1
|
Abstract
![]()
We
explore the process of base-flipping for four central bases,
adenine, guanine, cytosine, and thymine, in a deoxyribonucleic acid
(DNA) duplex using the energy landscape perspective. NMR imino-proton
exchange and fluorescence correlation spectroscopy studies have been
used in previous experiments to obtain lifetimes for bases in paired
and extrahelical states. However, the difference of almost 4 orders
of magnitude in the base-flipping rates obtained by the two methods
implies that they are exploring different pathways and possibly different
open states. Our results support the previous suggestion that minor
groove opening may be favored by distortions in the DNA backbone and
reveal links between sequence effects and the direction of opening,
i.e., whether the base flips toward the major or the minor groove
side. In particular, base flipping along the minor groove pathway
was found to align toward the 5′ side of the backbone. We find
that bases align toward the 3′ side of the backbone when flipping
along the major groove pathway. However, in some cases for cytosine
and thymine, the base flipping along the major groove pathway also
aligns toward the 5′ side. The sequence effect may be caused
by the polar interactions between the flipping-base and its neighboring
bases on either of the strands. For guanine flipping toward the minor
groove side, we find that the equilibrium constant for opening is
large compared to flipping via the major groove. We find that the
estimated rates of base opening, and hence the lifetimes of the closed
state, obtained for thymine flipping through small and large angles
along the major groove differ by 6 orders of magnitude, whereas for
thymine flipping through small angles along the minor groove and large
angles along the major groove, the rates differ by 3 orders of magnitude.
Collapse
Affiliation(s)
- Nicy
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - David J. Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| |
Collapse
|
2
|
Abstract
Base pairing plays a pivotal role in DNA functions and replication fidelity. But while the complementarity between Watson-Crick matched bases is generally believed to arise from the different number of hydrogen bonds in G|C pairs versus A|T, the energetics of these interactions are heavily renormalized by the aqueous solvent. Employing large-scale Monte Carlo simulations, we have extracted the solvent contribution to the free energy for canonical and some noncanonical and stacked base pairs. For all of them, the solvent's contribution to the base pairing free energy is exclusively destabilizing. While the direct hydrogen bonding interactions in the G|C pair is much stronger than A|T, the thermodynamic resistance produced by the solvent also pushes back much stronger against G|C compared to A|T, generating an only ∼1 kcal/mol free energy difference between them. We have profiled the density of water molecules in the solvent adjacent to the bases and observed a "freezing" behavior where waters are recruited into the gap between the bases to compensate for the unsatisfied hydrogen bonds between them. A very small number of water molecules that are associated with the Watson-Crick donor/acceptor atoms turn out to be responsible for the majority of the solvent's thermodynamic resistance to base pairing. The absence or presence of these near-field waters can be used to enhance fidelity during DNA replication.
Collapse
|
3
|
Kingsland A, Maibaum L. DNA Base Pair Mismatches Induce Structural Changes and Alter the Free-Energy Landscape of Base Flip. J Phys Chem B 2018; 122:12251-12259. [DOI: 10.1021/acs.jpcb.8b06007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Addie Kingsland
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Lutz Maibaum
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
4
|
Wang Y, Wang Z, Wang Y, Liu T, Zhang W. The nearest neighbor and next nearest neighbor effects on the thermodynamic and kinetic properties of RNA base pair. J Chem Phys 2018; 148:045101. [PMID: 29390847 DOI: 10.1063/1.5013282] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The thermodynamic and kinetic parameters of an RNA base pair with different nearest and next nearest neighbors were obtained through long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The results indicate that thermodynamic parameters of GC base pair are dependent on the nearest neighbor base pair, and the next nearest neighbor base pair has little effect, which validated the nearest-neighbor model. The closing and opening rates of the GC base pair also showed nearest neighbor dependences. At certain temperature, the closing and opening rates of the GC pair with nearest neighbor AU is larger than that with the nearest neighbor GC, and the next nearest neighbor plays little role. The free energy landscape of the GC base pair with the nearest neighbor GC is rougher than that with nearest neighbor AU.
