1
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Zheng CC, Chen YL, Dong HL, Zhang XH, Tan ZJ. Effect of ethanol on the elasticities of double-stranded RNA and DNA revealed by magnetic tweezers and simulations. J Chem Phys 2024; 161:075101. [PMID: 39145565 DOI: 10.1063/5.0211869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 07/29/2024] [Indexed: 08/16/2024] Open
Abstract
The elasticities of double-stranded (ds) DNA and RNA, which are critical to their biological functions and applications in materials science, can be significantly modulated by solution conditions such as ions and temperature. However, there is still a lack of a comprehensive understanding of the role of solvents in the elasticities of dsRNA and dsDNA in a comparative way. In this work, we explored the effect of ethanol solvent on the elasticities of dsRNA and dsDNA by magnetic tweezers and all-atom molecular dynamics simulations. We found that the bending persistence lengths and contour lengths of dsRNA and dsDNA decrease monotonically with the increase in ethanol concentration. Furthermore, the addition of ethanol weakens the positive twist-stretch coupling of dsRNA, while promotes the negative twist-stretch coupling of dsDNA. Counter-intuitively, the lower dielectric environment of ethanol causes a significant re-distribution of counterions and enhanced ion neutralization, which overwhelms the enhanced repulsion along dsRNA/dsDNA, ultimately leading to the softening in bending for dsRNA and dsDNA. Moreover, for dsRNA, ethanol causes slight ion-clamping across the major groove, which weakens the major groove-mediated twist-stretch coupling, while for dsDNA, ethanol promotes the stretch-radius correlation due to enhanced ion binding and consequently enhances the helical radius-mediated twist-stretch coupling.
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Affiliation(s)
- Chen-Chen Zheng
- School of Physics and Technology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yun-Long Chen
- School of Physics and Technology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hai-Long Dong
- School of Physics and Technology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xing-Hua Zhang
- School of Physics and Technology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhi-Jie Tan
- School of Physics and Technology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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2
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Laeremans W, Segers M, Voorspoels A, Carlon E, Hooyberghs J. Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs cgDNA. J Chem Phys 2024; 160:144105. [PMID: 38591677 DOI: 10.1063/5.0197053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/19/2024] [Indexed: 04/10/2024] Open
Abstract
Coarse-grained models have emerged as valuable tools to simulate long DNA molecules while maintaining computational efficiency. These models aim at preserving interactions among coarse-grained variables in a manner that mirrors the underlying atomistic description. We explore here a method for testing coarse-grained vs all-atom models using stiffness matrices in Fourier space (q-stiffnesses), which are particularly suited to probe DNA elasticity at different length scales. We focus on a class of coarse-grained rigid base DNA models known as cgDNA and its most recent version, cgDNA+. Our analysis shows that while cgDNA+ closely follows the q-stiffnesses of the all-atom model, the original cgDNA shows some deviations for twist and bending variables, which are rather strong in the q → 0 (long length scale) limit. The consequence is that while both cgDNA and cgDNA+ give a suitable description of local elastic behavior, the former misses some effects that manifest themselves at longer length scales. In particular, cgDNA performs poorly on twist stiffness, with a value much lower than expected for long DNA molecules. Conversely, the all-atom and cgDNA+ twist are strongly length scale dependent: DNA is torsionally soft at a few base pair distances but becomes more rigid at distances of a few dozen base pairs. Our analysis shows that the bending persistence length in all-atom and cgDNA+ is somewhat overestimated.
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Affiliation(s)
- Wout Laeremans
- Soft Matter and Biological Physics, Department of Applied Physics, and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, Netherlands
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
- UHasselt, Faculty of Sciences, Data Science Institute, Theory Lab, Agoralaan, 3590 Diepenbeek, Belgium
| | - Midas Segers
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Aderik Voorspoels
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Enrico Carlon
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Jef Hooyberghs
- UHasselt, Faculty of Sciences, Data Science Institute, Theory Lab, Agoralaan, 3590 Diepenbeek, Belgium
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3
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Curuksu JD. Spectral analysis of DNA superhelical dynamics from molecular minicircle simulations. J Chem Phys 2023; 159:105101. [PMID: 37694753 DOI: 10.1063/5.0164440] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023] Open
Abstract
Torsional and bending deformations of DNA molecules often occur in vivo and are important for biological functions. DNA "under stress" is a conformational state, which is by far the most frequent state during DNA-protein and gene regulation. In DNA minicircles of length <100 base pairs (bp), the combined effect of torsional and bending stresses can cause local unusual conformations, with certain base pair steps often absorbing most of the stress, leaving other steps close to their relaxed conformation. To better understand the superhelical dynamics of DNA under stress, molecular simulations of 94 bp minicircles with different torsional linking numbers were interpreted using Fourier analyses and principal component analyses. Sharp localized bends of nearly 90° in the helical axis were observed, which in turn decreased fluctuations of the rotational register and helped redistribute the torsional stress into writhe, i.e., superhelical turn up to 360°. In these kinked minicircles, only two-thirds of the DNA molecule bends and writhes and the remaining segment stays close to straight and preserves a conformational flexibility typical of canonical B-DNA (bending of 39° ± 17° distributed parsimoniously across 36 bp), which was confirmed and visualized by principal component analysis. These results confirm that stressed DNA molecules are highly heterogeneous along their sequence, with segments designed to locally store and release stress so that nearby segments can stay relaxed.
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Affiliation(s)
- Jeremy D Curuksu
- Amazon.com, Inc., New York, New York 10001, USA and Center for Data Science, New York University, New York, New York 10011, USA
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4
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Voorspoels A, Vreede J, Carlon E. Rigid Base Biasing in Molecular Dynamics Enables Enhanced Sampling of DNA Conformations. J Chem Theory Comput 2023; 19:902-909. [PMID: 36695645 DOI: 10.1021/acs.jctc.2c00889] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
All-atom simulations have become increasingly popular to study conformational and dynamical properties of nucleic acids as they are accurate and provide high spatial and time resolutions. This high resolution, however, comes at a heavy computational cost, and, within the time scales of simulations, nucleic acids weakly fluctuate around their ideal structure exploring a limited set of conformations. We introduce the RBB-NA algorithm (available as a package in the Open Source Library PLUMED), which is capable of controlling rigid base parameters in all-atom simulations of nucleic acids. With suitable biasing potentials, this algorithm can "force" a DNA or RNA molecule to assume specific values of the six rotational (tilt, roll, twist, buckle, propeller, opening) and/or the six translational parameters (shift, slide, rise, shear, stretch, stagger). The algorithm enables the use of advanced sampling techniques to probe the structure and dynamics of locally strongly deformed nucleic acids. We illustrate its performance showing some examples in which DNA is strongly twisted, bent, or locally buckled. In these examples, RBB-NA reproduces well the unconstrained simulations data and other known features of DNA mechanics, but it also allows one to explore the anharmonic behavior characterizing the mechanics of nucleic acids in the high deformation regime.
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Affiliation(s)
- Aderik Voorspoels
- Soft Matter and Biophysics, Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, 3000 Leuven, Belgium
| | - Jocelyne Vreede
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Enrico Carlon
- Soft Matter and Biophysics, Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, 3000 Leuven, Belgium
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5
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Kim M, Hong CC, Lee S, Kim JS. Dynamics of a
DNA
minicircle: Poloidal rotation and in‐plane circular vibration. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Minjung Kim
- Department of Chemistry and Nanoscience Ewha Womans University Seoul South Korea
| | - Chi Cheng Hong
- Department of Chemistry and Nanoscience Ewha Womans University Seoul South Korea
- School of Chemistry University of Edinburgh Edinburgh UK
| | - Saeyeon Lee
- Department of Chemistry and Nanoscience Ewha Womans University Seoul South Korea
| | - Jun Soo Kim
- Department of Chemistry and Nanoscience Ewha Womans University Seoul South Korea
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6
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Kim M, Bae S, Oh I, Yoo J, Kim JS. Sequence-dependent twist-bend coupling in DNA minicircles. NANOSCALE 2021; 13:20186-20196. [PMID: 34847218 DOI: 10.1039/d1nr04672a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Looping of double-stranded DNA molecules with 100-200 base pairs into minicircles, catenanes, and rotaxanes has been suggested as a potential tool for DNA nanotechnologies. However, sharp DNA bending into a minicircle with a diameter of several to ten nanometers occurs with alterations in the DNA helical structure and may lead to defective kink formation that hampers the use of DNA minicircles, catenanes, and rotaxanes in nanoscale DNA applications. Here, we investigated local variations of a helical twist in sharply bent DNA using microsecond-long all-atom molecular dynamics simulations of six different DNA minicircles, focusing on the sequence dependence of the coupling between DNA bending and its helical twist. Twist angles between consecutive base pairs were analyzed at different locations relative to the direction of DNA bending and, among 10 unique dinucleotide steps, we identified four dinucleotide steps with strong twist-bend coupling, the pyrimidine-purine dinucleotide steps of TA/TA, CG/CG, and CA/TG and the purine-purine dinucleotide step of GA/TC. This work suggests the sequence-dependent structural responses of DNA to strong mechanical deformation, providing new molecular-level insights into the structure and stability of sharply bent DNA minicircles for nanoscale applications.
