My Bibliography

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Acharya N, Prakash L, Prakash S. Yeast 9-1-1 complex acts as a sliding clamp for DNA synthesis by DNA polymerase ε. J Biol Chem. 2023 Jan;299(1):102727. doi: 10.1016/j.jbc.2022.102727. Epub 2022 Nov 19. PubMed PMID: 36410434; PubMed Central PMCID: PMC9791402.

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Malik R, Johnson RE, Prakash L, Prakash S, Ubarretxena-Belandia I, Aggarwal AK. Cryo-EM structure of translesion DNA synthesis polymerase ζ with a base pair mismatch. Nat Commun. 2022 Feb 25;13(1):1050. doi: 10.1038/s41467-022-28644-7. PubMed PMID: 35217661; PubMed Central PMCID: PMC8881453.

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Yoon JH, Johnson RE, Prakash L, Prakash S. Implications of inhibition of Rev1 interaction with Y family DNA polymerases for cisplatin chemotherapy. Genes Dev. 2021 Sep 1;35(17-18):1256-1270. doi: 10.1101/gad.348662.121. Epub 2021 Aug 12. PubMed PMID: 34385260; PubMed Central PMCID: PMC8415319.

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Yoon JH, Basu D, Choudhury JR, Prakash S, Prakash L. DNA polymerase λ promotes error-free replication through Watson-Crick impairing N1-methyl-deoxyadenosine adduct in conjunction with DNA polymerase ζ. J Biol Chem. 2021 Jul;297(1):100868. doi: 10.1016/j.jbc.2021.100868. Epub 2021 Jun 10. PubMed PMID: 34119520; PubMed Central PMCID: PMC8260881.

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Rechkoblit O, Johnson RE, Gupta YK, Prakash L, Prakash S, Aggarwal AK. Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase. Nat Commun. 2021 Jun 29;12(1):4020. doi: 10.1038/s41467-021-24317-z. PubMed PMID: 34188055; PubMed Central PMCID: PMC8241999.

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Yoon JH, Basu D, Sellamuthu K, Johnson RE, Prakash S, Prakash L. A novel role of DNA polymerase λ in translesion synthesis in conjunction with DNA polymerase ζ. Life Sci Alliance. 2021 Apr;4(4). doi: 10.26508/lsa.202000900. Print 2021 Apr. PubMed PMID: 33514655; PubMed Central PMCID: PMC7898466.

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Malik R, Kopylov M, Gomez-Llorente Y, Jain R, Johnson RE, Prakash L, Prakash S, Ubarretxena-Belandia I, Aggarwal AK. Structure and mechanism of B-family DNA polymerase ζ specialized for translesion DNA synthesis. Nat Struct Mol Biol. 2020 Oct;27(10):913-924. doi: 10.1038/s41594-020-0476-7. Epub 2020 Aug 17. PubMed PMID: 32807989; PubMed Central PMCID: PMC7554088.

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Yoon JH, Johnson RE, Prakash L, Prakash S. Genetic evidence for reconfiguration of DNA polymerase θ active site for error-free translesion synthesis in human cells. J Biol Chem. 2020 May 1;295(18):5918-5927. doi: 10.1074/jbc.RA120.012816. Epub 2020 Mar 13. PubMed PMID: 32169903; PubMed Central PMCID: PMC7196657.

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Yoon JH, Roy Choudhury J, Prakash L, Prakash S. Translesion synthesis DNA polymerases η, ι, and ν promote mutagenic replication through the anticancer nucleoside cytarabine. J Biol Chem. 2019 Dec 13;294(50):19048-19054. doi: 10.1074/jbc.RA119.011381. Epub 2019 Nov 4. PubMed PMID: 31685662; PubMed Central PMCID: PMC6916505.

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Rechkoblit O, Johnson RE, Buku A, Prakash L, Prakash S, Aggarwal AK. Structural insights into mutagenicity of anticancer nucleoside analog cytarabine during replication by DNA polymerase η. Sci Rep. 2019 Nov 8;9(1):16400. doi: 10.1038/s41598-019-52703-7. PubMed PMID: 31704958; PubMed Central PMCID: PMC6841716.

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Jain R, Rice WJ, Malik R, Johnson RE, Prakash L, Prakash S, Ubarretxena-Belandia I, Aggarwal AK. Cryo-EM structure and dynamics of eukaryotic DNA polymerase δ holoenzyme. Nat Struct Mol Biol. 2019 Oct;26(10):955-962. doi: 10.1038/s41594-019-0305-z. Epub 2019 Oct 3. PubMed PMID: 31582849; PubMed Central PMCID: PMC7309520.

