1
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Orndorff PB, van der Vaart A. Systematic assessment of the flexibility of uracil damaged DNA. J Biomol Struct Dyn 2024; 42:3958-3968. [PMID: 37261803 DOI: 10.1080/07391102.2023.2217683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023]
Abstract
Uracil is a common DNA lesion which is recognized and removed by uracil DNA-glycosylase (UDG) as a part of the base excision repair pathway. Excision proceeds by base flipping, and UDG efficiency is thought to depend on the ease of deformability of the bases neighboring the lesion. We used molecular dynamics simulations to assess the flexibility of a large library of dsDNA strands, containing all tetranucleotide motifs with U:A, U:G, T:A or C:G base pairs. Our study demonstrates that uracil damaged DNA largely follows trends in flexibility of undamaged DNA. Measured bending persistence lengths, groove widths, step parameters and base flipping propensities demonstrate that uracil increases the flexibility of DNA, and that U:G base paired strands are more flexible than U:A strands. Certain sequence contexts are more deformable than others, with a key role for the 3' base next to uracil. Flexibilities are large when this base is an A or G, and repressed for a C or T. A 5' T adjacent to the uracil strongly promotes flexibility, but other 5' bases are less influential. DNA bending is correlated to step deformations and base flipping, and bending aids flipping. Our study implies that the link between substrate flexibility and UDG efficiency is widely valid, helps explain why UDG prefers to bind U:G base paired strands, and suggests that the DNA bending angle of the UDG-substrate complex is optimal for base flipping.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Paul B Orndorff
- Department of Chemistry, University of South Florida, Tampa, Florida, USA
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2
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Orndorff PB, van der Vaart A. Register-Shifted Structures in Base-Flipped Uracil-Damaged DNA. J Am Chem Soc 2023. [PMID: 37478299 DOI: 10.1021/jacs.3c05890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
We report the occurrence of register-shifted structures in simulations of uracil-containing dsDNA. These occur when the 3' base vicinal to uracil is thymine in U:A base-paired DNA. Upon base flipping of uracil, this 3' thymine hydrogen bonds with the adenine across the uracil instead of its complementary base. The register-shifted structure is persistent and sterically blocks re-entry of uracil into the helix stack. Register shifting might be important for DNA repair since the longer exposure of the lesion in register-shifted structures could facilitate enzymatic recognition and repair.
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Affiliation(s)
- Paul B Orndorff
- 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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3
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Orndorff PB, Poddar S, Owens AM, Kumari N, Ugaz BT, Amin S, Van Horn WD, van der Vaart A, Levitus M. Uracil-DNA glycosylase efficiency is modulated by substrate rigidity. Sci Rep 2023; 13:3915. [PMID: 36890276 PMCID: PMC9995336 DOI: 10.1038/s41598-023-30620-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/27/2023] [Indexed: 03/10/2023] Open
Abstract
Uracil DNA-glycosylase (UNG) is a DNA repair enzyme that removes the highly mutagenic uracil lesion from DNA using a base flipping mechanism. Although this enzyme has evolved to remove uracil from diverse sequence contexts, UNG excision efficiency depends on DNA sequence. To provide the molecular basis for rationalizing UNG substrate preferences, we used time-resolved fluorescence spectroscopy, NMR imino proton exchange measurements, and molecular dynamics simulations to measure UNG specificity constants (kcat/KM) and DNA flexibilities for DNA substrates containing central AUT, TUA, AUA, and TUT motifs. Our study shows that UNG efficiency is dictated by the intrinsic deformability around the lesion, establishes a direct relationship between substrate flexibility modes and UNG efficiency, and shows that bases immediately adjacent to the uracil are allosterically coupled and have the greatest impact on substrate flexibility and UNG activity. The finding that substrate flexibility controls UNG efficiency is likely significant for other repair enzymes and has major implications for the understanding of mutation hotspot genesis, molecular evolution, and base editing.