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Affiliation(s)
- Minjung Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
| | - Sehui Bae
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
| | - Inrok Oh
- LG Chem Ltd, LG Science Park, Seoul 07796, Republic of Korea
| | - Jejoong Yoo
- Department of Physics, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jun Soo Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
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7
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Alves CC, Donadi EA, Giuliatti S. Structural Characterization of the Interaction of Hypoxia Inducible Factor-1 with Its Hypoxia Responsive Element at the -964G > A Variation Site of the HLA-G Promoter Region. Int J Mol Sci 2021; 22:ijms222313046. [PMID: 34884849 PMCID: PMC8657931 DOI: 10.3390/ijms222313046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
Human Antigen Leukocyte-G (HLA-G) gene encodes an immune checkpoint molecule that has restricted tissue expression in physiological conditions; however, the gene may be induced in hypoxic conditions by the interaction with the hypoxia inducible factor-1 (HIF1). Hypoxia regulatory elements (HRE) located at the HLA-G promoter region and at exon 2 are the major HIF1 target sites. Since the G allele of the −964G > A transversion induces higher HLA-G expression when compared to the A allele in hypoxic conditions, here we analyzed HIF1-HRE complex interaction at the pair-atom level considering both −964G > A polymorphism alleles. Mouse HIF2 dimer crystal (Protein Data Bank ID: 4ZPK) was used as template to perform homology modelling of human HIF1 quaternary structure using MODELLER v9.14. Two 3D DNA structures were built from 5′GCRTG’3 HRE sequence containing the −964G/A alleles using x3DNA. Protein-DNA docking was performed using the HADDOCK v2.4 server, and non-covalent bonds were computed by DNAproDB server. Molecular dynamic simulation was carried out per 200 ns, using Gromacs v.2019. HIF1 binding in the HRE containing −964G allele results in more hydrogen bonds and van der Waals contact formation than HRE with −964A allele. Protein-DNA complex trajectory analysis revealed that HIF1-HRE-964G complex is more stable. In conclusion, HIF1 binds in a more stable and specific manner at the HRE with G allele.
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Affiliation(s)
- Cinthia C. Alves
- Department of Genetic, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil;
| | - Eduardo A. Donadi
- Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil;
| | - Silvana Giuliatti
- Department of Genetic, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil;
- Correspondence:
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8
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Abstract
Mismatched base pairs alter the flexibility and intrinsic curvature of DNA. The role of such DNA features is not fully understood in the mismatch repair pathway. MutS/DNA complexes exhibit DNA bending, PHE intercalation, and changes of base-pair parameters near the mismatch. Recently, we have shown that base-pair opening in the absence of MutS can discriminate mismatches from canonical base pairs better than DNA bending. However, DNA bending in the absence of MutS was found to be rather challenging to describe correctly. Here, we present a computational study on the DNA bending of canonical and G/T mismatched DNAs. Five types of geometric parameters covering template-based bending toward the experimental DNA structure, global, and local geometry parameters were employed in biased molecular dynamics in the absence of MutS. None of these parameters showed higher discrimination than the base-pair opening. Only roll could induce a sharply localized bending of DNA as observed in the experimental MutS/DNA structure. Further, we demonstrated that the intercalation of benzene mimicking PHE decreases the energetic cost of DNA bending without any effect on mismatch discrimination.
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Affiliation(s)
- Tomáš Bouchal
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,CEITEC─Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Ivo Durník
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,CEITEC─Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petr Kulhánek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,CEITEC─Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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9
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Fogg JM, Judge AK, Stricker E, Chan HL, Zechiedrich L. Supercoiling and looping promote DNA base accessibility and coordination among distant sites. Nat Commun 2021; 12:5683. [PMID: 34584096 PMCID: PMC8478907 DOI: 10.1038/s41467-021-25936-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022] Open
Abstract
DNA in cells is supercoiled and constrained into loops and this supercoiling and looping influence every aspect of DNA activity. We show here that negative supercoiling transmits mechanical stress along the DNA backbone to disrupt base pairing at specific distant sites. Cooperativity among distant sites localizes certain sequences to superhelical apices. Base pair disruption allows sharp bending at superhelical apices, which facilitates DNA writhing to relieve torsional strain. The coupling of these processes may help prevent extensive denaturation associated with genomic instability. Our results provide a model for how DNA can form short loops, which are required for many essential processes, and how cells may use DNA loops to position nicks to facilitate repair. Furthermore, our results reveal a complex interplay between site-specific disruptions to base pairing and the 3-D conformation of DNA, which influences how genomes are stored, replicated, transcribed, repaired, and many other aspects of DNA activity.
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Affiliation(s)
- Jonathan M Fogg
- Department of Molecular Virology and Microbiology, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, TX, USA
- Department of Pharmacology and Chemical Biology, Houston, TX, USA
| | - Allison K Judge
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, TX, USA
| | - Erik Stricker
- Department of Molecular Virology and Microbiology, Houston, TX, USA
| | - Hilda L Chan
- Graduate Program in Immunology and Microbiology, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, Houston, TX, USA.
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, TX, USA.
- Department of Pharmacology and Chemical Biology, Houston, TX, USA.
- Graduate Program in Immunology and Microbiology, Houston, TX, USA.
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10
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Dohnalová H, Lankaš F. Deciphering the mechanical properties of
B‐DNA
duplex. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1575] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hana Dohnalová
- Department of Informatics and Chemistry University of Chemistry and Technology Prague Praha 6 Czech Republic
| | - Filip Lankaš
- Department of Informatics and Chemistry University of Chemistry and Technology Prague Praha 6 Czech Republic
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11
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Abstract
DNA dynamics can only be understood by taking into account its complex mechanical behavior at different length scales. At the micrometer level, the mechanical properties of single DNA molecules have been well-characterized by polymer models and are commonly quantified by a persistence length of 50 nm (~150 bp). However, at the base pair level (~3.4 Å), the dynamics of DNA involves complex molecular mechanisms that are still being deciphered. Here, we review recent single-molecule experiments and molecular dynamics simulations that are providing novel insights into DNA mechanics from such a molecular perspective. We first discuss recent findings on sequence-dependent DNA mechanical properties, including sequences that resist mechanical stress and sequences that can accommodate strong deformations. We then comment on the intricate effects of cytosine methylation and DNA mismatches on DNA mechanics. Finally, we review recently reported differences in the mechanical properties of DNA and double-stranded RNA, the other double-helical carrier of genetic information. A thorough examination of the recent single-molecule literature permits establishing a set of general 'rules' that reasonably explain the mechanics of nucleic acids at the base pair level. These simple rules offer an improved description of certain biological systems and might serve as valuable guidelines for future design of DNA and RNA nanostructures.
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12
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Prokhorov VV, Barinov NA, Prusakov KA, Dubrovin EV, Frank-Kamenetskii MD, Klinov DV. Anomalous Laterally Stressed Kinetically Trapped DNA Surface Conformations. NANO-MICRO LETTERS 2021; 13:130. [PMID: 34138333 PMCID: PMC8141082 DOI: 10.1007/s40820-021-00626-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
DNA kinking is inevitable for the highly anisotropic 1D-1D electrostatic interaction with the one-dimensionally periodically charged surface. The double helical structure of the DNA kinetically trapped on positively charged monomolecular films comprising the lamellar templates is strongly laterally stressed and extremely perturbed at the nanometer scale. The DNA kinetic trapping is not a smooth 3D-> 2D conformational flattening but is a complex nonlinear in-plane mechanical response (bending, tensile and unzipping) driven by the physics beyond the scope of the applicability of the linear worm-like chain approximation. Up to now, the DNA molecule adsorbed on a surface was believed to always preserve its native structure. This belief implies a negligible contribution of lateral surface forces during and after DNA adsorption although their impact has never been elucidated. High-resolution atomic force microscopy was used to observe that stiff DNA molecules kinetically trapped on monomolecular films comprising one-dimensional periodically charged lamellar templates as a single layer or as a sublayer are oversaturated by sharp discontinuous kinks and can also be locally melted and supercoiled. We argue that kink/anti-kink pairs are induced by an overcritical lateral bending stress (> 30 pNnm) inevitable for the highly anisotropic 1D-1D electrostatic interaction of DNA and underlying rows of positive surface charges. In addition, the unexpected kink-inducing mechanical instability in the shape of the template-directed DNA confined between the positively charged lamellar sides is observed indicating the strong impact of helicity. The previously reported anomalously low values of the persistence length of the surface-adsorbed DNA are explained by the impact of the surface-induced low-scale bending. The sites of the local melting and supercoiling are convincingly introduced as other lateral stress-induced structural DNA anomalies by establishing a link with DNA high-force mechanics. The results open up the study in the completely unexplored area of the principally anomalous kinetically trapped DNA surface conformations in which the DNA local mechanical response to the surface-induced spatially modulated lateral electrostatic stress is essentially nonlinear. The underlying rich and complex in-plane nonlinear physics acts at the nanoscale beyond the scope of applicability of the worm-like chain approximation.
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Affiliation(s)
- Valery V Prokhorov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.
- A.N.Frumkin Institute of Physical Chemistry and Electrochemistry, RAS, Leninsky prospect 31, Moscow, 199071, Russian Federation.
| | - Nikolay A Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
| | - Kirill A Prusakov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, 141700, Moscow, Russian Federation
| | - Evgeniy V Dubrovin
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
- Lomonosov Moscow State University, Leninskie gory, 1-2, Moscow, 119991, Russian Federation
| | | | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, 141700, Moscow, Russian Federation.
