1
|
Lombardo Z, Mukerji I. Site-Specific Investigation of DNA Holliday Junction Dynamics and Structure with 6-Methylisoxanthopterin, a Fluorescent Guanine Analog. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590264. [PMID: 38659790 PMCID: PMC11042373 DOI: 10.1101/2024.04.19.590264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
DNA Holliday Junction (HJ) formation and resolution is requisite for maintaining genomic stability in processes such as replication fork reversal and double-strand break repair. If HJs are not resolved, chromosome disjunction and aneuploidy result, hallmarks of tumor cells. To understand the structural features that lead to processing of these four-stranded joint molecule structures, we seek to identify structural and dynamic features unique to the central junction core. We incorporate the fluorescent guanine analog 6-methylisoxanthopterin (6-MI) at ten different locations throughout a model HJ structure to obtain site-specific information regarding the structure and dynamics of bases relative to those in a comparable sequence context in duplex DNA. These comparisons were accomplished through measuring fluorescence lifetime, relative brightness, fluorescence anisotropy, and thermodynamic stability, along with fluorescence quenching assays. These time-resolved and steady-state fluorescence measurements demonstrate that the structural distortions imposed by strand crossing result in increased solvent exposure, less stacking of bases and greater extrahelical nature of bases within the junction core. The 6-MI base analogs in the junction reflect these structural changes through an increase in intensity relative to those in the duplex. Molecular dynamics simulations performed using a model HJ indicate the primary sources of deformation are in the shift and twist parameters of the bases at the central junction step. These results suggest that junction-binding proteins may use the unique structure and dynamics of the bases at the core for recognition.
Collapse
Affiliation(s)
- Zane Lombardo
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | - Ishita Mukerji
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Mahmoud R, Dhakal S. Single-Molecule Analysis of DNA Branch Migration under Biomimetic Environments. J Phys Chem B 2022; 126:7252-7261. [DOI: 10.1021/acs.jpcb.2c03153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Roaa Mahmoud
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
| |
Collapse
|
4
|
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.
Collapse
Affiliation(s)
- Subhas C Bera
- Chemical Sciences Division, Saha Institute of Nuclear Physics, HBNI Mumbai, 1/AF Bidhannagar, Kolkata 700064, India.
| | | | | | | |
Collapse
|
5
|
Maffeo C, Chou HY, Aksimentiev A. Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations. ADVANCED THEORY AND SIMULATIONS 2019; 2:1800191. [PMID: 31728433 PMCID: PMC6855400 DOI: 10.1002/adts.201800191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 12/15/2022]
Abstract
Reproduction, the hallmark of biological activity, requires making an accurate copy of the genetic material to allow the progeny to inherit parental traits. In all living cells, the process of DNA replication is carried out by a concerted action of multiple protein species forming a loose protein-nucleic acid complex, the replisome. Proofreading and error correction generally accompany replication but also occur independently, safeguarding genetic information through all phases of the cell cycle. Advances in biochemical characterization of intracellular processes, proteomics and the advent of single-molecule biophysics have brought about a treasure trove of information awaiting to be assembled into an accurate mechanistic model of the DNA replication process. In this review, we describe recent efforts to model elements of DNA replication and repair processes using computer simulations, an approach that has gained immense popularity in many areas of molecular biophysics but has yet to become mainstream in the DNA metabolism community. We highlight the use of diverse computational methods to address specific problems of the fields and discuss unexplored possibilities that lie ahead for the computational approaches in these areas.
Collapse
Affiliation(s)
- Christopher Maffeo
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign,1110 W Green St, Urbana, IL 61801, USA
| | - Han-Yi Chou
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign,1110 W Green St, Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign,1110 W Green St, Urbana, IL 61801, USA
| |
Collapse
|
6
|
Prior C, Danilāne L, Oganesyan VS. All-atom molecular dynamics simulations of spin labelled double and single-strand DNA for EPR studies. Phys Chem Chem Phys 2018; 20:13461-13472. [DOI: 10.1039/c7cp08625c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Prediction of motional EPR spectra of spin labelled DNA structures from fully atomistic MD simulations.