Collapse
Affiliation(s)
- Yujie Wang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Zhen Wang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Yanli Wang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Taigang Liu
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Wenbing Zhang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| |
Collapse
|
5
|
Lindahl V, Villa A, Hess B. Sequence dependency of canonical base pair opening in the DNA double helix. PLoS Comput Biol 2017; 13:e1005463. [PMID: 28369121 PMCID: PMC5393899 DOI: 10.1371/journal.pcbi.1005463] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 04/17/2017] [Accepted: 03/17/2017] [Indexed: 12/15/2022] Open
Abstract
The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base flipping and the exact mechanism is still not well understood. We investigate sequence effects on base pair opening using extensive classical molecular dynamics simulations targeting the opening of 11 different canonical base pairs in two DNA sequences. Two popular biomolecular force fields are applied. To enhance sampling and calculate free energies, we bias the simulation along a simple distance coordinate using a newly developed adaptive sampling algorithm. The simulation is guided back and forth along the coordinate, allowing for multiple opening pathways. We compare the calculated free energies with those from an NMR study and check assumptions of the model used for interpreting the NMR data. Our results further show that the neighboring sequence is an important factor for the opening free energy, but also indicates that other sequence effects may play a role. All base pairs are observed to have a propensity for opening toward the major groove. The preferred opening base is cytosine for GC base pairs, while for AT there is sequence dependent competition between the two bases. For AT opening, we identify two non-canonical base pair interactions contributing to a local minimum in the free energy profile. For both AT and CG we observe long-lived interactions with water and with sodium ions at specific sites on the open base pair. The DNA double helix, a molecule that stores biological information, has become an iconic image of biomedical research. In order to use or repair the information it carries, the bases that are stacked in the helix need to be chemically exposed. This can happen either by separating the two strands in the helix or by flipping out individual bases. Here, we focus on the latter process. Usually proteins are involved in interactions with bases, but it is still unclear if bases are pulled out actively by proteins or if they act on spontaneously flipped bases. Although experiments can detect base pair opening, it is difficult to detect which base moves in which direction. Here, we present results from molecular dynamics simulations using a recently developed sampling method which improves the statistics in the simulations by enhancing the probability of the base pair opening event. We observe differences in probability, modes and mechanism of opening that depend not only on the types of the bases in the pair, but also strongly on their neighbors. This provides essential information for understanding how DNA functions.
Collapse
Affiliation(s)
- Viveca Lindahl
- Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Stockholm and Uppsala, Stockholm, Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Berk Hess
- Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Stockholm and Uppsala, Stockholm, Sweden
- * E-mail:
| |
Collapse
|
6
|
Knips A, Zacharias M. Both DNA global deformation and repair enzyme contacts mediate flipping of thymine dimer damage. Sci Rep 2017; 7:41324. [PMID: 28128222 PMCID: PMC5269681 DOI: 10.1038/srep41324] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/16/2016] [Indexed: 01/31/2023] Open
Abstract
The photo-induced cis-syn-cyclobutane pyrimidine (CPD) dimer is a frequent DNA lesion. In bacteria photolyases efficiently repair dimers employing a light-driven reaction after flipping out the CPD damage to the active site. How the repair enzyme identifies a damaged site and how the damage is flipped out without external energy is still unclear. Employing molecular dynamics free energy calculations, the CPD flipping process was systematically compared to flipping undamaged nucleotides in various DNA global states and bound to photolyase enzyme. The global DNA deformation alone (without protein) significantly reduces the flipping penalty and induces a partially looped out state of the damage but not undamaged nucleotides. Bound enzyme further lowers the penalty for CPD damage flipping with a lower free energy of the flipped nucleotides in the active site compared to intra-helical state (not for undamaged DNA). Both the reduced penalty and partial looping by global DNA deformation contribute to a significantly shorter mean first passage time for CPD flipping compared to regular nucleotides which increases the repair likelihood upon short time encounter between repair enzyme and DNA.