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13
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Pyne ALB, Noy A, Main KHS, Velasco-Berrelleza V, Piperakis MM, Mitchenall LA, Cugliandolo FM, Beton JG, Stevenson CEM, Hoogenboom BW, Bates AD, Maxwell A, Harris SA. Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides. Nat Commun 2021; 12:1053. [PMID: 33594049 PMCID: PMC7887228 DOI: 10.1038/s41467-021-21243-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 01/16/2021] [Indexed: 12/16/2022] Open
Abstract
In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled) structures. It remains unclear how this supercoiling affects the detailed double-helical structure of DNA, largely because of limitations in spatial resolution of the available biophysical tools. Here, we overcome these limitations, by a combination of atomic force microscopy (AFM) and atomistic molecular dynamics (MD) simulations, to resolve structures of negatively-supercoiled DNA minicircles at base-pair resolution. We observe that negative superhelical stress induces local variation in the canonical B-form DNA structure by introducing kinks and defects that affect global minicircle structure and flexibility. We probe how these local and global conformational changes affect DNA interactions through the binding of triplex-forming oligonucleotides to DNA minicircles. We show that the energetics of triplex formation is governed by a delicate balance between electrostatics and bonding interactions. Our results provide mechanistic insight into how DNA supercoiling can affect molecular recognition, that may have broader implications for DNA interactions with other molecular species.
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Affiliation(s)
- Alice L B Pyne
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, UK.
- London Centre for Nanotechnology, University College London, London, UK.
| | - Agnes Noy
- Department of Physics, Biological Physical Sciences Institute, University of York, York, UK.
| | - Kavit H S Main
- London Centre for Nanotechnology, University College London, London, UK
- UCL Cancer Institute, University College London, London, UK
| | | | - Michael M Piperakis
- Department of Biological Chemistry, John Innes Centre, Norwich, UK
- Department of Chemistry, University of Reading, Whiteknights, Reading, UK
| | | | - Fiorella M Cugliandolo
- Department of Biological Chemistry, John Innes Centre, Norwich, UK
- Department of Pathology, Division of Immunology, University of Cambridge, Cambridge, UK
| | - Joseph G Beton
- London Centre for Nanotechnology, University College London, London, UK
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, UK
| | | | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London, UK
- Department of Physics and Astronomy, University College London, London, UK
| | - Andrew D Bates
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich, UK
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, Leeds, UK.
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
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14
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Park G, Cho MK, Jung Y. Sequence-Dependent Kink Formation in Short DNA Loops: Theory and Molecular Dynamics Simulations. J Chem Theory Comput 2021; 17:1308-1317. [PMID: 33570937 DOI: 10.1021/acs.jctc.0c01116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Kink formation is essential in highly bent DNA complexed with gene regulatory proteins such as histones to release the bending stress stored within the DNA duplex. Local opening of the double-stranded DNA creates a sharp turn along the specific sequence, which leads to the global bending of the DNA strand. Despite the critical role of kink formation, it is still challenging to predict the position of kink formation for a given DNA sequence. In this study, we propose a theoretical model and perform molecular dynamics simulations to quantify the sequence-dependent kink probability of a strongly bent DNA. By incorporating the elastic bending energy and the sequence-specific thermodynamic parameters, we investigate the importance of the DNA sequence on kink formation. We find that the sequence with TA dinucleotide repeats flanked by GC steps increases the kink propensity by more than an order of magnitude under the same bending stress. The number of base pairs involved in the local opening is found to be coupled with the sequence-specific bubble formation free energy. Our study elucidates the molecular origin of the sequence heterogeneity on kink formation, which is fundamental to understanding protein-DNA recognition.
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Affiliation(s)
- Gyehyun Park
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Myung Keun Cho
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - YounJoon Jung
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
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15
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Saran R, Wang Y, Li ITS. Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology. SENSORS (BASEL, SWITZERLAND) 2020; 20:E7019. [PMID: 33302459 PMCID: PMC7764255 DOI: 10.3390/s20247019] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023]
Abstract
The mechanical properties of DNA have enabled it to be a structural and sensory element in many nanotechnology applications. While specific base-pairing interactions and secondary structure formation have been the most widely utilized mechanism in designing DNA nanodevices and biosensors, the intrinsic mechanical rigidity and flexibility are often overlooked. In this article, we will discuss the biochemical and biophysical origin of double-stranded DNA rigidity and how environmental and intrinsic factors such as salt, temperature, sequence, and small molecules influence it. We will then take a critical look at three areas of applications of DNA bending rigidity. First, we will discuss how DNA's bending rigidity has been utilized to create molecular springs that regulate the activities of biomolecules and cellular processes. Second, we will discuss how the nanomechanical response induced by DNA rigidity has been used to create conformational changes as sensors for molecular force, pH, metal ions, small molecules, and protein interactions. Lastly, we will discuss how DNA's rigidity enabled its application in creating DNA-based nanostructures from DNA origami to nanomachines.
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Affiliation(s)
- Runjhun Saran
- Department of Chemistry, Biochemistry and Molecular Biology, Irving K. Barber Faculty of Science, The University of British Columbia, Kelowna, BC V1V1V7, Canada;
| | - Yong Wang
- Department of Physics, Materials Science and Engineering Program, Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Isaac T. S. Li
- Department of Chemistry, Biochemistry and Molecular Biology, Irving K. Barber Faculty of Science, The University of British Columbia, Kelowna, BC V1V1V7, Canada;
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16
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Desai PR, Brahmachari S, Marko JF, Das S, Neuman KC. Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches. Nucleic Acids Res 2020; 48:10713-10725. [PMID: 33045724 DOI: 10.1093/nar/gkaa836] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 09/14/2020] [Accepted: 09/18/2020] [Indexed: 12/27/2022] Open
Abstract
Damaged or mismatched DNA bases result in the formation of physical defects in double-stranded DNA. In vivo, defects in DNA must be rapidly and efficiently repaired to maintain cellular function and integrity. Defects can also alter the mechanical response of DNA to bending and twisting constraints, both of which are important in defining the mechanics of DNA supercoiling. Here, we use coarse-grained molecular dynamics (MD) simulation and supporting statistical-mechanical theory to study the effect of mismatched base pairs on DNA supercoiling. Our simulations show that plectoneme pinning at the mismatch site is deterministic under conditions of relatively high force (>2 pN) and high salt concentration (>0.5 M NaCl). Under physiologically relevant conditions of lower force (0.3 pN) and lower salt concentration (0.2 M NaCl), we find that plectoneme pinning becomes probabilistic and the pinning probability increases with the mismatch size. These findings are in line with experimental observations. The simulation framework, validated with experimental results and supported by the theoretical predictions, provides a way to study the effect of defects on DNA supercoiling and the dynamics of supercoiling in molecular detail.
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Affiliation(s)
- Parth Rakesh Desai
- Department of Mechanical Engineering, University of Maryland, College Park, MD 20742, USA.,Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - John F Marko
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA.,Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Siddhartha Das
- Department of Mechanical Engineering, University of Maryland, College Park, MD 20742, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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17
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Bouchal T, Durník I, Illík V, Réblová K, Kulhánek P. Importance of base-pair opening for mismatch recognition. Nucleic Acids Res 2020; 48:11322-11334. [PMID: 33080020 PMCID: PMC7672436 DOI: 10.1093/nar/gkaa896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 09/09/2020] [Accepted: 09/30/2020] [Indexed: 01/04/2023] Open
Abstract
Mismatch repair is a highly conserved cellular pathway responsible for repairing mismatched dsDNA. Errors are detected by the MutS enzyme, which most likely senses altered mechanical property of damaged dsDNA rather than a specific molecular pattern. While the curved shape of dsDNA in crystallographic MutS/DNA structures suggests the role of DNA bending, the theoretical support is not fully convincing. Here, we present a computational study focused on a base-pair opening into the minor groove, a specific base-pair motion observed upon interaction with MutS. Propensities for the opening were evaluated in terms of two base-pair parameters: Opening and Shear. We tested all possible base pairs in anti/anti, anti/syn and syn/anti orientations and found clear discrimination between mismatches and canonical base-pairs only for the opening into the minor groove. Besides, the discrimination gap was also confirmed in hotspot and coldspot sequences, indicating that the opening could play a more significant role in the mismatch recognition than previously recognized. Our findings can be helpful for a better understanding of sequence-dependent mutability. Further, detailed structural characterization of mismatches can serve for designing anti-cancer drugs targeting mismatched base pairs.