Collapse
Affiliation(s)
- C. Prior
- School of Chemistry
- University of East Anglia
- Norwich
- UK
| | - L. Danilāne
- School of Chemistry
- University of East Anglia
- Norwich
- UK
| | | |
Collapse
|
7
|
Single-molecule fluorescence-based analysis of protein conformation, interaction, and oligomerization in cellular systems. Biophys Rev 2017; 10:317-326. [PMID: 29243093 PMCID: PMC5899725 DOI: 10.1007/s12551-017-0366-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/19/2017] [Indexed: 12/23/2022] Open
Abstract
Single-molecule imaging (SMI) of proteins in operation has a history of intensive investigations over 20 years and is now widely used in various fields of biology and biotechnology. We review the recent advances in SMI of fluorescently-tagged proteins in structural biology, focusing on technical applicability of SMI to the measurements in living cells. Basic technologies and recent applications of SMI in structural biology are introduced. Distinct from other methods in structural biology, SMI directly observes single molecules and single-molecule events one-by-one, thus, explicitly analyzing the distribution of protein structures and the history of protein dynamics. It also allows one to detect single events of protein interaction. One unique feature of SMI is that it is applicable in complicated and heterogeneous environments, including living cells. The numbers, location, movements, interaction, oligomerization, and conformation of single-protein molecules have been determined using SMI in cellular systems.
Collapse
|
8
|
Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments. Sci Rep 2016; 6:22863. [PMID: 26971574 PMCID: PMC4789735 DOI: 10.1038/srep22863] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/22/2016] [Indexed: 02/08/2023] Open
Abstract
Holliday junctions play a central role in genetic recombination, DNA repair and other cellular processes. We combine simulations and experiments to evaluate the ability of the 3SPN.2 model, a coarse-grained representation designed to mimic B-DNA, to predict the properties of DNA Holliday junctions. The model reproduces many experimentally determined aspects of junction structure and stability, including the temperature dependence of melting on salt concentration, the bias between open and stacked conformations, the relative populations of conformers at high salt concentration, and the inter-duplex angle (IDA) between arms. We also obtain a close correspondence between the junction structure evaluated by all-atom and coarse-grained simulations. We predict that, for salt concentrations at physiological and higher levels, the populations of the stacked conformers are independent of salt concentration, and directly observe proposed tetrahedral intermediate sub-states implicated in conformational transitions. Our findings demonstrate that the 3SPN.2 model captures junction properties that are inaccessible to all-atom studies, opening the possibility to simulate complex aspects of junction behavior.
Collapse
|
9
|
Okamoto K, Sako Y. State transition analysis of spontaneous branch migration of the Holliday junction by photon-based single-molecule fluorescence resonance energy transfer. Biophys Chem 2016; 209:21-7. [DOI: 10.1016/j.bpc.2015.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 11/27/2015] [Accepted: 11/28/2015] [Indexed: 11/17/2022]
|
10
|
Cannon B, Kachroo AH, Jarmoskaite I, Jayaram M, Russell R. Hexapeptides that inhibit processing of branched DNA structures induce a dynamic ensemble of Holliday junction conformations. J Biol Chem 2015; 290:22734-46. [PMID: 26209636 PMCID: PMC4566245 DOI: 10.1074/jbc.m115.663930] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 07/23/2015] [Indexed: 11/06/2022] Open
Abstract
Holliday junctions are critical intermediates in DNA recombination, repair, and restart of blocked replication. Hexapeptides have been identified that bind to junctions and inhibit various junction-processing enzymes, and these peptides confer anti-microbial and anti-tumor properties. Earlier studies suggested that inhibition results from stabilization of peptide-bound Holliday junctions in the square planar conformation. Here, we use single molecule fluorescence resonance energy transfer (smFRET) and two model junctions, which are AT- or GC-rich at the branch points, to show that binding of the peptide KWWCRW induces a dynamic ensemble of junction conformations that differs from both the square planar and stacked X conformations. The specific features of the conformational distributions differ for the two peptide-bound junctions, but both junctions display greatly decreased Mg(2+) dependence and increased conformational fluctuations. The smFRET results, complemented by gel mobility shift and small angle x-ray scattering analyses, reveal structural effects of peptides and highlight the sensitivity of smFRET for analyzing complex mixtures of DNA structures. The peptide-induced conformational dynamics suggest multiple stacking arrangements of aromatic amino acids with the nucleobases at the junction core. This conformational heterogeneity may inhibit DNA processing by increasing the population of inactive junction conformations, thereby preventing the binding of processing enzymes and/or resulting in their premature dissociation.