Collapse
Affiliation(s)
- Alexander Knips
- Physik-Department T38, Technische Universität München, James-Franck-Str. 1, D-85748 Garching, Germany
| | - Martin Zacharias
- Physik-Department T38, Technische Universität München, James-Franck-Str. 1, D-85748 Garching, Germany
| |
Collapse
|
7
|
Wang Y, Gong S, Wang Z, Zhang W. The thermodynamics and kinetics of a nucleotide base pair. J Chem Phys 2017; 144:115101. [PMID: 27004898 DOI: 10.1063/1.4944067] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption of hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian.
Collapse
Affiliation(s)
- Yujie Wang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Sha Gong
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Zhen Wang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Wenbing Zhang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| |
Collapse
|
8
|
Yang D, Boyer B, Prévost C, Danilowicz C, Prentiss M. Integrating multi-scale data on homologous recombination into a new recognition mechanism based on simulations of the RecA-ssDNA/dsDNA structure. Nucleic Acids Res 2015; 43:10251-63. [PMID: 26384422 PMCID: PMC4666392 DOI: 10.1093/nar/gkv883] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/23/2015] [Indexed: 12/11/2022] Open
Abstract
RecA protein is the prototypical recombinase. Members of the recombinase family can accurately repair double strand breaks in DNA. They also provide crucial links between pairs of sister chromatids in eukaryotic meiosis. A very broad outline of how these proteins align homologous sequences and promote DNA strand exchange has long been known, as are the crystal structures of the RecA-DNA pre- and postsynaptic complexes; however, little is known about the homology searching conformations and the details of how DNA in bacterial genomes is rapidly searched until homologous alignment is achieved. By integrating a physical model of recognition to new modeling work based on docking exploration and molecular dynamics simulation, we present a detailed structure/function model of homology recognition that reconciles extremely quick searching with the efficient and stringent formation of stable strand exchange products and which is consistent with a vast body of previously unexplained experimental results.
Collapse
Affiliation(s)
- Darren Yang
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Benjamin Boyer
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, IBPC, Paris, France
| | - Chantal Prévost
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, IBPC, Paris, France
| | | | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| |
Collapse
|
9
|
Saladin A, Amourda C, Poulain P, Férey N, Baaden M, Zacharias M, Delalande O, Prévost C. Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments. Nucleic Acids Res 2010; 38:6313-23. [PMID: 20507912 PMCID: PMC2965220 DOI: 10.1093/nar/gkq459] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Homologous recombination is a fundamental process enabling the repair of double-strand breaks with a high degree of fidelity. In prokaryotes, it is carried out by RecA nucleofilaments formed on single-stranded DNA (ssDNA). These filaments incorporate genomic sequences that are homologous to the ssDNA and exchange the homologous strands. Due to the highly dynamic character of this process and its rapid propagation along the filament, the sequence recognition and strand exchange mechanism remains unknown at the structural level. The recently published structure of the RecA/DNA filament active for recombination (Chen et al., Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structure, Nature 2008, 453, 489) provides a starting point for new exploration of the system. Here, we investigate the possible geometries of association of the early encounter complex between RecA/ssDNA filament and double-stranded DNA (dsDNA). Due to the huge size of the system and its dense packing, we use a reduced representation for protein and DNA together with state-of-the-art molecular modeling methods, including systematic docking and virtual reality simulations. The results indicate that it is possible for the double-stranded DNA to access the RecA-bound ssDNA while initially retaining its Watson–Crick pairing. They emphasize the importance of RecA L2 loop mobility for both recognition and strand exchange.
Collapse
Affiliation(s)
- Adrien Saladin
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005 Paris, MTI, France
| | | | | | | | | | | | | | | |
Collapse
|
10
|
de Marco G, Várnai P. Molecular simulation of conformational transitions in biomolecules using a combination of structure-based potential and empirical valence bond theory. Phys Chem Chem Phys 2009; 11:10694-700. [DOI: 10.1039/b917109f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
11
|
Mura C, McCammon JA. Molecular dynamics of a kappaB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation. Nucleic Acids Res 2008; 36:4941-55. [PMID: 18653524 PMCID: PMC2528173 DOI: 10.1093/nar/gkn473] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better understand DNA structure, function, and dynamics in general, and protein···DNA recognition in the ‘κB’ family of genetic regulatory elements in particular, we performed molecular dynamics simulations of a 20-bp DNA encompassing a cognate κB site recognized by the proto-oncogenic ‘c-Rel’ subfamily of NF-κB transcription factors. Simulations of the κB DNA in explicit water were extended to microsecond duration, providing a broad, atomically detailed glimpse into the structural and dynamical behavior of double helical DNA over many timescales. Of particular note, novel (and structurally plausible) conformations of DNA developed only at the long times sampled in this simulation—including a peculiar state arising at ≈0.7 μs and characterized by cross-strand intercalative stacking of nucleotides within a longitudinally sheared base pair, followed (at ≈1 μs) by spontaneous base flipping of a neighboring thymine within the A-rich duplex. Results and predictions from the microsecond-scale simulation include implications for a dynamical NF-κB recognition motif, and are amenable to testing and further exploration via specific experimental approaches that are suggested herein.