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Affiliation(s)
- Tomáš Bouchal
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Ivo Durník
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Viktor Illík
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Kamila Réblová
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petr Kulhánek
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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18
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Drozdetski AV, Mukhopadhyay A, Onufriev AV. Strongly Bent Double-Stranded DNA: Reconciling Theory and Experiment. FRONTIERS IN PHYSICS 2019; 7:195. [PMID: 32601596 PMCID: PMC7323118 DOI: 10.3389/fphy.2019.00195] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general physical principle. As the bending deformation increases beyond a certain (polymer-specific) point, the change in the convexity properties of the effective bending energy of the polymer makes the harmonic deformation energetically unfavorable: in this strong bending regime the energy of the polymer varies linearly with the average bending angle as the system follows the convex hull of the deformation energy function. For double-stranded DNA, the effective bending deformation energy becomes non-convex for bends greater than ~ 2° per base-pair, equivalent to the curvature of a closed circular loop of ~ 160 base pairs. A simple equation is derived for the polymer loop energy that covers both the weak and strong bending regimes. The theory shows quantitative agreement with recent DNA cyclization experiments on short DNA fragments, while maintaining the expected agreement with experiment in the weak bending regime. Counter-intuitively, cyclization probability (j-factor) of very short DNA loops is predicted to increase with decreasing loop length; the j-factor reaches its minimum for loops of ≃ 45 base pairs. Atomistic simulations reveal that the attractive component of the short-range Lennard-Jones interaction between the backbone atoms can explain the underlying non-convexity of the DNA effective bending energy, leading to the linear bending regime. Applicability of the theory to protein-DNA complexes, including the nucleosome, is discussed.
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Affiliation(s)
| | | | - Alexey V. Onufriev
- Department of Physics, Virginia Tech, Blacksburg, VA, United States
- Department of Computer Science, Virginia Tech, Blacksburg, VA, United States
- Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, United States
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19
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Růžička M, Souček P, Kulhánek P, Radová L, Fajkusová L, Réblová K. Bending of DNA duplexes with mutation motifs. DNA Res 2019; 26:341-352. [PMID: 31230075 PMCID: PMC6704406 DOI: 10.1093/dnares/dsz013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/27/2019] [Indexed: 01/30/2023] Open
Abstract
Mutations can be induced by environmental factors but also arise spontaneously during DNA replication or due to deamination of methylated cytosines at CpG dinucleotides. Sites where mutations occur with higher frequency than would be expected by chance are termed hotspots while sites that contain mutations rarely are termed coldspots. Mutations are permanently scanned and repaired by repair systems. Among them, the mismatch repair targets base pair mismatches, which are discriminated from canonical base pairs by probing altered elasticity of DNA. Using biased molecular dynamics simulations, we investigated the elasticity of coldspots and hotspots motifs detected in human genes associated with inherited disorders, and also of motifs with Czech population hotspots and de novo mutations. Main attention was paid to mutations leading to G/T and A+/C pairs. We observed that hotspots without CpG/CpHpG sequences are less flexible than coldspots, which indicates that flexible sequences are more effectively repaired. In contrary, hotspots with CpG/CpHpG sequences exhibited increased flexibility as coldspots. Their mutability is more likely related to spontaneous deamination of methylated cytosines leading to C > T mutations, which are primarily targeted by base excision repair. We corroborated conclusions based on computer simulations by measuring melting curves of hotspots and coldspots containing G/T mismatch.
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Affiliation(s)
- Michal Růžička
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Přemysl Souček
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Petr Kulhánek
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lenka Radová
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Lenka Fajkusová
- Centre of Molecular Biology and Gene Therapy, University Hospital Brno, Brno, Czech Republic
| | - Kamila Réblová
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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20
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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.
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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
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21
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Marin-Gonzalez A, Vilhena JG, Moreno-Herrero F, Perez R. DNA Crookedness Regulates DNA Mechanical Properties at Short Length Scales. PHYSICAL REVIEW LETTERS 2019; 122:048102. [PMID: 30768347 DOI: 10.1103/physrevlett.122.048102] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Indexed: 05/13/2023]
Abstract
Sequence-dependent DNA conformation and flexibility play a fundamental role in the specificity of DNA-protein interactions. Here we quantify the DNA crookedness: a sequence-dependent deformation of DNA that consists of periodic bends of the base pair centers chain. Using extensive 100 μs-long, all-atom molecular dynamics simulations, we found that DNA crookedness and its associated flexibility are bijective, which unveils a one-to-one relation between DNA structure and dynamics. This allowed us to build a predictive model to compute the stretch moduli of different DNA sequences from solely their structure. Sequences with very little crookedness show extremely high stretching stiffness and have been previously shown to form unstable nucleosomes and promote gene expression. Interestingly, the crookedness can be tailored by epigenetic modifications, known to affect gene expression. Our results rationalize the idea that the DNA sequence is not only a chemical code, but also a physical one that allows finely regulating its mechanical properties and, possibly, its 3D arrangement inside the cell.
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Affiliation(s)
- Alberto Marin-Gonzalez
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - J G Vilhena
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH 4056 Basel, Switzerland
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Ruben Perez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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22
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Simonov KA. Strong deformations of DNA: Effect on the persistence length. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:114. [PMID: 30259229 DOI: 10.1140/epje/i2018-11722-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/30/2018] [Indexed: 06/08/2023]
Abstract
Extreme deformations of the DNA double helix attracted a lot of attention during the past decades. Particularly, the determination of the persistence length of DNA with extreme local disruptions, or kinks, has become a crucial problem in the studies of many important biological processes. In this paper we review an approach to calculate the persistence length of the double helix by taking into account the formation of kinks of arbitrary configuration. The reviewed approach improves the Kratky-Porod model to determine the type and nature of kinks that occur in the double helix, by measuring a reduction of the persistence length of the kinkable DNA.
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Affiliation(s)
- Kyryło A Simonov
- Fakultät für Mathematik, Universität Wien, Oskar-Morgenstern-Platz 1, 1090, Vienna, Austria.
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23
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Ghoshdastidar D, Bansal M. Dynamics of physiologically relevant noncanonical DNA structures: an overview from experimental and theoretical studies. Brief Funct Genomics 2018; 18:192-204. [DOI: 10.1093/bfgp/ely026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 06/23/2018] [Accepted: 07/09/2018] [Indexed: 12/23/2022] Open
Abstract
Abstract
DNA is a complex molecule with phenomenal inherent plasticity and the ability to form different hydrogen bonding patterns of varying stabilities. These properties enable DNA to attain a variety of structural and conformational polymorphic forms. Structurally, DNA can exist in single-stranded form or as higher-order structures, which include the canonical double helix as well as the noncanonical duplex, triplex and quadruplex species. Each of these structural forms in turn encompasses an ensemble of dynamically heterogeneous conformers depending on the sequence composition and environmental context. In vivo, the widely populated canonical B-DNA attains these noncanonical polymorphs during important cellular processes. While several investigations have focused on the structure of these noncanonical DNA, studying their dynamics has remained nontrivial. Here, we outline findings from some recent advanced experimental and molecular simulation techniques that have significantly contributed toward understanding the complex dynamics of physiologically relevant noncanonical forms of DNA.
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Affiliation(s)
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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24
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Sandmann A, Sticht H. Probing the role of intercalating protein sidechains for kink formation in DNA. PLoS One 2018; 13:e0192605. [PMID: 29432448 PMCID: PMC5809078 DOI: 10.1371/journal.pone.0192605] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/28/2018] [Indexed: 11/18/2022] Open
Abstract
Protein binding can induce DNA kinks, which are for example important to enhance the specificity of the interaction and to facilitate the assembly of multi protein complexes. The respective proteins frequently exhibit amino acid sidechains that intercalate between the DNA base steps at the site of the kink. However, on a molecular level there is only little information available about the role of individual sidechains for kink formation. To unravel structural principles of protein-induced DNA kinking we have performed molecular dynamics (MD) simulations of five complexes that varied in their architecture, function, and identity of intercalated residues. Simulations were performed for the DNA complexes of wildtype proteins (Sac7d, Sox-4, CcpA, TFAM, TBP) and for mutants, in which the intercalating residues were individually or combined replaced by alanine. The work revealed that for systems with multiple intercalated residues, not all of them are necessarily required for kink formation. In some complexes (Sox-4, TBP), one of the residues proved to be essential for kink formation, whereas the second residue has only a very small effect on the magnitude of the kink. In other systems (e.g. Sac7d) each of the intercalated residues proved to be individually capable of conferring a strong kink suggesting a partially redundant role of the intercalating residues. Mutation of the key residues responsible for kinking either resulted in stable complexes with reduced kink angles or caused conformational instability as evidenced by a shift of the kink to an adjacent base step. Thus, MD simulations can help to identify the role of individual inserted residues for kinking, which is not readily apparent from an inspection of the static structures. This information might be helpful for understanding protein-DNA interactions in more detail and for designing proteins with altered DNA binding properties in the future.
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Affiliation(s)
- Achim Sandmann
- Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Heinrich Sticht
- Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- * E-mail:
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25
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Role of Macromolecular Crowding on the Intracellular Diffusion of DNA Binding Proteins. Sci Rep 2018; 8:844. [PMID: 29339733 PMCID: PMC5770392 DOI: 10.1038/s41598-017-18933-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 12/20/2017] [Indexed: 11/08/2022] Open
Abstract
Recent experiments suggest that cellular crowding facilitates the target search dynamics of proteins on DNA, the mechanism of which is not yet known. By using large scale computer simulations, we show that two competing factors, namely the width of the depletion layer that separates the crowder cloud from the DNA molecule and the degree of protein-crowder crosstalk, act in harmony to affect the target search dynamics of proteins. The impacts vary from nonspecific to specific target search regime. During a nonspecific search, dynamics of a protein is only minimally affected, whereas, a significantly different behaviour is observed when the protein starts forming a specific protein-DNA complex. We also find that the severity of impacts largely depends upon physiological crowder concentration and deviation from it leads to attenuation in the binding kinetics. Based on extensive kinetic study and binding energy landscape analysis, we further present a comprehensive molecular description of the search process that allows us to interpret the experimental findings.