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Affiliation(s)
- Paul B Orndorff
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA
| | - Souvik Poddar
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Institute Center for Single Molecule Biophysics, Arizona State University, Tempe, AZ, 85287, USA
| | - Aerial M Owens
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Institute Virginia G. Piper Center for Personalized Diagnostics, Arizona State University, Tempe, AZ, 85287, USA
| | - Nikita Kumari
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Institute Center for Single Molecule Biophysics, Arizona State University, Tempe, AZ, 85287, USA
| | - Bryan T Ugaz
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Institute Center for Single Molecule Biophysics, Arizona State University, Tempe, AZ, 85287, USA
| | - Samrat Amin
- Magnetic Resonance Research Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Wade D Van Horn
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
- The Biodesign Institute Virginia G. Piper Center for Personalized Diagnostics, Arizona State University, Tempe, AZ, 85287, USA.
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA.
| | - Marcia Levitus
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
- The Biodesign Institute Center for Single Molecule Biophysics, Arizona State University, Tempe, AZ, 85287, USA.
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4
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Wang SD, Zhang RB, Eriksson LA. Markov state models elucidate the stability of DNA influenced by the chiral 5S-Tg base. Nucleic Acids Res 2022; 50:9072-9082. [PMID: 35979954 PMCID: PMC9458442 DOI: 10.1093/nar/gkac691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/15/2022] [Accepted: 07/30/2022] [Indexed: 12/24/2022] Open
Abstract
The static and dynamic structures of DNA duplexes affected by 5S-Tg (Tg, Thymine glycol) epimers were studied using MD simulations and Markov State Models (MSMs) analysis. The results show that the 5S,6S-Tg base caused little perturbation to the helix, and the base-flipping barrier was determined to be 4.4 kcal mol-1 through the use of enhanced sampling meta-eABF calculations, comparable to 5.4 kcal mol-1 of the corresponding thymine flipping. Two conformations with the different hydrogen bond structures between 5S,6R-Tg and A19 were identified in several independent MD trajectories. The 5S,6R-Tg:O6HO6•••N1:A19 hydrogen bond is present in the high-energy conformation displaying a clear helical distortion, and near barrier-free Tg base flipping. The low-energy conformation always maintains Watson-Crick base pairing between 5S,6R-Tg and A19, and 5S-Tg base flipping is accompanied by a small barrier of ca. 2.0 KBT (T = 298 K). The same conformations are observed in the MSMs analysis. Moreover, the transition path and metastable structures of the damaged base flipping are for the first time verified through MSMs analysis. The data clearly show that the epimers have completely different influence on the stability of the DNA duplex, thus implying different enzymatic mechanisms for DNA repair.
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Affiliation(s)
- Shu-dong Wang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, South Street No. 5, Zhongguancun, Haidan District, 100081 Beijing, China
| | - Ru-bo Zhang
- Correspondence may also be addressed to Ru-bo Zhang.
| | - Leif A Eriksson
- To whom correspondence should be addressed. Tel: +46 31 786 9117;
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5
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Nicy, Chakraborty D, Wales DJ. Energy Landscapes for Base-Flipping in a Model DNA Duplex. J Phys Chem B 2022; 126:3012-3028. [PMID: 35427136 PMCID: PMC9098180 DOI: 10.1021/acs.jpcb.2c00340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/24/2022] [Indexed: 12/31/2022]
Abstract
We explore the process of base-flipping for four central bases, adenine, guanine, cytosine, and thymine, in a deoxyribonucleic acid (DNA) duplex using the energy landscape perspective. NMR imino-proton exchange and fluorescence correlation spectroscopy studies have been used in previous experiments to obtain lifetimes for bases in paired and extrahelical states. However, the difference of almost 4 orders of magnitude in the base-flipping rates obtained by the two methods implies that they are exploring different pathways and possibly different open states. Our results support the previous suggestion that minor groove opening may be favored by distortions in the DNA backbone and reveal links between sequence effects and the direction of opening, i.e., whether the base flips toward the major or the minor groove side. In particular, base flipping along the minor groove pathway was found to align toward the 5' side of the backbone. We find that bases align toward the 3' side of the backbone when flipping along the major groove pathway. However, in some cases for cytosine and thymine, the base flipping along the major groove pathway also aligns toward the 5' side. The sequence effect may be caused by the polar interactions between the flipping-base and its neighboring bases on either of the strands. For guanine flipping toward the minor groove side, we find that the equilibrium constant for opening is large compared to flipping via the major groove. We find that the estimated rates of base opening, and hence the lifetimes of the closed state, obtained for thymine flipping through small and large angles along the major groove differ by 6 orders of magnitude, whereas for thymine flipping through small angles along the minor groove and large angles along the major groove, the rates differ by 3 orders of magnitude.