Collapse
Affiliation(s)
- Cameron Mura
- Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA 92093-0365, USA.
| | | |
Collapse
|
12
|
Villani G. A time-dependent quantum dynamics investigation of the guanine-cytosine system: A six-dimensional model. J Chem Phys 2008; 128:114306. [DOI: 10.1063/1.2890040] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
|
13
|
Roy A, Panigrahi S, Bhattacharyya M, Bhattacharyya D. Structure, Stability, and Dynamics of Canonical and Noncanonical Base Pairs: Quantum Chemical Studies. J Phys Chem B 2008; 112:3786-96. [DOI: 10.1021/jp076921e] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Ashim Roy
- Biophysics Division and Center for Applied Mathematics and Computational Science, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Swati Panigrahi
- Biophysics Division and Center for Applied Mathematics and Computational Science, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Malyasri Bhattacharyya
- Biophysics Division and Center for Applied Mathematics and Computational Science, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Dhananjay Bhattacharyya
- Biophysics Division and Center for Applied Mathematics and Computational Science, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| |
Collapse
|
14
|
Villani G. Theoretical investigation of the coupling between the hydrogen transfer and the base pair opening in the adenine–thymine system. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2007.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
15
|
Bouvier B, Grubmüller H. A molecular dynamics study of slow base flipping in DNA using conformational flooding. Biophys J 2007; 93:770-86. [PMID: 17496048 PMCID: PMC1913169 DOI: 10.1529/biophysj.106.091751] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Individual DNA bases are known to be able to flip out of the helical stack, providing enzymes with access to the genetic information otherwise hidden inside the helix. Consequently, base flipping is a necessary first step to many more complex biological processes such as DNA transcription or replication. Much remains unknown about this elementary step, despite a wealth of experimental and theoretical studies. From the theoretical point of view, the involved timescale of milliseconds or longer requires the use of enhanced sampling techniques. In contrast to previous theoretical studies employing umbrella sampling along a predefined flipping coordinate, this study attempts to induce flipping without prior knowledge of the pathway, using information from a molecular dynamics simulation of a B-DNA fragment and the conformational flooding method. The relevance to base flipping of the principal components of the simulation is assayed, and a combination of modes optimally related to the flipping of the base through either helical groove is derived for each of the two bases of the central guanine-cytosine basepair. By applying an artificial flooding potential along these collective coordinates, the flipping mechanism is accelerated to within the scope of molecular dynamics simulations. The associated free energy surface is found to feature local minima corresponding to partially flipped states, particularly relevant to flipping in isolated DNA; further transitions from these minima to the fully flipped conformation are accelerated by additional flooding potentials. The associated free energy profiles feature similar barrier heights for both bases and pathways; the flipped state beyond is a broad and rugged attraction basin, only a few kcal/mol higher in energy than the closed conformation. This result diverges from previous works but echoes some aspects of recent experimental findings, justifying the need for novel approaches to this difficult problem: this contribution represents a first step in this direction. Important structural factors involved in flipping, both local (sugar-phosphate backbone dihedral angles) and global (helical axis bend), are also identified.