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26
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Gantchev TG, Petkov PS, Hunting DJ. Conformational rearrangement of 1,2-d(GG) intrastrand cis-diammineplatinum crosslinked DNA is driven by counter-ion penetration within the minor groove of the modified site. J Mol Model 2017; 23:278. [PMID: 28913561 DOI: 10.1007/s00894-017-3445-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 08/25/2017] [Indexed: 11/27/2022]
Abstract
The major structural aberrations of DNA induced by a cis-diammineplatinum (II) 1,2-d(GG) intrastrand cross-link (CPT) have been known for decades. To gain deeper insights into the structural dynamics of the sequence-dependent DNA distortions adjacent to the CPT adduct, we employed molecular modeling and molecular dynamics (MD) simulations. The structural dynamics of native (N-DNA) and cisPt 1,2-d(GG) crosslinked (CPT-DNA) in the form of symmetric 36 nt d(G2T15G*G*T15G2)●C2A15CCA15C2) oligonucleotide duplexes is compared. The selected sequence context enabled tracking of the origin of the DNA axis curvature at the YpR flexible points (N-DNA), the enhancement of axis bending, and further distortions due to steric/electrostatic perturbations arising from the CPT-crosslink. In addition to the known structural distortions of CPT-DNA: helix bend towards the major groove; local helix unwinding; high roll angle between cross-linked guanine bases; and adoption of A-form DNA on the 5'-side of the CPT-crosslink (TpG junction); our results show the existence of a singular irreversible and reproducible conformational rearrangement, not previously observed, resulting in two stable CPT-DNA1 and CPT-DNA2 conformers. The CPT-DNA2 conformation presents an enhanced DNA axis bend and a wider and shallower minor grove with increased solvent accessibility within the modified site. It is concluded that the polymorphous (unstable) DNA environment near the cisPt 1,2-d(GG) unit in synergy with specific dynamic events, such as prolonged minor groove retention of particular Na+ ions and water redistribution within the d(TG*G*T) site, together with the formation of extra and more stable H-bonds between Pt(NH3)2 amines and neighboring nucleotides, are cooperatively responsible for the initiation of the conformational rearrangement leading to the CPT-DNA2 conformer, which, surprisingly, closely resembles the HMGB1-bound CPT-DNA structure. Graphical abstract Superimposed averaged structures of normal (N-DNA, green) and cisplatin intrastrand cross-linked (CPT-DNA, orange). Global DNA axes: N-DNA (blue beads); CPT-DNA (red beads); PT (yellow sphere); crosslinked dGs viewed from the minor groove (bold).
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Affiliation(s)
- Tsvetan G Gantchev
- Department of Nuclear Medicine & Radiobiology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada. .,"Roumen Tsanev" Institute of Molecular Biology, Bulgarian Academy of Sciences, 1113, Sofia, Bulgaria.
| | - Peicho St Petkov
- Department of Atomic Physics, Faculty of Physics, Sofia University, 5 James Bourchier Blvd., 1164, Sofia, Bulgaria
| | - Darel J Hunting
- Department of Nuclear Medicine & Radiobiology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada
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27
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Simulation of DNA Supercoil Relaxation. Biophys J 2017; 110:2176-84. [PMID: 27224483 DOI: 10.1016/j.bpj.2016.03.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 03/24/2016] [Accepted: 03/28/2016] [Indexed: 01/17/2023] Open
Abstract
Several recent single-molecule experiments observe the response of supercoiled DNA to nicking endonucleases and topoisomerases. Typically in these experiments, indirect measurements of supercoil relaxation are obtained by observing the motion of a large micron-sized bead. The bead, which also serves to manipulate DNA, experiences significant drag and thereby obscures supercoil dynamics. Here we employ our discrete wormlike chain model to bypass experimental limitations and simulate the dynamic response of supercoiled DNA to a single strand nick. From our simulations, we make three major observations. First, extension is a poor dynamic measure of supercoil relaxation; in fact, the linking number relaxes so fast that it cannot have much impact on extension. Second, the rate of linking number relaxation depends upon its initial partitioning into twist and writhe as determined by tension. Third, the extensional response strongly depends upon the initial position of plectonemes.
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28
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Bilto IM, Guha TK, Wai A, Hausner G. Three new active members of the I-OnuI family of homing endonucleases. Can J Microbiol 2017; 63:671-681. [PMID: 28414922 DOI: 10.1139/cjm-2017-0067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In vitro characterization of 3 LAGLIDADG-type homing endonucleases (HEs) (I-CcaI, I-CcaII, and I-AstI) that belong to the I-OnuI family showed that they are functional HEs that cleave their respective cognate target sites. These endonucleases are encoded within group ID introns and appear to be orthologues that have inserted into 3 different mitochondrial genes: rns, rnl, and cox3. The endonuclease activity of I-CcaI was tested using various substrates, and its minimum DNA recognition sequence was estimated to be 26 nt. This set of HEs may provide some insight into how these types of mobile elements can migrate into new locations. This study provides additional endonucleases that can be added to the catalog of currently available HEs that may have various biotechnology applications.
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Affiliation(s)
- Iman M Bilto
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Tuhin K Guha
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Alvan Wai
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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29
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Sutthibutpong T, Matek C, Benham C, Slade GG, Noy A, Laughton C, K Doye JP, Louis AA, Harris SA. Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation. Nucleic Acids Res 2016; 44:9121-9130. [PMID: 27664220 PMCID: PMC5100592 DOI: 10.1093/nar/gkw815] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 09/03/2016] [Indexed: 12/14/2022] Open
Abstract
It is well established that gene regulation can be achieved through activator and repressor proteins that bind to DNA and switch particular genes on or off, and that complex metabolic networks determine the levels of transcription of a given gene at a given time. Using three complementary computational techniques to study the sequence-dependence of DNA denaturation within DNA minicircles, we have observed that whenever the ends of the DNA are constrained, information can be transferred over long distances directly by the transmission of mechanical stress through the DNA itself, without any requirement for external signalling factors. Our models combine atomistic molecular dynamics (MD) with coarse-grained simulations and statistical mechanical calculations to span three distinct spatial resolutions and timescale regimes. While they give a consensus view of the non-locality of sequence-dependent denaturation in highly bent and supercoiled DNA loops, each also reveals a unique aspect of long-range informational transfer that occurs as a result of restraining the DNA within the closed loop of the minicircles.
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Affiliation(s)
- Thana Sutthibutpong
- School of Physics and Astronomy, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.,Theoretical and Computational Science Center (TaCS), Science Laboratory Building, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand
| | - Christian Matek
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Craig Benham
- UC Davis Genome Centre, Health Sciences Drive, Davis, CA 95616, USA
| | - Gabriel G Slade
- Department of Physics, São Paulo State University, Rua Cristovão, São José do Rio Preto, SP 15054-000, Brazil
| | - Agnes Noy
- Department of Physics, Biological Physical Sciences Institute, University of York, York, YO10 5DD, UK
| | - Charles Laughton
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK .,Astbury Centre for Structural and Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
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30
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Cong P, Dai L, Chen H, van der Maarel JRC, Doyle PS, Yan J. Revisiting the Anomalous Bending Elasticity of Sharply Bent DNA. Biophys J 2016; 109:2338-51. [PMID: 26636945 PMCID: PMC4675846 DOI: 10.1016/j.bpj.2015.10.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 11/25/2022] Open
Abstract
Several recent experiments suggest that sharply bent DNA has a surprisingly high bending flexibility, but the cause of this flexibility is poorly understood. Although excitation of flexible defects can explain these results, whether such excitation can occur with the level of DNA bending in these experiments remains unclear. Intriguingly, the DNA contained preexisting nicks in most of these experiments but whether nicks might play a role in flexibility has never been considered in the interpretation of experimental results. Here, using full-atom molecular dynamics simulations, we show that nicks promote DNA basepair disruption at the nicked sites, which drastically reduces DNA bending energy. In addition, lower temperatures suppress the nick-dependent basepair disruption. In the absence of nicks, basepair disruption can also occur but requires a higher level of DNA bending. Therefore, basepair disruption inside B-form DNA can be suppressed if the DNA contains preexisting nicks. Overall, our results suggest that the reported mechanical anomaly of sharply bent DNA is likely dependent on preexisting nicks, therefore the intrinsic mechanisms of sharply bent nick-free DNA remain an open question.
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Affiliation(s)
- Peiwen Cong
- Mechanobiology Institute, National University of Singapore, Singapore; Singapore-MIT Alliance, National University of Singapore, Singapore; Department of Physics, National University of Singapore, Singapore
| | - Liang Dai
- BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology Centre, Singapore
| | - Hu Chen
- Department of Physics, Xiamen University, Xiamen, Fujian, China
| | | | - Patrick S Doyle
- BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology Centre, Singapore; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore; Department of Physics, National University of Singapore, Singapore; BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology Centre, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore.