Collapse
Affiliation(s)
- Brian Cannon
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Aashiq H Kachroo
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Inga Jarmoskaite
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Makkuni Jayaram
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Rick Russell
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| |
Collapse
|
11
|
Castro CE, Su HJ, Marras AE, Zhou L, Johnson J. Mechanical design of DNA nanostructures. NANOSCALE 2015; 7:5913-21. [PMID: 25655237 DOI: 10.1039/c4nr07153k] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Structural DNA nanotechnology is a rapidly emerging field that has demonstrated great potential for applications such as single molecule sensing, drug delivery, and templating molecular components. As the applications of DNA nanotechnology expand, a consideration of their mechanical behavior is becoming essential to understand how these structures will respond to physical interactions. This review considers three major avenues of recent progress in this area: (1) measuring and designing mechanical properties of DNA nanostructures, (2) designing complex nanostructures based on imposed mechanical stresses, and (3) designing and controlling structurally dynamic nanostructures. This work has laid the foundation for mechanically active nanomachines that can generate, transmit, and respond to physical cues in molecular systems.
Collapse
Affiliation(s)
- Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.
| | | | | | | | | |
Collapse
|
12
|
Chen SH, Plank JL, Willcox S, Griffith JD, Hsieh TS. Top3α is required during the convergent migration step of double Holliday junction dissolution. PLoS One 2014; 9:e83582. [PMID: 24392087 PMCID: PMC3879244 DOI: 10.1371/journal.pone.0083582] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 11/06/2013] [Indexed: 11/19/2022] Open
Abstract
Although Blm and Top3α are known to form a minimal dissolvasome that can uniquely undo a double Holliday junction structure, the details of the mechanism remain unknown. It was originally suggested that Blm acts first to create a hemicatenane structure from branch migration of the junctions, followed by Top3α performing strand passage to decatenate the interlocking single strands. Recent evidence suggests that Top3α may also be important for assisting in the migration of the junctions. Using a mismatch-dHJ substrate (MM-DHJS) and eukaryotic Top1 (in place of Top3α), we show that the presence of a topoisomerase is required for Blm to substantially migrate a topologically constrained Holliday junction. When investigated by electron microscopy, these migrated structures did not resemble a hemicatenane. However, when Blm is together with Top3α, the dissolution reaction is processive with no pausing at a partially migrated structure. Potential mechanisms are discussed.
Collapse
Affiliation(s)
- Stefanie Hartman Chen
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Jody L. Plank
- Department of Microbiology, University of California Davis, Davis, California, United States of America
| | - Smaranda Willcox
- Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jack D. Griffith
- Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Tao-shih Hsieh
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- * E-mail:
| |
Collapse
|
13
|
Abstract
Single-molecule fluorescence studies of nucleic acids are revolutionizing our understanding of fundamental cellular processes related to DNA and RNA processing mechanisms. Detailed molecular insights into DNA repair, replication, transcription, and RNA folding and function are continuously being uncovered by using the full repertoire of single-molecule fluorescence techniques. The fundamental reason behind the stunning growth in the application of single-molecule techniques to study nucleic acid structure and dynamics is the unmatched ability of single-molecule fluorescence, and mostly single-molecule FRET, to resolve heterogeneous static and dynamic populations and identify transient and low-populated states without the need for sample synchronization. New advances in DNA and RNA synthesis, post-synthetic dye-labeling methods, immobilization and passivation strategies, improved dye photophysics, and standardized analysis methods have enabled the implementation of single-molecule techniques beyond specialized laboratories. In this chapter, we introduce the practical aspects of applying single-molecule techniques to investigate nucleic acid structure, dynamics, and function.