Collapse
Affiliation(s)
- Benjamin Bouvier
- Theoretical and Computational Biophysics Department, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | |
Collapse
|
16
|
Singh M. Friccohenics of Continuum and Non‐Continuum Models for Liquid Flow Applied for Heteromolecular Interaction of DNA Bases and Sugars Estimated with Mansingh Equation. J DISPER SCI TECHNOL 2007. [DOI: 10.1080/01932690701341850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
17
|
Wiggins PA, Phillips R, Nelson PC. Exact theory of kinkable elastic polymers. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2005; 71:021909. [PMID: 15783354 PMCID: PMC3496790 DOI: 10.1103/physreve.71.021909] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2004] [Indexed: 05/05/2023]
Abstract
The importance of nonlinearities in material constitutive relations has long been appreciated in the continuum mechanics of macroscopic rods. Although the moment (torque) response to bending is almost universally linear for small deflection angles, many rod systems exhibit a high-curvature softening. The signature behavior of these rod systems is a kinking transition in which the bending is localized. Recent DNA cyclization experiments by Cloutier and Widom have offered evidence that the linear-elastic bending theory fails to describe the high-curvature mechanics of DNA. Motivated by this recent experimental work, we develop a simple and exact theory of the statistical mechanics of linear-elastic polymer chains that can undergo a kinking transition. We characterize the kinking behavior with a single parameter and show that the resulting theory reproduces both the low-curvature linear-elastic behavior which is already well described by the worm-like chain model, as well as the high-curvature softening observed in recent cyclization experiments.
Collapse
|
18
|
Huang N, MacKerell AD. Atomistic view of base flipping in DNA. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2004; 362:1439-1460. [PMID: 15306460 DOI: 10.1098/rsta.2004.1383] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Base flipping is essential for the enzyme-catalysed methylation of DNA. In our previous studies, the flipping of bases out of duplex DNA in DNA alone and when bound to the (cytosine-C5)-methyltransferase from HhaI (M.HhaI) were investigated via potential of mean force calculations. Insights into various experimental observations were obtained. In the present paper we present an overview of previous computational studies of base flipping along with new detailed structural and energetic analysis on atomic events that contribute to the free energy surfaces. The contributions from different intrinsic and environmental effects to the base-flipping process are explored, and experimental data derived from a variety of methods are reconciled. A detailed protein-facilitated base-flipping mechanism is proposed. Ground-state destabilization is achieved via disruption of the target base Watson-Crick interactions by substitution with favourable DNA-protein interactions. In addition, specific DNA-protein interactions and favourable solvation effects further promote target base flipping along the major groove through the protein matrix, and maximal interactions occur between the DNA and the protein upon reaching the fully flipped state. Other DNA binding proteins that involve distortion of DNA's conformation may use a similar mechanism to that by which M.HhaI facilitates base flipping.
Collapse
Affiliation(s)
- Niu Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, Baltimore, MD 21201, USA
| | | |
Collapse
|
19
|
Ababneh AM, Large CC, Georghiou S. Solvation of nucleosides in aqueous mixtures of organic solvents: relevance to DNA open basepairs. Biophys J 2003; 85:1111-27. [PMID: 12885656 PMCID: PMC1303230 DOI: 10.1016/s0006-3495(03)74548-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2002] [Accepted: 04/16/2003] [Indexed: 10/21/2022] Open
Abstract
Toward the goal of understanding how open basepairs in DNA interact with their heterogeneous environment, we have studied the steady-state intrinsic fluorescence properties of the purine and pyrimidine deoxynucleosides in organic solvents in the presence of small amounts of water. The organic solvents used in the present study were: n-butanol, acetonitrile, methanol, n-propanol, isopropanol, and isobutanol. For n-butanol and acetonitrile, which have a high degree of amphiphilicity and weak hydrogen bonding ability, respectively, the fluorescence spectral properties of the purines are found to depend on the sequence of steps in which the aqueous mixtures were formed. By contrast, no such dependence was observed in the mixtures with any of the other solvents used in the present study. Moreover, no such dependence was observed for the pyrimidines. These findings suggest that the final solvation network around the purines is dependent on the nature of the environment to which they were initially exposed. This would tend to present an impediment to the closing of AT or GC basepairs in DNA that become open as a result of structural fluctuations, DNA bending, or protein-DNA interactions.
