Abstract
Translation is initiated within the RNA of the hepatitis C virus at the internal ribosome entry site (IRES). The IRES is a 341-nucleotide element that contains a four-way helical junction (IIIabc) as a functionally important element of the secondary structure. The junction has three additional, nonpaired nucleotides at the point of strand exchange on one diagonal. We have studied the global conformation and folding of this junction in solution, using comparative gel electrophoresis and steady-state and time-resolved fluorescence resonance energy transfer. In the absence of divalent metal ions, the junction adopts an extended-square structure, in contrast to perfect four-way RNA junctions, which retain coaxial helical stacking under all conditions. The IIIabc junction is induced to fold on addition of Mg(2+), by pairwise coaxial stacking of arms, into the conformer in which the unpaired bases are located on the exchanging strands. Fluorescence lifetime measurements indicate that in the presence of Mg(2+) ions, the IIIabc junction exists in a dynamic equilibrium comprising approximately equal populations of antiparallel and parallel species. These dynamic properties may be important in mediating interactions between the IRES and the ribosome and initiation factors.
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Affiliation(s)
- Sonya E Melcher
- Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, UK
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Li G, Tolstonog GV, Sabasch M, Traub P. Type III intermediate filament proteins interact with four-way junction DNA and facilitate its cleavage by the junction-resolving enzyme T7 endonuclease I. DNA Cell Biol 2003; 22:261-91. [PMID: 12823903 DOI: 10.1089/104454903321908656] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The isolation from proliferating mouse and human embryo fibroblasts of SDS-stable crosslinkage products of vimentin with DNA fragments containing inverted repeats capable of cruciform formation under superhelical stress and the competitive effect of a synthetic Holliday junction on the binding of cytoplasmic intermediate filament (cIF) proteins to supercoiled DNA prompted a detailed investigation of the proteins' capacity to associate with four-way junction DNA and to influence its processing by junction-resolving endonucleases. Electrophoretic mobility shift analysis of reaction products obtained from vimentin and Holliday junctions under varying ionic conditions revealed efficient complex formation of the filament protein not only with the unstacked, square-planar configuration of the junctions but also with their coaxially stacked X-conformation. Glial fibrillary acidic protein (GFAP) was less efficient and desmin virtually inactive in complex formation. Electron microscopy showed binding of vimentin tetramers or octamers almost exclusively to the branchpoint of the Holliday junctions under physiological ionic conditions. Even at several hundredfold molar excess, sequence-related single- and double-stranded DNAs were unable to chase Holliday junctions from their complexes with vimentin. Vimentin also stimulated bacteriophage T7 endonuclease I in introducing single-strand cuts diametrically across the branchpoint and thus in the resolution of the Holliday junctions. This effect is very likely due to vimentin-induced structural distortion of the branchpoint, as suggested by the results of hydroxyl radical footprinting of Holliday junctions in the absence and the presence of vimentin. Moreover, vimentin, and to a lesser extent GFAP and desmin, interacted with the cruciform structures of inverted repeats inserted into a supercoiled vector plasmid, thereby changing their configuration via branch migration and sensibilizing them to processing by T7 endonuclease I. This refers to both plasmid relaxation caused by unilateral scission and, particularly, linearization via bilateral scission at primary and cIF protein-induced secondary cruciform branchpoints that were identified by T7 endonuclease I footprinting. cIF proteins share these activities with a variety of other architectural proteins interacting with and structurally modulating four-way DNA junctions. In view of the known and hypothetical functions of four-way DNA junctions and associated protein factors in DNA metabolism, cIF proteins as complementary nuclear matrix proteins may play important roles in such nuclear matrix-associated processes as DNA replication, recombination, repair, and transcription, with special emphasis on both the preservation and evolution of the genome.
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Affiliation(s)
- Guohong Li
- Max-Planck-Institut für Zellbiologie, Rosenhof, 68526 Ladenburg, Germany
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Radman-Livaja M, Shaw C, Azaro M, Biswas T, Ellenberger T, Landy A. Arm sequences contribute to the architecture and catalytic function of a lambda integrase-Holliday junction complex. Mol Cell 2003; 11:783-94. [PMID: 12667459 DOI: 10.1016/s1097-2765(03)00111-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
lambda integrase (Int) mediates recombination between attachment sites on lambda phage and E. coli DNAs. With the assistance of accessory proteins that induce DNA loops, Int bridges pairs of distinct arm- and core-type DNA binding sites to form synapsed recombination complexes, which then recombine via a Holliday junction (HJ) intermediate. We show that, in addition to promoting the proper positioning of Int protomers, the arm sequences facilitate the catalytic activities of the Int tetramer, independent of accessory proteins or physical continuity between the arm and core sites. We have determined the architecture of ternary complexes containing a HJ, Int, and P'1,2 arm-type DNA. These structures accommodate simultaneous binding of Int to direct-repeat arm sites and indirect-repeat core sites and afford a new view of the higher-order recombinogenic complexes.
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Affiliation(s)
- Marta Radman-Livaja
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Box G-J360, Providence, RI 02912, USA
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