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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 101201152.

In-vitro validated methods for encoding digital data in deoxyribonucleic acid (DNA)

Golam Md Mortuza, Jorge Guerrero, Shoshanna Llewellyn, Michael D. Tobiason, George D. Dickinson, William L. Hughes, Reza Zadegan, Tim Andersen

BMC Bioinformatics. 2023; 24: 160. Published online 2023 Apr 21. doi: 10.1186/s12859-023-05264-6

PMCID:: PMC10120115

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Select item 87890633.

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 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 82501865.

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 69804246.

RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment

Amir H. Bayegan, Peter Clote

PLoS One. 2020; 15(1): e0227177. Published online 2020 Jan 24. doi: 10.1371/journal.pone.0227177

PMCID:: PMC6980424

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Select item 107284167.

Reverse transcription loop-mediated isothermal amplification (RT-LAMP) primer design based on Indonesia SARS-CoV-2 RNA sequence

Irsyad Ibadurrahman, Suryani, Desriani

J Genet Eng Biotechnol. 2023 Dec; 21: 168. Published online 2023 Dec 18. doi: 10.1186/s43141-023-00580-z

PMCID:: PMC10728416

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Select item 91469018.

Revisiting DNA Sequence-Dependent Deformability in High-Resolution Structures: Effects of Flanking Base Pairs on Dinucleotide Morphology and Global Chain Configuration

Robert T. Young, Luke Czapla, Zoe O. Wefers, Benjamin M. Cohen, Wilma K. Olson

Life (Basel) 2022 May; 12(5): 759. Published online 2022 May 20. doi: 10.3390/life12050759

PMCID:: PMC9146901

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Select item 75842509.

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

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Select item 843909810.

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

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Select item 738497511.

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 455191812.

Identifying novel sequence variants of RNA 3D motifs

Craig L. Zirbel, James Roll, Blake A. Sweeney, Anton I. Petrov, Meg Pirrung, Neocles B. Leontis

Nucleic Acids Res. 2015 Sep 3; 43(15): 7504–7520. Published online 2015 Jun 29. doi: 10.1093/nar/gkv651

PMCID:: PMC4551918

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Select item 1040196513.

Molecular insight into how the position of an abasic site and its sequence environment influence DNA duplex stability and dynamics

Brennan Ashwood, Michael S. Jones, Yumin Lee, Joseph R. Sachleben, Andrew L. Ferguson, Andrei Tokmakoff

Version 1. bioRxiv. Preprint. 2023 Jul 25. doi: 10.1101/2023.07.22.550182

Published in:: Biophys J. 2024 Jan 16; 123(2): 118–133.

PMCID:: PMC10401965

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Select item 644263214.

Interplay between DNA sequence and negative superhelicity drives R-loop structures

Robert Stolz, Shaheen Sulthana, Stella R. Hartono, Maika Malig, Craig J. Benham, Frederic Chedin

Proc Natl Acad Sci U S A. 2019 Mar 26; 116(13): 6260–6269. Published online 2019 Mar 8. doi: 10.1073/pnas.1819476116

PMCID:: PMC6442632

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Select item 996939415.

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 1051006516.

DBTRG: De Bruijn Trim rotation graph encoding for reliable DNA storage

Yunzhu Zhao, Ben Cao, Penghao Wang, Kun Wang, Bin Wang

Comput Struct Biotechnol J. 2023; 21: 4469–4477. Published online 2023 Sep 11. doi: 10.1016/j.csbj.2023.09.004

PMCID:: PMC10510065

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Select item 530078217.

Contributions of Sequence to the Higher-Order Structures of DNA

Stefjord Todolli, Pamela J. Perez, Nicolas Clauvelin, Wilma K. Olson

Biophys J. 2017 Feb 7; 112(3): 416–426. Published online 2016 Dec 9. doi: 10.1016/j.bpj.2016.11.017

PMCID:: PMC5300782

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Select item 864840218.