Collapse
Affiliation(s)
- Anas M Ababneh
- Molecular Biophysics Laboratory, Department of Physics, The University of Tennessee, Knoxville, Tennessee 37996, USA
| | | | | |
Collapse
|
20
|
Seibert E, Ross JBA, Osman R. Contribution of opening and bending dynamics to specific recognition of DNA damage. J Mol Biol 2003; 330:687-703. [PMID: 12850140 DOI: 10.1016/s0022-2836(03)00598-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Guanine-uracil (G.U) wobble base-pairs are a detrimental lesion in DNA. Previous investigations have shown that such wobble base-pairs are more prone to base-opening than the normal G.C base-pairs. To investigate the sequence-dependence of base-pair opening we have performed 5ns molecular dynamics simulations on G.U wobble base-pairs in two different sequence contexts, TGT/AUA and CGC/GUG. Furthermore, we have investigated the effect of replacing the guanine base in each sequence with a fluorescent guanine analogue, 6-methylisoxanthopterin (6MI). Our results indicate that each sequence opens spontaneously towards the major groove in the course of the simulations. The TGT/AUA sequence has a greater proportion of structures in the open state than the CGC/GUG sequence. Incorporation of 6MI yields wobble base-pairs that open more readily than their guanine counterparts. In order of increasing open population, the sequences are ordered as CGC<TGT<CMC<TMT, where M represents 6MI. Both members of the base-pair open towards the major groove in a symmetrically coupled motion. Opening results in breakage of the H3(U)-O6(G/6MI) hydrogen bond, and distortion of the H1(G/6MI)-O2(U) hydrogen bond. Structural consequences of the opening include the formation of the H21(G/6MI)-O2(U) hydrogen bond and a change in local solvation in the grooves and particularly near N3-H3 of uracil. Additionally, DNA flexibility is reduced in the open state for bending towards the major groove generating two nearly discrete states: closed unbent and open bent. The observed differences in the local structural and dynamical properties of the G.U base-pair may play an important role in the activity of DNA repair enzymes that initiate base excision by distorting the DNA and flipping the target base from inside the DNA helix.
Collapse
Affiliation(s)
- Eleanore Seibert
- Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, NY 10029, USA
| | | | | |
Collapse
|
21
|
Fuxreiter M, Luo N, Jedlovszky P, Simon I, Osman R. Role of base flipping in specific recognition of damaged DNA by repair enzymes. J Mol Biol 2002; 323:823-34. [PMID: 12417196 DOI: 10.1016/s0022-2836(02)00999-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA repair enzymes induce base flipping in the process of damage recognition. Endonuclease V initiates the repair of cis, syn thymine dimers (TD) produced in DNA by UV radiation. The enzyme is known to flip the base opposite the damage into a non-specific binding pocket inside the protein. Uracil DNA glycosylase removes a uracil base from G.U mismatches in DNA by initially flipping it into a highly specific pocket in the enzyme. The contribution of base flipping to specific recognition has been studied by molecular dynamics simulations on the closed and open states of undamaged and damaged models of DNA. Analysis of the distributions of bending and opening angles indicates that enhanced base flipping originates in increased flexibility of the damaged DNA and the lowering of the energy difference between the closed and open states. The increased flexibility of the damaged DNA gives rise to a DNA more susceptible to distortions induced by the enzyme, which lowers the barrier for base flipping. The free energy profile of the base-flipping process was constructed using a potential of mean force representation. The barrier for TD-containing DNA is 2.5 kcal mol(-1) lower than that in the undamaged DNA, while the barrier for uracil flipping is 11.6 kcal mol(-1) lower than the barrier for flipping a cytosine base in the undamaged DNA. The final barriers for base flipping are approximately 10 kcal mol(-1), making the rate of base flipping similar to the rate of linear scanning of proteins on DNA. These results suggest that damage recognition based on lowering the barrier for base flipping can provide a general mechanism for other DNA-repair enzymes.