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Affiliation(s)
- Nicy
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K.
| | - Debayan Chakraborty
- Department
of Chemistry, The University of Texas at
Austin, Austin, Texas 78712, United States
| | - David J. Wales
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K.
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6
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Wang SD, Eriksson LA, Zhang RB. Dynamics of 5R-Tg Base Flipping in DNA Duplexes Based on Simulations─Agreement with Experiments and Beyond. J Chem Inf Model 2022; 62:386-398. [PMID: 34994562 PMCID: PMC8790752 DOI: 10.1021/acs.jcim.1c01169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Damaged or mismatched
DNA bases are normally thought to be able
to flip out of the helical stack, providing enzymes with access to
the faulty genetic information otherwise hidden inside the helix.
Thymine glycol (Tg) is one of the most common products of nucleic
acid damage. However, the static and dynamic structures of DNA duplexes
affected by 5R-Tg epimers are still not clearly understood, including
the ability of these to undergo spontaneous base flipping. Structural
effects of the 5R-Tg epimers on the duplex DNA are herein studied
using molecular dynamics together with reliable DFT based calculations.
In comparison with the corresponding intact DNA, the cis-5R,6S-Tg epimer base causes little perturbation to the duplex DNA,
and a barrier of 4.9 kcal mol–1 is obtained by meta-eABF
for cis-5R,6S-Tg base flipping out of the duplex
DNA, comparable to the 5.4 kcal mol–1 obtained for
the corresponding thymine flipping in intact DNA. For the trans-5R,6R-Tg epimer, three stable local structures were
identified, of which the most stable disrupts the Watson–Crick
hydrogen-bonded G5/C20 base pair, leading to conformational distortion
of the duplex. Interestingly, the relative barrier height of the 5R-Tg
flipping is only 1.0 kcal mol–1 for one of these trans-5R,6R-Tg epimers. Water bridge interactions were identified
to be essential for 5R-Tg flipping. The study clearly demonstrates
the occurrence of partial trans-5R,6R-Tg epimer flipping
in solution.
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Affiliation(s)
- Shu Dong Wang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, South Street no 5, Zhongguancun, Haidian District, 100081 Beijing, China
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9c, 405 30 Göteborg, Sweden
| | - Ru Bo Zhang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, South Street no 5, Zhongguancun, Haidian District, 100081 Beijing, China
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7
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Ray D, Stone SE, Andricioaei I. Markovian Weighted Ensemble Milestoning (M-WEM): Long-Time Kinetics from Short Trajectories. J Chem Theory Comput 2021; 18:79-95. [PMID: 34910499 DOI: 10.1021/acs.jctc.1c00803] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We introduce a rare-event sampling scheme, named Markovian Weighted Ensemble Milestoning (M-WEM), which inlays a weighted ensemble framework within a Markovian milestoning theory to efficiently calculate thermodynamic and kinetic properties of long-time-scale biomolecular processes from short atomistic molecular dynamics simulations. M-WEM is tested on the Müller-Brown potential model, the conformational switching in alanine dipeptide, and the millisecond time-scale protein-ligand unbinding in a trypsin-benzamidine complex. Not only can M-WEM predict the kinetics of these processes with quantitative accuracy but it also allows for a scheme to reconstruct a multidimensional free-energy landscape along additional degrees of freedom, which are not part of the milestoning progress coordinate. For the ligand-receptor system, the experimental residence time, association and dissociation kinetics, and binding free energy could be reproduced using M-WEM within a simulation time of a few hundreds of nanoseconds, which is a fraction of the computational cost of other currently available methods, and close to 4 orders of magnitude less than the experimental residence time. Due to the high accuracy and low computational cost, the M-WEM approach can find potential applications in kinetics and free-energy-based computational drug design.