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31
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Abstract
DNA bending is critical for DNA packaging, recognition, and repair, and occurs toward either the major or the minor groove. The anisotropy of B-DNA groove bending was quantified for eight DNA sequences by free energy simulations employing a novel reaction coordinate. The simulations show that bending toward the major groove is preferred for non-A-tracts while the A-tract has a high tendency of bending toward the minor groove. Persistence lengths were generally larger for bending toward the minor groove, which is thought to originate from differences in groove hydration. While this difference in stiffness is one of the factors determining the overall preference of bending direction, the dominant contribution is shown to be a free energy offset between major and minor groove bending. The data suggests that, for the A-tract, this offset is largely determined by inherent structural properties, while differences in groove hydration play a large role for non-A-tracts. By quantifying the energetics of DNA groove bending and rationalizing the origins of the anisotropy, the calculations provide important new insights into a key biological process.
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Affiliation(s)
- Ning Ma
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, CHE 205, Tampa, Florida 33620, United States
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, CHE 205, Tampa, Florida 33620, United States
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32
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Pasi M, Mornico D, Volant S, Juchet A, Batisse J, Bouchier C, Parissi V, Ruff M, Lavery R, Lavigne M. DNA minicircles clarify the specific role of DNA structure on retroviral integration. Nucleic Acids Res 2016; 44:7830-47. [PMID: 27439712 PMCID: PMC5027509 DOI: 10.1093/nar/gkw651] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/11/2016] [Indexed: 01/26/2023] Open
Abstract
Chromatin regulates the selectivity of retroviral integration into the genome of infected cells. At the nucleosome level, both histones and DNA structure are involved in this regulation. We propose a strategy that allows to specifically study a single factor: the DNA distortion induced by the nucleosome. This strategy relies on mimicking this distortion using DNA minicircles (MCs) having a fixed rotational orientation of DNA curvature, coupled with atomic-resolution modeling. Contrasting MCs with linear DNA fragments having identical sequences enabled us to analyze the impact of DNA distortion on the efficiency and selectivity of integration. We observed a global enhancement of HIV-1 integration in MCs and an enrichment of integration sites in the outward-facing DNA major grooves. Both of these changes are favored by LEDGF/p75, revealing a new, histone-independent role of this integration cofactor. PFV integration is also enhanced in MCs, but is not associated with a periodic redistribution of integration sites, thus highlighting its distinct catalytic properties. MCs help to separate the roles of target DNA structure, histone modifications and integrase (IN) cofactors during retroviral integration and to reveal IN-specific regulation mechanisms.
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Affiliation(s)
- Marco Pasi
- MMSB UMR5086 University of Lyon I/CNRS, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
| | - Damien Mornico
- Institut Pasteur-Bioinformatics and Biostatistics Hub-C3BI, USR 3756 IP-CNRS, Paris 75015, France
| | - Stevenn Volant
- Institut Pasteur-Bioinformatics and Biostatistics Hub-C3BI, USR 3756 IP-CNRS, Paris 75015, France
| | - Anna Juchet
- Institut Pasteur, Unité de Virologie Moléculaire et Vaccinologie, UMR 3569 IP-CNRS, Paris 75015, France
| | - Julien Batisse
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Dpt de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, Illkirch 67400, France
| | - Christiane Bouchier
- Institut Pasteur, PF1, Plate-forme Génomique-Pôle Biomics, Citech, Paris 75015, France
| | - Vincent Parissi
- Laboratoire de Microbiologie Fondamentale et Pathogénicité, UMR 5234 CNRS-Université de Bordeaux, Bordeaux 33000, France
| | - Marc Ruff
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Dpt de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, Illkirch 67400, France
| | - Richard Lavery
- MMSB UMR5086 University of Lyon I/CNRS, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
| | - Marc Lavigne
- Institut Pasteur, Unité de Virologie Moléculaire et Vaccinologie, UMR 3569 IP-CNRS, Paris 75015, France
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33
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Pasi M, Lavery R. Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics. Nucleic Acids Res 2016; 44:5450-6. [PMID: 27098037 PMCID: PMC4914111 DOI: 10.1093/nar/gkw293] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/08/2016] [Accepted: 04/08/2016] [Indexed: 01/25/2023] Open
Abstract
DNA loop formation on nucleosomes is strongly implicated in chromatin remodeling and occurs spontaneously in nucleosomes subjected to superhelical stress. The nature of such loops depends crucially on the balance between DNA deformation and DNA interaction with the nucleosome core. Currently, no high-resolution structural data on these loops exist. Although uniform rod models have been used to study loop size and shape, these models make assumptions concerning DNA mechanics and DNA-core binding. We present here atomic-scale molecular dynamics simulations for two different loop sizes. The results point to the key role of localized DNA kinking within the loops. Kinks enable the relaxation of DNA bending strain to be coupled with improved DNA-core interactions. Kinks lead to small, irregularly shaped loops that are asymmetrically positioned with respect to the nucleosome core. We also find that loop position can influence the dynamics of the DNA segments at the extremities of the nucleosome.
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Affiliation(s)
- Marco Pasi
- MMSB, University Lyon I/CNRS UMR 5086, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, 69367 Lyon, France
| | - Richard Lavery
- MMSB, University Lyon I/CNRS UMR 5086, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, 69367 Lyon, France
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34
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Lambert AR, Hallinan JP, Shen BW, Chik JK, Bolduc JM, Kulshina N, Robins LI, Kaiser BK, Jarjour J, Havens K, Scharenberg AM, Stoddard BL. Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity. Structure 2016; 24:862-73. [PMID: 27133026 DOI: 10.1016/j.str.2016.03.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/07/2016] [Accepted: 03/21/2016] [Indexed: 11/29/2022]
Abstract
LAGLIDADG meganucleases are DNA cleaving enzymes used for genome engineering. While their cleavage specificity can be altered using several protein engineering and selection strategies, their overall targetability is limited by highly specific indirect recognition of the central four base pairs within their recognition sites. In order to examine the physical basis of indirect sequence recognition and to expand the number of such nucleases available for genome engineering, we have determined the target sites, DNA-bound structures, and central four cleavage fidelities of nine related enzymes. Subsequent crystallographic analyses of a meganuclease bound to two noncleavable target sites, each containing a single inactivating base pair substitution at its center, indicates that a localized slip of the mutated base pair causes a small change in the DNA backbone conformation that results in a loss of metal occupancy at one binding site, eliminating cleavage activity.
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Affiliation(s)
- Abigail R Lambert
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-025, Seattle, WA 98109, USA
| | - Jazmine P Hallinan
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-025, Seattle, WA 98109, USA
| | - Betty W Shen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-025, Seattle, WA 98109, USA
| | - Jennifer K Chik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-025, Seattle, WA 98109, USA
| | - Jill M Bolduc
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-025, Seattle, WA 98109, USA
| | - Nadia Kulshina
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-025, Seattle, WA 98109, USA
| | - Lori I Robins
- Physical Sciences Division, School of STEM, University of Washington, 18115 Campus Way Northeast, Bothell, WA 98011, USA
| | - Brett K Kaiser
- Department of Biology, Seattle University, 901 12th Avenue, Seattle, WA 98122, USA
| | - Jordan Jarjour
- bluebird bio Inc. Suite 207, 1616 Eastlake Avenue East, Seattle, WA 98102, USA
| | - Kyle Havens
- bluebird bio Inc. Suite 207, 1616 Eastlake Avenue East, Seattle, WA 98102, USA
| | - Andrew M Scharenberg
- Seattle Children's Research Institute, 1900 Ninth Avenue, Seattle, WA 98101, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-025, Seattle, WA 98109, USA.
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35
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Menzies GE, Reed SH, Brancale A, Lewis PD. Base damage, local sequence context and TP53 mutation hotspots: a molecular dynamics study of benzo[a]pyrene induced DNA distortion and mutability. Nucleic Acids Res 2015; 43:9133-46. [PMID: 26400171 PMCID: PMC4627081 DOI: 10.1093/nar/gkv910] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/26/2015] [Indexed: 12/22/2022] Open
Abstract
The mutational pattern for the TP53 tumour suppressor gene in lung tumours differs to other cancer types by having a higher frequency of G:C>T:A transversions. The aetiology of this differing mutation pattern is still unknown. Benzo[a]pyrene,diol epoxide (BPDE) is a potent cigarette smoke carcinogen that forms guanine adducts at TP53 CpG mutation hotspot sites including codons 157, 158, 245, 248 and 273. We performed molecular modelling of BPDE-adducted TP53 duplex sequences to determine the degree of local distortion caused by adducts which could influence the ability of nucleotide excision repair. We show that BPDE adducted codon 157 has greater structural distortion than other TP53 G:C>T:A hotspot sites and that sequence context more distal to adjacent bases must influence local distortion. Using TP53 trinucleotide mutation signatures for lung cancer in smokers and non-smokers we further show that codons 157 and 273 have the highest mutation probability in smokers. Combining this information with adduct structural data we predict that G:C>T:A mutations at codon 157 in lung tumours of smokers are predominantly caused by BPDE. Our results provide insight into how different DNA sequence contexts show variability in DNA distortion at mutagen adduct sites that could compromise DNA repair at well characterized cancer related mutation hotspots.