Collapse
Affiliation(s)
- Monika Fuxreiter
- Institute of Enzymology, H-1113, Budapest, Karolina ut 29, Hungary
| | | | | | | | | |
Collapse
|
22
|
Banavali NK, MacKerell AD. Free energy and structural pathways of base flipping in a DNA GCGC containing sequence. J Mol Biol 2002; 319:141-60. [PMID: 12051942 DOI: 10.1016/s0022-2836(02)00194-8] [Citation(s) in RCA: 139] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Structural distortions of DNA are essential for its biological function due to the genetic information of DNA not being physically accessible in the duplex state. Base flipping is one of the simplest structural distortions of DNA and may represent an initial event in strand separation required to access the genetic code. Flipping is also utilized by DNA-modifying and repair enzymes to access specific bases. It is typically thought that base flipping (or base-pair opening) occurs via the major groove whereas minor groove flipping is only possible when mediated by DNA-binding proteins. Here, umbrella sampling with a novel center-of-mass pseudodihedral reaction coordinate was used to calculate the individual potentials of mean force (PMF) for flipping of the Watson-Crick (WC) paired C and G bases in the CCATGCGCTGAC DNA dodecamer. The novel reaction coordinate allowed explicit investigation of the complete flipping process via both the minor and major groove pathways. The minor and major groove barriers to flipping are similar for C base flipping while the major groove barrier is slightly lower for G base flipping. Minor groove flipping requires distortion of the WC partner while the flipping base pulls away from its partner during major groove flipping. The flipped states are represented by relatively flat free energy surfaces, with a small, local minimum observed for the flipped G base. Conserved patterns of phosphodiester backbone dihedral distortions during flipping indicate their essential role in the flipping process. During flipping, the target base tracks along the respective grooves, leading to hydrogen-bonding interactions with neighboring base-pairs. Such hydrogen-bonding interactions with the neighboring sequence suggest a novel mechanism of sequence dependence in DNA dynamics.
Collapse
Affiliation(s)
- Nilesh K Banavali
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 North Pine Street, Baltimore, MD 21201, USA
| | | |
Collapse
|
23
|
Abstract
We describe an original approach to determining sequence-structure relationships for DNA. This approach, termed ADAPT, combines all-atom molecular mechanics with a multicopy algorithm to build nucleotides that contain all four standard bases in variable proportions. These nucleotides enable us to search very rapidly for base sequences that energetically favor chosen types of DNA deformation or chosen DNA-protein or DNA-ligand interactions. Sequences satisfying the chosen criteria can be found by energy minimization, combinatorial sequence searching, or genome scanning, in a manner similar to the threading approaches developed for protein structure prediction. In the latter case, we are able to analyze roughly 2000 base pairs per second. Applications of the method to DNA allomorphic transitions, DNA deformation, and specific DNA interactions are presented.
Collapse
Affiliation(s)
- I Lafontaine
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France
| | | |
Collapse
|
24
|
Giudice E, Várnai P, Lavery R. Energetic and Conformational Aspects of A:T Base-Pair Opening within the DNA Double Helix. Chemphyschem 2001; 2:673-7. [DOI: 10.1002/1439-7641(20011119)2:11<673::aid-cphc673>3.0.co;2-s] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2001] [Indexed: 11/09/2022]
|
25
|
Abstract
We use internal coordinate molecular mechanics calculations to study the impact of abasic sites on the conformation and the mechanics of the DNA double helix. Abasic sites, which are common mutagenic lesions, are shown to locally modify both the groove geometry and the curvature of DNA in a sequence dependent manner. By controlled twisting and bending, it is also shown that these lesions modify the deformability of the duplex, generally increasing its flexibility, but again to an extent which depends on the nature of the abasic site and on the surrounding base sequence. Both the conformational and mechanical influence of this type of DNA damage may be significant for recognition and repair mechanisms.