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Affiliation(s)
- Dhiman Ray
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Sharon Emily Stone
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Ioan Andricioaei
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States.,Department of Physics and Astronomy, University of California Irvine, Irvine, California 92697, United States
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8
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Yamada D, Yamamoto J, Getzoff ED, Iwata T, Kandori H. Structural Changes during the Photorepair and Binding Processes of Xenopus (6-4) Photolyase with (6-4) Photoproducts in Single- and Double-Stranded DNA. Biochemistry 2021; 60:3253-3261. [PMID: 34658241 DOI: 10.1021/acs.biochem.1c00413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photolyases (PHRs) repair ultraviolet (UV)-induced DNA photoproducts into normal bases. In this study, we measured the conformational changes upon photoactivation and photorepair processes of a PHR and its specific substrates, (6-4)PHR and a pyrimidine(6-4)pyrimidone photoproduct ((6-4)PP), by light-induced difference Fourier transform infrared (FT-IR) spectroscopy. The single-stranded DNA with (6-4)PP (ss(6-4)PP) was used as a substrate and the resultant FT-IR spectra were compared with the previous results on double-stranded DNA with (6-4)PP (ds(6-4)PP). In the excess amount of substrate to the enzyme, different ss(6-4)PP photorepair FT-IR signals were obtained in an illumination time-dependent manner. As reported for ds(6-4)PP, the early stages of the photoreaction involve the changes in the ss(6-4)PP only, while the late stages of the reaction involve the ss(6-4)PP repair-associated changes and dissociation from (6-4)PHR. From these spectra, difference spectra originating from the binding/dissociation spectrum were extracted. The signals of the C═O stretches of (6-4)PP and repaired thymines in the single- and double-stranded DNA were tentatively assigned. The C═O stretches of (6-4)PP were observed at frequencies that reflect single- and double-stranded DNA environments in aqueous solution, reflecting the different hydrogen-bonding environments. The conformational changes of PHR upon binding of ss(6-4)PP and ds(6-4)PP were similar, suggesting that the conformational change is limited to the (6-4)PP binding pocket region. We interpreted that ds(6-4)PP may be bound together without any special mechanism for flipping out.
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Affiliation(s)
- Daichi Yamada
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.,Graduate School of Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Elizabeth D Getzoff
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States.,Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Tatsuya Iwata
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.,Faculty of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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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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Gillet N, Bartocci A, Dumont E. Assessing the sequence dependence of pyrimidine-pyrimidone (6-4) photoproduct in a duplex double-stranded DNA: A pitfall for microsecond range simulation. J Chem Phys 2021; 154:135103. [PMID: 33832258 DOI: 10.1063/5.0041332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Sequence dependence of the (6-4) photoproduct conformational landscape when embedded in six 25-bp duplexes is evaluated along extensive unbiased and enhanced (replica exchange with solute tempering, REST2) molecular dynamics simulations. The structural reorganization as the central pyrimidines become covalently tethered is traced back in terms of non-covalent interactions, DNA bending, and extrusion of adenines of the opposite strands. The close sequence pattern impacts the conformational landscape around the lesion, inducing different upstream and downstream flexibilities. Moreover, REST2 simulations allow us to probe structures possibly important for damaged DNA recognition.