Collapse
Affiliation(s)
- Kaley McCluskey
- SUPA School of Physics and Astronomy, University of St. Andrews, St. Andrews, Scotland, UK
| | | | | | | |
Collapse
|
14
|
Chen P, Keller AM, Joshi CP, Martell DJ, Andoy NM, Benítez JJ, Chen TY, Santiago AG, Yang F. Single-molecule dynamics and mechanisms of metalloregulators and metallochaperones. Biochemistry 2013; 52:7170-83. [PMID: 24053279 DOI: 10.1021/bi400597v] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Understanding how cells regulate and transport metal ions is an important goal in the field of bioinorganic chemistry, a frontier research area that resides at the interface of chemistry and biology. This Current Topic reviews recent advances from the authors' group in using single-molecule fluorescence imaging techniques to identify the mechanisms of metal homeostatic proteins, including metalloregulators and metallochaperones. It emphasizes the novel mechanistic insights into how dynamic protein-DNA and protein-protein interactions offer efficient pathways via which MerR-family metalloregulators and copper chaperones can fulfill their functions. This work also summarizes other related single-molecule studies of bioinorganic systems and provides an outlook toward single-molecule imaging of metalloprotein functions in living cells.
Collapse
Affiliation(s)
- Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Okamoto K, Sako Y. Variational Bayes analysis of a photon-based hidden Markov model for single-molecule FRET trajectories. Biophys J 2013; 103:1315-24. [PMID: 22995504 DOI: 10.1016/j.bpj.2012.07.047] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 07/27/2012] [Accepted: 07/30/2012] [Indexed: 11/29/2022] Open
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) measurement is a powerful technique for investigating dynamics of biomolecules, for which various efforts have been made to overcome significant stochastic noise. Time stamp (TS) measurement has been employed experimentally to enrich information within the signals, while data analyses such as the hidden Markov model (HMM) have been successfully applied to recover the trajectories of molecular state transitions from time-binned photon counting signals or images. In this article, we introduce the HMM for TS-FRET signals, employing the variational Bayes (VB) inference to solve the model, and demonstrate the application of VB-HMM-TS-FRET to simulated TS-FRET data. The same analysis using VB-HMM is conducted for other models and the previously reported change point detection scheme. The performance is compared to other analysis methods or data types and we show that our VB-HMM-TS-FRET analysis can achieve the best performance and results in the highest time resolution. Finally, an smFRET experiment was conducted to observe spontaneous branch migration of Holliday-junction DNA. VB-HMM-TS-FRET was successfully applied to reconstruct the state transition trajectory with the number of states consistent with the nucleotide sequence. The results suggest that a single migration process frequently involves rearrangement of multiple basepairs.
Collapse
Affiliation(s)
- Kenji Okamoto
- Advanced Science Institute, RIKEN, Wako, Saitama, Japan.
| | | |
Collapse
|
16
|
Wheatley E, Pieniazek S, Mukerji I, Beveridge D. Molecular dynamics of a DNA Holliday junction: the inverted repeat sequence d(CCGGTACCGG)₄. Biophys J 2012; 102:552-60. [PMID: 22325278 PMCID: PMC3274787 DOI: 10.1016/j.bpj.2011.11.4023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 11/08/2011] [Accepted: 11/10/2011] [Indexed: 12/01/2022] Open
Abstract
All-atom molecular dynamics (MD) computer simulations have been applied successfully to duplex DNA structures in solution for some years and found to give close accord with observed results. However, the MD force fields have generally not been parameterized against unusual DNA structures, and their use to obtain dynamical models for this class of systems needs to be independently validated. The four-way junction (4WJ), or Holliday junction, is a dynamic DNA structure involved in central cellular processes of homologous replication and double strand break repair. Two conformations are observed in solution: a planar open-X form (OPN) with a mobile center and four duplex arms, and an immobile stacked-X (STX) form with two continuous strands and two crossover strands, stabilized by high salt conditions. To characterize the accuracy of MD modeling on 4WJ, we report a set of explicit solvent MD simulations of ∼100 ns on the repeat sequence d(CCGGTACCGG)(4) starting from the STX structure (PDB code 1dcw), and an OPN structure built for the same sequence. All 4WJ MD simulations converged to a stable STX structure in close accord with the crystal structure. Our MD beginning in the OPN form converts to the STX form spontaneously at both high and low salt conditions, providing a model for the conformational transition. Thus, these simulations provide a successful account of the dynamical structure of the STX form of d(CCGGTACCGG)(4) in solution, and provide new, to our knowledge, information on the conformational stability of the junction and distribution of counterions in the junction interior.
