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Select item 34792141.

Nucleotide excision repair of 2-acetylaminofluorene- and 2-aminofluorene-(C8)-guanine adducts: molecular dynamics simulations elucidate how lesion structure and base sequence context impact repair efficiencies

Hong Mu, Konstantin Kropachev, Lihua Wang, Lu Zhang, Alexander Kolbanovskiy, Marina Kolbanovskiy, Nicholas E. Geacintov, Suse Broyde

Nucleic Acids Res. 2012 Oct; 40(19): 9675–9690. Published online 2012 Aug 13. doi: 10.1093/nar/gks788

PMCID:: PMC3479214

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Select item 87890632.

Computational investigation of the impact of core sequence on immobile DNA four-way junction structure and dynamics

Matthew R Adendorff, Guo Qing Tang, David P Millar, Mark Bathe, William P Bricker

Nucleic Acids Res. 2022 Jan 25; 50(2): 717–730. Published online 2021 Dec 22. doi: 10.1093/nar/gkab1246

PMCID:: PMC8789063

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Select item 29230963.

Distant neighbor base sequence context effects in human nucleotide excision repair of a benzo[a]pyrene-derived DNA lesion

Yuqin Cai, Konstantin Kropachev, Rong Xu, Yijin Tang, Marina Kolbanovskii, Alexander Kolbanovskii, Shantu Amin, Dinshaw J. Patel, Suse Broyde, Nicholas E. Geacintov

J Mol Biol. Author manuscript; available in PMC 2011 Jun 11.

Published in final edited form as: J Mol Biol. 2010 Jun 11; 399(3): 397–409. Published online 2010 Apr 22. doi: 10.1016/j.jmb.2010.04.004

PMCID:: PMC2923096

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Select item 102125714.

Statistical inference reveals the role of length, GC content, and local sequence in V(D)J nucleotide trimming

Magdalena L Russell, Noah Simon, Philip Bradley, Frederick A Matsen, IV

eLife. 2023; 12: e85145. Published online 2023 May 25. doi: 10.7554/eLife.85145

PMCID:: PMC10212571

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Select item 99693945.

Sequence-Dependent Melting and Refolding Dynamics of RNA UNCG Tetraloops Using Temperature-Jump/Drop Infrared Spectroscopy

C. P. Howe, G. M. Greetham, B. Procacci, A. W. Parker, N. T. Hunt

J Phys Chem B. 2023 Feb 23; 127(7): 1586–1597. Published online 2023 Feb 14. doi: 10.1021/acs.jpcb.2c08709

PMCID:: PMC9969394

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Select item 73816446.

DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation

Sabrina Adam, Hiwot Anteneh, Maximilian Hornisch, Vincent Wagner, Jiuwei Lu, Nicole E. Radde, Pavel Bashtrykov, Jikui Song, Albert Jeltsch

Nat Commun. 2020; 11: 3723. Published online 2020 Jul 24. doi: 10.1038/s41467-020-17531-8

PMCID:: PMC7381644

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Select item 82501867.

Evolutionary conservation of RNA sequence and structure

Elena Rivas

Wiley Interdiscip Rev RNA. 2021 Sep-Oct; 12(5): e1649. Published online 2021 Mar 22. doi: 10.1002/wrna.1649

PMCID:: PMC8250186

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Select item 84390988.

Carcinogen-induced DNA structural distortion differences in the RAS gene isoforms; the importance of local sequence

Georgina E. Menzies, Ian A. Prior, Andrea Brancale, Simon H. Reed, Paul D. Lewis

BMC Chem. 2021 Dec; 15(1): 51. Published online 2021 Sep 14. doi: 10.1186/s13065-021-00777-8

PMCID:: PMC8439098

Article PDF–1.7M

Select item 29431119.

Base Sequence Context Effects on Nucleotide Excision Repair

Yuqin Cai, Dinshaw J. Patel, Suse Broyde, Nicholas E. Geacintov

J Nucleic Acids. 2010; 2010: 174252. Published online 2010 Aug 23. doi: 10.4061/2010/174252

PMCID:: PMC2943111

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Select item 858691010.

Translesion synthesis past 5-formylcytosine mediated DNA-peptide crosslinks by hPolη is dependent on the local DNA sequence

Jenna Thomforde, Iwen Fu, Freddys Rodriguez, Suresh S. Pujari, Suse Broyde, Natalia Tretyakova

Biochemistry. Author manuscript; available in PMC 2022 Jun 15.

Published in final edited form as: Biochemistry. 2021 Jun 15; 60(23): 1797–1807. Published online 2021 Jun 3. doi: 10.1021/acs.biochem.1c00130

PMCID:: PMC8586910

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Select item 443897311.

Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA

Christopher A. Lavender, Ronny Lorenz, Ge Zhang, Rita Tamayo, Ivo L. Hofacker, Kevin M. Weeks

PLoS Comput Biol. 2015 May; 11(5): e1004126. Published online 2015 May 20. doi: 10.1371/journal.pcbi.1004126

PMCID:: PMC4438973

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Select item 758425012.

New insights into the existing image encryption algorithms based on DNA coding

Xianglian Xue, Dongsheng Zhou, Changjun Zhou

PLoS One. 2020; 15(10): e0241184. Published online 2020 Oct 23. doi: 10.1371/journal.pone.0241184

PMCID:: PMC7584250

Article PDF–4.4M

Select item 280021513.

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

Richard Lavery, Krystyna Zakrzewska, David Beveridge, Thomas C. Bishop, David A. Case, Thomas Cheatham, III, Surjit Dixit, B. Jayaram, Filip Lankas, Charles Laughton, John H. Maddocks, Alexis Michon, Roman Osman, Modesto Orozco, Alberto Perez, Tanya Singh, Nada Spackova, Jiri Sponer

Nucleic Acids Res. 2010 Jan; 38(1): 299–313. Published online 2009 Oct 22. doi: 10.1093/nar/gkp834

PMCID:: PMC2800215

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Select item 738497514.

Determinants of Base Editing Outcomes from Target Library Analysis and Machine Learning

Mandana Arbab, Max W. Shen, Beverly Mok, Christopher Wilson, Żaneta Matuszek, Christopher A. Cassa, David R. Liu

Cell. Author manuscript; available in PMC 2021 Jul 23.

Published in final edited form as: Cell. 2020 Jul 23; 182(2): 463–480.e30. Published online 2020 Jun 12. doi: 10.1016/j.cell.2020.05.037

PMCID:: PMC7384975

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Select item 592094415.

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

Jiří Šponer, Giovanni Bussi, Miroslav Krepl, Pavel Banáš, Sandro Bottaro, Richard A. Cunha, Alejandro Gil-Ley, Giovanni Pinamonti, Simón Poblete, Petr Jurečka, Nils G. Walter, Michal Otyepka

Chem Rev. 2018 Apr 25; 118(8): 4177–4338. Published online 2018 Jan 3. doi: 10.1021/acs.chemrev.7b00427