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Affiliation(s)
- Natacha Gillet
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, F69364 Lyon, France
| | - Alessio Bartocci
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, F69364 Lyon, France
| | - Elise Dumont
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, F69364 Lyon, France
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11
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Mondal M, Yang L, Cai Z, Patra P, Gao YQ. A perspective on the molecular simulation of DNA from structural and functional aspects. Chem Sci 2021; 12:5390-5409. [PMID: 34168783 PMCID: PMC8179617 DOI: 10.1039/d0sc05329e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
As genetic material, DNA not only carries genetic information by sequence, but also affects biological functions ranging from base modification to replication, transcription and gene regulation through its structural and dynamic properties and variations. The motion and structural properties of DNA involved in related biological processes are also multi-scale, ranging from single base flipping to local DNA deformation, TF binding, G-quadruplex and i-motif formation, TAD establishment, compartmentalization and even chromosome territory formation, just to name a few. The sequence-dependent physical properties of DNA play vital role in all these events, and thus it is interesting to examine how simple sequence information affects DNA and the formation of the chromatin structure in these different hierarchical orders. Accordingly, molecular simulations can provide atomistic details of interactions and conformational dynamics involved in different biological processes of DNA, including those inaccessible by current experimental methods. In this perspective, which is mainly based on our recent studies, we provide a brief overview of the atomistic simulations on how the hierarchical structure and dynamics of DNA can be influenced by its sequences, base modifications, environmental factors and protein binding in the context of the protein-DNA interactions, gene regulation and structural organization of chromatin. We try to connect the DNA sequence, the hierarchical structures of DNA and gene regulation.
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Affiliation(s)
- Manas Mondal
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory 518055 Shenzhen China
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China
| | - Zhicheng Cai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China.,Biomedical Pioneering Innovation Center, Peking University 100871 Beijing China
| | - Piya Patra
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory 518055 Shenzhen China .,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China
| | - Yi Qin Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory 518055 Shenzhen China .,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China.,Biomedical Pioneering Innovation Center, Peking University 100871 Beijing China.,Beijing Advanced Innovation Center for Genomics, Peking University 100871 Beijing China
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12
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Ray D, Andricioaei I. Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA. Biophys J 2020; 119:1568-1579. [PMID: 32946766 DOI: 10.1016/j.bpj.2020.08.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 05/10/2020] [Accepted: 08/25/2020] [Indexed: 10/23/2022] Open
Abstract
Genetic information is encoded in the DNA double helix, which, in its physiological milieu, is characterized by the iconical Watson-Crick nucleo-base pairing. Recent NMR relaxation experiments revealed the transient presence of an alternative, Hoogsteen (HG) base pairing pattern in naked DNA duplexes, and estimated its relative stability and lifetime. In contrast with DNA, such structures were not observed in RNA duplexes. Understanding HG base pairing is important because the underlying "breathing" motion between the two conformations can significantly modulate protein binding. However, a detailed mechanistic insight into the transition pathways and kinetics is still missing. We performed enhanced sampling simulation (with combined metadynamics and adaptive force-bias method) and Markov state modeling to obtain accurate free energy, kinetics, and the intermediates in the transition pathway between Watson-Crick and HG base pairs for both naked B-DNA and A-RNA duplexes. The Markov state model constructed from our unbiased MD simulation data revealed previously unknown complex extrahelical intermediates in the seemingly simple process of base flipping in B-DNA. Extending our calculation to A-RNA, for which HG base pairing is not observed experimentally, resulted in relatively unstable, single-hydrogen-bonded, distorted Hoogsteen-like bases. Unlike B-DNA, the transition pathway primarily involved base paired and intrahelical intermediates with transition timescales much longer than that of B-DNA. The seemingly obvious flip-over reaction coordinate (i.e., the glycosidic torsion angle) is unable to resolve the intermediates. Instead, a multidimensional picture involving backbone dihedral angles and distance between hydrogen bond donor and acceptor atoms is required to gain insight into the molecular mechanism.