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Affiliation(s)
- Georgina E Menzies
- Institute of Life Science, Swansea University School of Medicine, Swansea University, SA2 8PP, UK
| | - Simon H Reed
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, CF14 4XN, UK
| | - Andrea Brancale
- School of Pharmacy and Pharmacology, Cardiff University, CF10 3NB, UK
| | - Paul D Lewis
- Institute of Life Science, Swansea University School of Medicine, Swansea University, SA2 8PP, UK
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36
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Singh RK, Sasikala WD, Mukherjee A. Molecular Origin of DNA Kinking by Transcription Factors. J Phys Chem B 2015; 119:11590-6. [PMID: 26258468 DOI: 10.1021/acs.jpcb.5b06229] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Binding of transcription factor (TF) proteins with DNA may cause severe kinks in the latter. Here, we investigate the molecular origin of the DNA kinks observed in the TF-DNA complexes using small molecule intercalation pathway, crystallographic analysis, and free energy calculations involving four different transcription factor (TF) protein-DNA complexes. We find that although protein binding may bend the DNA, bending alone is not sufficient to kink the DNA. We show that partial, not complete, intercalation is required to form the kink at a particular place in the DNA. It turns out that while amino acid alone can induce the desired kink through partial intercalation, protein provides thermodynamic stabilization of the kinked state in TF-DNA complexes.
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Affiliation(s)
- Reman Kumar Singh
- Department of Chemistry, Indian Institute of Science Education and Research , Pune, Maharashtra 411021, India
| | - Wilbee D Sasikala
- Department of Chemistry, Indian Institute of Science Education and Research , Pune, Maharashtra 411021, India
| | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research , Pune, Maharashtra 411021, India
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37
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Dršata T, Lankaš F. Multiscale modelling of DNA mechanics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:323102. [PMID: 26194779 DOI: 10.1088/0953-8984/27/32/323102] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Mechanical properties of DNA are important not only in a wide range of biological processes but also in the emerging field of DNA nanotechnology. We review some of the recent developments in modeling these properties, emphasizing the multiscale nature of the problem. Modern atomic resolution, explicit solvent molecular dynamics simulations have contributed to our understanding of DNA fine structure and conformational polymorphism. These simulations may serve as data sources to parameterize rigid base models which themselves have undergone major development. A consistent buildup of larger entities involving multiple rigid bases enables us to describe DNA at more global scales. Free energy methods to impose large strains on DNA, as well as bead models and other approaches, are also briefly discussed.
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Affiliation(s)
- Tomáš Dršata
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague, Czech Republic. Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University Prague, Albertov 6, 128 43 Prague, Czech Republic
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38
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Kim C, Lee OC, Kim JY, Sung W, Lee NK. Dynamic Release of Bending Stress in Short dsDNA by Formation of a Kink and Forks. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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39
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Kim C, Lee OC, Kim JY, Sung W, Lee NK. Dynamic Release of Bending Stress in Short dsDNA by Formation of a Kink and Forks. Angew Chem Int Ed Engl 2015; 54:8943-7. [PMID: 26046547 PMCID: PMC4744731 DOI: 10.1002/anie.201502055] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Indexed: 11/21/2022]
Abstract
Bending with high curvature is one of the major mechanical properties of double-stranded DNA (dsDNA) that is essential for its biological functions. The emergence of a kink arising from local melting in the middle of dsDNA has been suggested as a mechanism of releasing the energy cost of bending. Herein, we report that strong bending induces two types of short dsDNA deformations, induced by two types of local melting, namely, a kink in the middle and forks at the ends, which we demonstrate using D-shaped DNA nanostructures. The two types of deformed dsDNA structures dynamically interconvert on a millisecond timescale. The transition from a fork to a kink is dominated by entropic contribution (anti-Arrhenius behavior), while the transition from a kink to a fork is dominated by enthalpic contributions. The presence of mismatches in dsDNA accelerates kink formation, and the transition from a kink to a fork is removed when the mismatch size is three base pairs.
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Affiliation(s)
- Cheolhee Kim
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea)
| | - O-chul Lee
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea)
| | - Jae-Yeol Kim
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea)
| | - Wokyung Sung
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea)
- IBS Center for Self-assembly and Complexity, Pohang 790-784 (Republic of Korea)
| | - Nam Ki Lee
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea).
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40
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Gresh N, Sponer JE, Devereux M, Gkionis K, de Courcy B, Piquemal JP, Sponer J. Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics. J Phys Chem B 2015; 119:9477-95. [DOI: 10.1021/acs.jpcb.5b01695] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Nohad Gresh
- Chemistry & Biology, Nucleo(s)tides & Immunology for Therapy (CBNIT), CNRS UMR8601, Université Paris Descartes, PRES Sorbonne Paris Cité, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
- Laboratoire
de Chimie Théorique, Sorbonne Universités, UPMC, Paris 6, case courrier
137, 4, place Jussieu, Paris, F75252, France
- Laboratoire
de Chimie Théorique, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, Paris, F75252, France
| | - Judit E. Sponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska,
135, 612 65 Brno, Czech Republic
- CEITEC − Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Mike Devereux
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, Basel CH 4056, Switzerland
| | - Konstantinos Gkionis
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska,
135, 612 65 Brno, Czech Republic
| | - Benoit de Courcy
- Chemistry & Biology, Nucleo(s)tides & Immunology for Therapy (CBNIT), CNRS UMR8601, Université Paris Descartes, PRES Sorbonne Paris Cité, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
- Laboratoire
de Chimie Théorique, Sorbonne Universités, UPMC, Paris 6, case courrier
137, 4, place Jussieu, Paris, F75252, France
- Laboratoire
de Chimie Théorique, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, Paris, F75252, France
| | - Jean-Philip Piquemal
- Laboratoire
de Chimie Théorique, Sorbonne Universités, UPMC, Paris 6, case courrier
137, 4, place Jussieu, Paris, F75252, France
- Laboratoire
de Chimie Théorique, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, Paris, F75252, France
| | - Jiri Sponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska,
135, 612 65 Brno, Czech Republic
- CEITEC − Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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41
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Wang Q, Myers CG, Pettitt BM. Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density. J Phys Chem B 2015; 119:4937-43. [PMID: 25793549 DOI: 10.1021/acs.jpcb.5b00865] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We consider the consequences of assuming that DNA inside of phages can be approximated as a strongly nonlinear persistence length polymer. Recent cryo-EM experiments find a hole in the density map of P-SSP7 phage, located in the DNA segment filling the portal channel of the phage. We use experimentally derived structural constraints with coarse-grained simulation techniques to consider contrasting model interpretations of reconstructed density in the portal channel. The coarse-grained DNA models used are designed to capture the effects of torsional strain and electrostatic environment. Our simulation results are consistent with the interpretation that the vacancy or hole in the experimental density map is due to DNA strain leading to strand separation. We further demonstrate that a moderate negative twisting strain is able to account for the strand separation. This effect of nonlinear persistence length may be important in other aspects of phage DNA packing.
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Affiliation(s)
- Qian Wang
- †Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-0304, United States
| | - Christopher G Myers
- ‡Structural and Computational Biology and Molecular Biophysics Program, Baylor College of Medicine, Houston, Texas 77030, United States
| | - B Montgomery Pettitt
- †Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-0304, United States.,‡Structural and Computational Biology and Molecular Biophysics Program, Baylor College of Medicine, Houston, Texas 77030, United States
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42
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Bascom G, Andricioaei I. Single-Walled Carbon Nanotubes Modulate the B- to A-DNA Transition. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2014; 118:29441-29447. [PMID: 25553205 PMCID: PMC4275165 DOI: 10.1021/jp5081274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/20/2014] [Indexed: 06/04/2023]
Abstract
We study the conformational equilibrium between B-to-A forms of ds-DNA adsorbed onto a single-walled carbon nanotube (SWNT) using free energy profile calculations based on all-atom molecular dynamics simulations. The potential of mean force (PMF) of the B-to-A transition of ds-DNA in the presence of an uncharged (10,0) carbon nanotube for two dodecamers with poly-AT or poly-GC sequences is calculated as a function of a root-mean-square-distance (ΔRMSD) difference metric for the B-to-A transition. The calculations reveal that in the presence of a SWNT DNA favors B-form DNA significantly in both poly-GC and poly-AT sequences. Furthermore, the poly-AT DNA:SWNT complex shows a higher energy penalty for adopting an A-like conformation than poly-GC DNA:SWNT by several kcal/mol. The presence of a SWNT on either poly-AT or poly-GC DNA affects the PMF of the transition such that the B form is favored by as much as 10 kcal/mol. In agreement with published data, we find a potential energy minimum between A and B-form DNA at ΔRMSD ≈ -1.5 Å and that the presence of the SWNT moves this minimum by as much as ΔRMSD = 3 Å.
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McHarris DM, Barr DA. Truncated variants of the GCN4 transcription activator protein bind DNA with dramatically different dynamical motifs. J Chem Inf Model 2014; 54:2869-75. [PMID: 25204850 DOI: 10.1021/ci500448e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The yeast protein GCN4 is a transcriptional activator in the basic leucine zipper (bZip) family, whose distinguishing feature is the "chopstick-like" homodimer of alpha helices formed at the DNA-binding interface. While experiments have shown that truncated versions of the protein retain biologically relevant DNA-binding affinity, we present the results of a computational study revealing that these variants show a wide variety of dynamical modes in their interaction with the target DNA sequence. We have performed all-atom molecular dynamics simulations of the full-length GCN4 protein as well as three truncated variants; our data indicate that the truncated mutants show dramatically different correlation patterns. We conclude that although the truncated mutants still retain DNA-binding ability, the bZip interface present in the full-length protein provides important stability for the protein-DNA complex.