Collapse
Affiliation(s)
- L Ayadi
- LEDSS, Laboratoire de Chimie Bioorganique, UMR CNRS 5616, Université Joseph Fourier Grenoble 1, France
| | | | | |
Collapse
|
26
|
Ayadi L, Coulombeau C, Lavery R. Abasic sites in duplex DNA: molecular modeling of sequence-dependent effects on conformation. Biophys J 1999; 77:3218-26. [PMID: 10585943 PMCID: PMC1300592 DOI: 10.1016/s0006-3495(99)77152-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Molecular modeling calculations using JUnction Minimization of Nucleic Acids (JUMNA) have been used to study sequence effects on the conformation of abasic sites within duplex DNA. We have considered lesions leading to all possible unpaired bases (X), adenine, guanine, cytosine, or thymine contained within two distinct sequence contexts, CXC and GXG. Calculations were carried out on DNA 11-mers using extensive conformational search techniques to locate the most stable abasic conformations and using Poisson-Boltzmann corrected electrostatics to account for solvation effects. The results, which are in very good agreement with available experimental data, point to strong sequence effects on both the position of the unpaired base (intra or extrahelical) and on the overall curvature induced by the abasic lesion. For CXC, unpaired purines are found to lie within the helix, while unpaired pyrimidines are either extrahelical or in equilibrium between the intra and extrahelical forms. For GXG, all unpaired bases lead to intrahelical forms, but with marked, sequence-dependent differences in induced curvature.
Collapse
Affiliation(s)
- L Ayadi
- Laboratoire d'Etudes Dynamiques et Structurales de la Sélectivité, Laboratoire de Chimie Bioorganique, Université Joseph Fourier, F-38041 Grenoble, Cedex 9, France
| | | | | |
Collapse
|
27
|
Bertucat G, Lavery R, Prévost C. A molecular model for RecA-promoted strand exchange via parallel triple-stranded helices. Biophys J 1999; 77:1562-76. [PMID: 10465767 PMCID: PMC1300444 DOI: 10.1016/s0006-3495(99)77004-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A number of studies have concluded that strand exchange between a RecA-complexed DNA single strand and a homologous DNA duplex occurs via a single-strand invasion of the minor groove of the duplex. Using molecular modeling, we have previously demonstrated the possibility of forming a parallel triple helix in which the single strand interacts with the intact duplex in the minor groove, via novel base interactions (Bertucat et al., J. Biomol. Struct. Dynam. 16:535-546). This triplex is stabilized by the stretching and unwinding imposed by RecA. In the present study, we show that the bases within this triplex are appropriately placed to undergo strand exchange. Strand exchange is found to be exothermic and to result in a triple helix in which the new single strand occupies the major groove. This structure, which can be equated to so-called R-form DNA, can be further stabilized by compression and rewinding. We are consequently able to propose a detailed, atomic-scale model of RecA-promoted strand exchange. This model, which is supported by a variety of experimental data, suggests that the role of RecA is principally to prepare the single strand for its future interactions, to guide a minor groove attack on duplex DNA, and to stabilize the resulting, stretched triplex, which intrinsically favors strand exchange. We also discuss how this mechanism can incorporate homologous recognition.
Collapse
Affiliation(s)
- G Bertucat
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | | | | |
Collapse
|
28
|
Bertucat G, Lavery R, Prévost C. A model for parallel triple helix formation by RecA: single-single association with a homologous duplex via the minor groove. J Biomol Struct Dyn 1998; 16:535-46. [PMID: 10052612 DOI: 10.1080/07391102.1998.10508268] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The nucleoproteic filaments of RecA polymerized on single stranded DNA are able to integrate double stranded DNA in a coaxial arrangement (with DNA stretched by a factor 1.5), to recognize homologous sequences in the duplex and to perform strand exchange between the single stranded and double stranded molecules. While experimental results favor the hypothesis of an invasion of the minor groove of the duplex by the single strand, parallel minor groove triple helices have never been isolated or even modeled, the minor groove offering little space for a third strand to interact. Based on an internal coordinate modeling study, we show here that such a structure is perfectly conceivable when the two interacting oligomers are stretched by a factor 1.5, in order to open the minor groove of the duplex. The model helix presents characteristics that coincide with known experimental data on unwinding, base pair inclination and inter-proton distances. Moreover, we show that extension and unwinding stabilize the triple helix. New patterns of triplet interaction via the minor groove are presented.
Collapse
Affiliation(s)
- G Bertucat
- Laboratoire de Biochimie Théorique, UPR 9080, Institut de Biologie Physico-Chimique, Paris, France
| | | | | |
Collapse
|