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Affiliation(s)
| | - Ioan Andricioaei
- Department of Chemistry; Department of Physics and Astronomy, University of California Irvine, Irvine, California.
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13
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Wang X, Sun Z. Determination of Base-Flipping Free-Energy Landscapes from Nonequilibrium Stratification. J Chem Inf Model 2019; 59:2980-2994. [PMID: 31124677 DOI: 10.1021/acs.jcim.9b00263] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Correct calculation of the variation of free energy upon base flipping is crucial in understanding the dynamics of DNA systems. The free-energy landscape along the flipping pathway gives the thermodynamic stability and the flexibility of base-paired states. Although numerous free-energy simulations are performed in the base flipping cases, no theoretically rigorous nonequilibrium techniques are devised and employed to investigate the thermodynamics of base flipping. In the current work, we report a general nonequilibrium stratification scheme for the efficient calculation of the free-energy landscape of base flipping in DNA duplex. We carefully monitor the convergence behavior of the equilibrium sampling based free-energy simulation and the nonequilibrium stratification and determine the empirical length of time blocks required for converged sampling. Comparison between the performances of the equilibrium umbrella sampling and the nonequilibrium stratification is given. The results show that nonequilibrium free-energy simulation achieves similar accuracy and efficiency compared with the equilibrium enhanced sampling technique in the base flipping cases. We further test a convergence criterion we previously proposed and it comes out that the convergence determined by this criterion agrees with those given by the time-invariant behavior of PMF and the nonlinear dependence of standard deviation on the sample size.
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Affiliation(s)
- Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , China.,Institute of Computational Science , Università della Svizzera Italiana (USI) , Via Giuseppe Buffi 13 , CH-6900 , Lugano , Ticino , Switzerland
| | - Zhaoxi Sun
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , China.,Computational Biomedicine (IAS-5/INM-9) , Forschungszentrum Jülich , Jülich 52425 , Germany
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Kanaan N, Imhof P. Interactions of the DNA Repair Enzyme Human Thymine DNA Glycosylase with Cognate and Noncognate DNA. Biochemistry 2018; 57:5654-5665. [PMID: 30067350 DOI: 10.1021/acs.biochem.8b00409] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glycosylases specifically recognize and flip their target base out of the DNA helix into the enzyme's active site. Our simulations show that a partially flipped state, already present in free DNA carrying a T:G mispair, becomes the more probable state compared to the closed state after binding of thymine DNA glycosylase (TDG). Paired thymine (T:A) or methyl-cytosine (mC:G) does not exhibit a partially flipped state in free or complexed DNA. Important enzyme-DNA interactions exhibit significant strength in the intrahelical and extrahelical TDG-DNA complexes. The computed binding free energy differences suggest these interactions account for the stabilization of the partially flipped state, thereby driving the T:G mispair toward base flip. In the fully flipped state, the cognate base thymine is significantly better accommodated in the enzyme's active site than noncognate bases are, suggesting the hydrolysis step as the last of several stages at which base recognition can be achieved.
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Affiliation(s)
- Natalia Kanaan
- Institute of Theoretical Physics , Freie Universität Berlin , Arnimallee 14 , D-14195 Berlin , Germany
| | - Petra Imhof
- Institute of Theoretical Physics , Freie Universität Berlin , Arnimallee 14 , D-14195 Berlin , Germany
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Hardwick JS, Lane AN, Brown T. Epigenetic Modifications of Cytosine: Biophysical Properties, Regulation, and Function in Mammalian DNA. Bioessays 2018; 40. [DOI: 10.1002/bies.201700199] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/13/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Jack S. Hardwick
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Andrew N. Lane
- Department of Toxicology and Cancer Biology; University of Kentucky; 789 S. Limestone St. Lexington KY 40536 USA
| | - Tom Brown
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
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