Fungal diversity notes 1387–1511: taxonomic and phylogenetic contributions on genera and species of fungal taxa

Saranyaphat Boonmee, Dhanushka N. Wanasinghe, Mark S. Calabon, Naruemon Huanraluek, Sajini K. U. Chandrasiri, Gareth E. B. Jones, Walter Rossi, Marco Leonardi, Sanjay K. Singh, Shiwali Rana, Paras N. Singh, Deepak K. Maurya, Ajay C. Lagashetti, Deepika Choudhary, Yu-Cheng Dai, Chang-Lin Zhao, Yan-Hong Mu, Hai-Sheng Yuan, Shuang-Hui He, Rungtiwa Phookamsak, Hong-Bo Jiang, María P. Martín, Margarita Dueñas, M. Teresa Telleria, Izabela L. Kałucka, Andrzej M. Jagodziński, Kare Liimatainen, Diana S. Pereira, Alan J. L. Phillips, Nakarin Suwannarach, Jaturong Kumla, Surapong Khuna, Saisamorn Lumyong, Tarynn B. Potter, Roger G. Shivas, Adam H. Sparks, Niloofar Vaghefi, Mohamed A. Abdel-Wahab, Faten A. Abdel-Aziz, Guo-Jie Li, Wen-Fei Lin, Upendra Singh, Rajendra P. Bhatt, Hyang Burm Lee, Thuong T. T. Nguyen, Paul M. Kirk, Arun Kumar Dutta, Krishnendu Acharya, V. Venkateswara Sarma, M. Niranjan, Kunhiraman C. Rajeshkumar, Nikhil Ashtekar, Sneha Lad, Nalin N. Wijayawardene, Darbe J. Bhat, Rong-Ju Xu, Subodini N. Wijesinghe, Hong-Wei Shen, Zong-Long Luo, Jing-Yi Zhang, Phongeun Sysouphanthong, Naritsada Thongklang, Dan-Feng Bao, Janith V. S. Aluthmuhandiram, Jafar Abdollahzadeh, Alireza Javadi, Francesco Dovana, Muhammad Usman, Abdul Nasir Khalid, Asha J. Dissanayake, Anusha Telagathoti, Maraike Probst, Ursula Peintner, Isaac Garrido-Benavent, Lilla Bóna, Zsolt Merényi, Lajos Boros, Bratek Zoltán, J. Benjamin Stielow, Ning Jiang, Cheng-Ming Tian, Esmaeil Shams, Farzaneh Dehghanizadeh, Adel Pordel, Mohammad Javan-Nikkhah, Teodor T. Denchev, Cvetomir M. Denchev, Martin Kemler, Dominik Begerow, Chun-Ying Deng, Emma Harrower, Tohir Bozorov, Tutigul Kholmuradova, Yusufjon Gafforov, Aziz Abdurazakov, Jian-Chu Xu, Peter E. Mortimer, Guang-Cong Ren, Rajesh Jeewon, Sajeewa S. N. Maharachchikumbura, Chayanard Phukhamsakda, Ausana Mapook, Kevin D. Hyde

Fungal Divers. 2021; 111(1): 1–335. Published online 2021 Dec 7. doi: 10.1007/s13225-021-00489-3

PMCID:: PMC8648402

Article PDF–139M

Select item 268023019.

Differential Nucleotide Excision Repair Susceptibility of Bulky DNA Adducts in Different Sequence Contexts: Hierarchies of Recognition Signals

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

J Mol Biol. Author manuscript; available in PMC 2009 May 11.

Published in final edited form as: J Mol Biol. 2009 Jan 9; 385(1): 30–44. Published online 2008 Oct 11. doi: 10.1016/j.jmb.2008.09.087

PMCID:: PMC2680230

Article PDF–3.9M

Select item 462708120.

Base damage, local sequence context and TP53 mutation hotspots: a molecular dynamics study of benzo[a]pyrene induced DNA distortion and mutability

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

Nucleic Acids Res. 2015 Oct 30; 43(19): 9133–9146. Published online 2015 Sep 22. doi: 10.1093/nar/gkv910

PMCID:: PMC4627081

Article PDF–439K

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