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Affiliation(s)
- Danielle M McHarris
- Department of Chemistry and Biochemistry, Utica College , 1600 Burrstone Road, Utica, New York 13502, United States
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Symmetric curvature descriptors for label-free analysis of DNA. Sci Rep 2014; 4:6459. [PMID: 25248631 PMCID: PMC5377314 DOI: 10.1038/srep06459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/26/2014] [Indexed: 11/13/2022] Open
Abstract
High-resolution microscopy techniques such as electron microscopy, scanning tunnelling microscopy and atomic force microscopy represent well-established, powerful tools for the structural characterization of adsorbed DNA molecules at the nanoscale. Notably, the analysis of DNA contours allows mapping intrinsic curvature and flexibility along the molecular backbone. This is particularly suited to address the impact of the base-pairs sequence on the local conformation of the strands and plays a pivotal role for investigations relating the inherent DNA shape and flexibility to other functional properties. Here, we introduce novel chain descriptors aimed to characterize the local intrinsic curvature and flexibility of adsorbed DNA molecules with unknown orientation. They consist of stochastic functions that couple the curvatures of two nanosized segments, symmetrically placed on the DNA contour. We show that the fine mapping of the ensemble-averaged functions along the molecular backbone generates characteristic patterns of variation that highlight all pairs of tracts with large intrinsic curvature or enhanced flexibility. We demonstrate the practical applicability of the method for DNA chains imaged by atomic force microscopy. Our approach paves the way for the label-free comparative analysis of duplexes, aimed to detect nanoscale conformational changes of physical or biological relevance in large sample numbers.
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van der Vaart A. Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations. Biochim Biophys Acta Gen Subj 2014; 1850:1091-1098. [PMID: 25161164 DOI: 10.1016/j.bbagen.2014.08.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/14/2014] [Accepted: 08/18/2014] [Indexed: 12/21/2022]
Abstract
BACKGROUND Protein-DNA binding often involves dramatic conformational changes such as protein folding and DNA bending. While thermodynamic aspects of this behavior are understood, and its biological function is often known, the mechanism by which the conformational changes occur is generally unclear. By providing detailed structural and energetic data, molecular dynamics simulations have been helpful in elucidating and rationalizing protein-DNA binding. SCOPE OF REVIEW This review will summarize recent atomistic molecular dynamics simulations of the conformational dynamics of DNA and protein-DNA binding. A brief overview of recent developments in DNA force fields is given as well. MAJOR CONCLUSIONS Simulations have been crucial in rationalizing the intrinsic flexibility of DNA, and have been instrumental in identifying the sequence of binding events, the triggers for the conformational motion, and the mechanism of binding for a number of important DNA-binding proteins. GENERAL SIGNIFICANCE Molecular dynamics simulations are an important tool for understanding the complex binding behavior of DNA-binding proteins. With recent advances in force fields and rapid increases in simulation time scales, simulations will become even more important for future studies. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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Affiliation(s)
- Arjan van der Vaart
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue CHE 205, Tampa, FL 33620, USA.
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Dršata T, Špačková N, Jurečka P, Zgarbová M, Šponer J, Lankaš F. Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning. Nucleic Acids Res 2014; 42:7383-94. [PMID: 24829460 PMCID: PMC4066768 DOI: 10.1093/nar/gku338] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/07/2014] [Accepted: 04/09/2014] [Indexed: 11/13/2022] Open
Abstract
A-tracts are functionally important DNA sequences which induce helix bending and have peculiar structural properties. While A-tract structure has been qualitatively well characterized, their mechanical properties remain controversial. A-tracts appear structurally rigid and resist nucleosome formation, but seem flexible in DNA looping. In this work, we investigate mechanical properties of symmetric AnTn and asymmetric A2n tracts for n = 3, 4, 5 using two types of coarse-grained models. The first model represents DNA as an ensemble of interacting rigid bases with non-local quadratic deformation energy, the second one treats DNA as an anisotropically bendable and twistable elastic rod. Parameters for both models are inferred from microsecond long, atomic-resolution molecular dynamics simulations. We find that asymmetric A-tracts are more rigid than the control G/C-rich sequence in localized distortions relevant for nucleosome formation, but are more flexible in global bending and twisting relevant for looping. The symmetric tracts, in contrast, are more rigid than asymmetric tracts and the control, both locally and globally. Our results can reconcile the contradictory stiffness data on A-tracts and suggest symmetric A-tracts to be more efficient in nucleosome exclusion than the asymmetric ones. This would open a new possibility of gene expression manipulation using A-tracts.
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Affiliation(s)
- Tomáš Dršata
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
| | - Nada Špačková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic CEITEC-Central European Institute of Technology, Campus Bohunice, Kamenice 5, 62500 Brno, Czech Republic
| | - Filip Lankaš
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
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Xiao S, Zhu H, Wang L, Liang H. DNA conformational flexibility study using phosphate backbone neutralization model. SOFT MATTER 2014; 10:1045-1055. [PMID: 24983118 DOI: 10.1039/c3sm52345d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Due to the critical role of DNA in the processes of the cell cycle, the structural and physicochemical properties of DNA have long been of concern. In the present work, the effect of interplay between the DNA duplex and metal ions in solution on the DNA structure and conformational flexibility is studied by comparing the structure and dynamic conformational behavior of a duplex in a normal form and its “null isomer” using molecular dynamics methods. It was found that the phosphate neutralization changes the cation atmosphere around the DNA duplex greatly, increases the major groove width, decreases the minor groove width, and reduces the global bending direction preference. We also noted that the probability of BI phosphate linkages increases significantly because of the charge reduction in the backbone phosphate groups. More importantly, we found that the electrostatic effect on the DNA conformational flexibility is dependent on the sequence; that is, the phosphate backbone neutralization induces the global dynamic bending to be less flexible for GC-rich sequences but more flexible for AT-rich sequences.
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Abstract
During the past decade, the issue of strong bending of the double helix has attracted a lot of attention. Here, we overview the major experimental and theoretical developments in the field sorting out reliably established facts from speculations and unsubstantiated claims. Theoretical analysis shows that sharp bends or kinks have to facilitate strong bending of the double helix. It remains to be determined what is the critical curvature of DNA that prompts the appearance of the kinks. Different experimental and computational approaches to the problem are analyzed. We conclude that there is no reliable evidence that any anomalous behavior of the double helix happens when DNA fragments in the range of 100 bp are circularized without torsional stress. The anomaly starts at the fragment length of about 70 bp when sharp bends or kinks emerge in essentially every molecule. Experimental data and theoretical analysis suggest that kinks may represent openings of isolated base pairs, which had been experimentally detected in linear DNA molecules. The calculation suggests that although the probability of these openings in unstressed DNA is close to 10−5, it increases sharply in small DNA circles reaching 1 open bp per circle of 70 bp.
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Sharma M, Predeus AV, Mukherjee S, Feig M. DNA bending propensity in the presence of base mismatches: implications for DNA repair. J Phys Chem B 2013; 117:6194-205. [PMID: 23621762 DOI: 10.1021/jp403127a] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA bending is believed to facilitate the initial recognition of the mismatched base for repair. The repair efficiencies are dependent on both the mismatch type and neighboring nucleotide sequence. We have studied bending of several DNA duplexes containing canonical matches: A:T and G:C; various mismatches: A:A, A:C, G:A, G:G, G:T, C:C, C:T, and T:T; and a bis-abasic site: X:X. Free-energy profiles were generated for DNA bending using umbrella sampling. The highest energetic cost associated with DNA bending is observed for canonical matches while bending free energies are lower in the presence of mismatches, with the lowest value for the abasic site. In all of the sequences, DNA duplexes bend toward the major groove with widening of the minor groove. For homoduplexes, DNA bending is observed to occur via smooth deformations, whereas for heteroduplexes, kinks are observed at the mismatch site during strong bending. In general, pyrimidine:pyrimidine mismatches are the most destabilizing, while purine:purine mismatches lead to intermediate destabilization, and purine:pyrimidine mismatches are the least destabilizing. The ease of bending is partially correlated with the binding affinity of MutS to the mismatch pairs and subsequent repair efficiencies, indicating that intrinsic DNA bending propensities are a key factor of mismatch recognition.
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Affiliation(s)
- Monika Sharma
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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Vafabakhsh R, Ha T. Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization. Science 2012; 337:1097-101. [PMID: 22936778 PMCID: PMC3565842 DOI: 10.1126/science.1224139] [Citation(s) in RCA: 223] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The classical view of DNA posits that DNA must be stiff below the persistence length [<150 base pairs (bp)], but recent studies addressing this have yielded contradictory results. We developed a fluorescence-based, protein-free assay for studying the cyclization of single DNA molecules in real time. The assay samples the equilibrium population of a sharply bent, transient species that is entirely suppressed in single-molecule mechanical measurements and is biologically more relevant than the annealed species sampled in the traditional ligase-based assay. The looping rate has a weak length dependence between 67 and 106 bp that cannot be described by the worm-like chain model. Many biologically important protein-DNA interactions that involve looping and bending of DNA below 100 bp likely use this intrinsic bendability of DNA.
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Affiliation(s)
- Reza Vafabakhsh
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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