Collapse
Affiliation(s)
| | | | - Ishita Mukerji
- Department of Molecular Biology and Biochemistry, and Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut
| | - D.L. Beveridge
- Department of Chemistry, Wesleyan University, Middletown, Connecticut
| |
Collapse
|
17
|
Torella JP, Holden SJ, Santoso Y, Hohlbein J, Kapanidis AN. Identifying molecular dynamics in single-molecule FRET experiments with burst variance analysis. Biophys J 2011; 100:1568-77. [PMID: 21402040 DOI: 10.1016/j.bpj.2011.01.066] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 12/31/2010] [Accepted: 01/20/2011] [Indexed: 12/22/2022] Open
Abstract
Histograms of single-molecule Förster resonance energy transfer (FRET) efficiency are often used to study the structures of biomolecules and relate these structures to function. Methods like probability distribution analysis analyze FRET histograms to detect heterogeneities in molecular structure, but they cannot determine whether this heterogeneity arises from dynamic processes or from the coexistence of several static structures. To this end, we introduce burst variance analysis (BVA), a method that detects dynamics by comparing the standard deviation of FRET from individual molecules over time to that expected from theory. Both simulations and experiments on DNA hairpins show that BVA can distinguish between static and dynamic sources of heterogeneity in single-molecule FRET histograms and can test models of dynamics against the observed standard deviation information. Using BVA, we analyzed the fingers-closing transition in the Klenow fragment of Escherichia coli DNA polymerase I and identified substantial dynamics in polymerase complexes formed prior to nucleotide incorporation; these dynamics may be important for the fidelity of DNA synthesis. We expect BVA to be broadly applicable to single-molecule FRET studies of molecular structure and to complement approaches such as probability distribution analysis and fluorescence correlation spectroscopy in studying molecular dynamics.
Collapse
Affiliation(s)
- Joseph P Torella
- Department of Physics and Biological Physics Research Group, University of Oxford, Oxford, United Kingdom
| | | | | | | | | |
Collapse
|
18
|
Palets D, Lushnikov AY, Karymov MA, Lyubchenko YL. Effect of single-strand break on branch migration and folding dynamics of Holliday junctions. Biophys J 2010; 99:1916-24. [PMID: 20858437 PMCID: PMC2941029 DOI: 10.1016/j.bpj.2010.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Revised: 06/29/2010] [Accepted: 07/13/2010] [Indexed: 10/19/2022] Open
Abstract
The Holliday junction (HJ), or four-way junction, is a central intermediate state of DNA for homologous genetic recombination and other genetic processes such as replication and repair. Branch migration is the process by which the exchange of homologous DNA regions occurs, and it can be spontaneous or driven by proteins. Unfolding of the HJ is required for branch migration. 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. Folding of the HJ in one of the folded conformations terminates the branch migration phase. At the same time, in the unfolded state HJ rapidly migrates over entire homology region of the HJ in one hop. This process can be affected by irregularities in the DNA double helical structure, so mismatches almost terminate a spontaneous branch migration. Single-stranded breaks or nicks are the most ubiquitous defects in the DNA helix; however, to date, their effect on the HJ branch migration has not been studied. In addition, although nicked HJs are specific substrates for a number of enzymes involved in DNA recombination and repair, the role of this substrate specificity remains unclear. Our main goal in this work was to study the effect of nicks on the efficiency of HJ branch migration and the dynamics of the HJ. To accomplish this goal, we applied two single-molecule methods: atomic force microscopy and fluorescence resonance energy transfer. The atomic force microscopy data show that the nick does not prevent branch migration, but it does decrease the probability that the HJ will pass the DNA lesion. The single-molecule fluorescence resonance energy transfer approaches were instrumental in detailing the effects of nicks. These studies reveal a dramatic change of the HJ dynamics. The nick changes the structure and conformational dynamics of the junctions, leading to conformations with geometries that are different from those for the intact HJ. On the basis of these data, we propose a model of branch migration in which the propensity of the junction to unfold decreases the lifetimes of folded states, thereby increasing the frequency of junction fluctuations between the folded states.
Collapse
Affiliation(s)
| | | | | | - Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska
| |
Collapse
|
19
|
Chen P, Andoy NM, Benítez JJ, Keller AM, Panda D, Gao F. Tackling metal regulation and transport at the single-molecule level. Nat Prod Rep 2010; 27:757-67. [PMID: 20442963 PMCID: PMC2992825 DOI: 10.1039/b906691h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To maintain normal metal metabolism, organisms utilize dynamic cooperation of many biomacromolecules for regulating metal ion concentrations and bioavailability. How these biomacromolecules work together to achieve their functions is largely unclear. For example, how do metalloregulators and DNA interact dynamically to control gene expression to maintain healthy cellular metal level? And how do metal transporters collaborate dynamically to deliver metal ions? Here we review recent advances in studying the dynamic interactions of macromolecular machineries for metal regulation and transport at the single-molecule level: (1) The development of engineered DNA Holliday junctions as single-molecule reporters for metalloregulator-DNA interactions, focusing onMerR-family regulators. And (2) The development of nanovesicle trapping coupled with single molecule fluorescence resonance energy transfer (smFRET) for studying weak, transient interactions between the copper chaperone Hah1 and the Wilson disease protein. We describe the methodologies,the information content of the single-molecule results, and the insights into the biological functions of the involved biomacromolecules for metal regulation and transport. We also discuss remaining challenges from our perspective.
Collapse
Affiliation(s)
- Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| | | | | | | | | | | |
Collapse
|
20
|
Andoy NM, Sarkar SK, Wang Q, Panda D, Benítez JJ, Kalininskiy A, Chen P. Single-molecule study of metalloregulator CueR-DNA interactions using engineered Holliday junctions. Biophys J 2009; 97:844-52. [PMID: 19651042 DOI: 10.1016/j.bpj.2009.05.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 05/03/2009] [Accepted: 05/21/2009] [Indexed: 12/19/2022] Open
Abstract
To maintain normal metal metabolism, bacteria use metal-sensing metalloregulators to control transcription of metal resistance genes. Depending on their metal-binding states, the MerR-family metalloregulators change their interactions with DNA to suppress or activate transcription. To understand their functions fundamentally, we study how CueR, a Cu(1+)-responsive MerR-family metalloregulator, interacts with DNA, using an engineered DNA Holliday junction (HJ) as a protein-DNA interaction reporter in single-molecule fluorescence resonance energy transfer measurements. By analyzing the single-molecule structural dynamics of the engineered HJ in the presence of various concentrations of both apo- and holo-CueR, we show how CueR interacts with the two conformers of the engineered HJ, forming variable protein-DNA complexes at different protein concentrations and changing the HJ structures. We also show how apo- and holo-CueR differ in their interactions with DNA, and discuss their similarities and differences with other MerR-family metalloregulators. The surprising finding that holo-CueR binds more strongly to DNA than to apo-CueR suggests functional differences among MerR-family metalloregulators, in particular in their mechanisms of switching off gene transcription after activation. The study also corroborates the general applicability of engineered HJs as single-molecule reporters for protein-DNA interactions, which are fundamental processes in gene replication, transcription, recombination, and regulation.
Collapse
Affiliation(s)
- Nesha May Andoy
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | | | | | | | | | | | | |
Collapse
|