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Yoon JH, McArthur MJ, Park J, Basu D, Wakamiya M, Prakash L, Prakash S. Error-Prone Replication through UV Lesions by DNA Polymerase θ Protects against Skin Cancers. Cell. 2019 Mar 7;176(6):1295-1309.e15. doi: 10.1016/j.cell.2019.01.023. Epub 2019 Feb 14. PubMed PMID: 30773314; PubMed Central PMCID: PMC6453116.

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Yoon JH, Johnson RE, Prakash L, Prakash S. DNA polymerase θ accomplishes translesion synthesis opposite 1,N(6)-ethenodeoxyadenosine with a remarkably high fidelity in human cells. Genes Dev. 2019 Mar 1;33(5-6):282-287. doi: 10.1101/gad.320531.118. Epub 2019 Feb 26. PubMed PMID: 30808656; PubMed Central PMCID: PMC6411006.

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Rechkoblit O, Choudhury JR, Buku A, Prakash L, Prakash S, Aggarwal AK. Structural basis for polymerase η-promoted resistance to the anticancer nucleoside analog cytarabine. Sci Rep. 2018 Aug 23;8(1):12702. doi: 10.1038/s41598-018-30796-w. PubMed PMID: 30140014; PubMed Central PMCID: PMC6107656.

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Yoon JH, Hodge RP, Hackfeld LC, Park J, Roy Choudhury J, Prakash S, Prakash L. Genetic control of predominantly error-free replication through an acrolein-derived minor-groove DNA adduct. J Biol Chem. 2018 Feb 23;293(8):2949-2958. doi: 10.1074/jbc.RA117.000962. Epub 2018 Jan 12. PubMed PMID: 29330301; PubMed Central PMCID: PMC5827445.

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Yoon JH, Roy Choudhury J, Park J, Prakash S, Prakash L. Translesion synthesis DNA polymerases promote error-free replication through the minor-groove DNA adduct 3-deaza-3-methyladenine. J Biol Chem. 2017 Nov 10;292(45):18682-18688. doi: 10.1074/jbc.M117.808659. Epub 2017 Sep 22. PubMed PMID: 28939775; PubMed Central PMCID: PMC5682974.

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Jain R, Choudhury JR, Buku A, Johnson RE, Prakash L, Prakash S, Aggarwal AK. Mechanism of error-free DNA synthesis across N1-methyl-deoxyadenosine by human DNA polymerase-ι. Sci Rep. 2017 Mar 8;7:43904. doi: 10.1038/srep43904. PubMed PMID: 28272441; PubMed Central PMCID: PMC5341039.

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Rechkoblit O, Gupta YK, Malik R, Rajashankar KR, Johnson RE, Prakash L, Prakash S, Aggarwal AK. Structure and mechanism of human PrimPol, a DNA polymerase with primase activity. Sci Adv. 2016 Oct;2(10):e1601317. doi: 10.1126/sciadv.1601317. eCollection 2016 Oct. PubMed PMID: 27819052; PubMed Central PMCID: PMC5088642.

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Coloma J, Johnson RE, Prakash L, Prakash S, Aggarwal AK. Human DNA polymerase α in binary complex with a DNA:DNA template-primer. Sci Rep. 2016 Apr 1;6:23784. doi: 10.1038/srep23784. PubMed PMID: 27032819; PubMed Central PMCID: PMC4817131.

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Johnson RE, Klassen R, Prakash L, Prakash S. Response to Burgers et al. Mol Cell. 2016 Feb 18;61(4):494-495. doi: 10.1016/j.molcel.2016.01.018. PubMed PMID: 26895422.

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Yoon JH, Park J, Conde J, Wakamiya M, Prakash L, Prakash S. Rev1 promotes replication through UV lesions in conjunction with DNA polymerases η, ι, and κ but not DNA polymerase ζ. Genes Dev. 2015 Dec 15;29(24):2588-602. doi: 10.1101/gad.272229.115. PubMed PMID: 26680302; PubMed Central PMCID: PMC4699387.

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Conde J, Yoon JH, Roy Choudhury J, Prakash L, Prakash S. Genetic Control of Replication through N1-methyladenine in Human Cells. J Biol Chem. 2015 Dec 11;290(50):29794-800. doi: 10.1074/jbc.M115.693010. Epub 2015 Oct 21. PubMed PMID: 26491020; PubMed Central PMCID: PMC4705973.

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Johnson RE, Klassen R, Prakash L, Prakash S. A Major Role of DNA Polymerase δ in Replication of Both the Leading and Lagging DNA Strands. Mol Cell. 2015 Jul 16;59(2):163-175. doi: 10.1016/j.molcel.2015.05.038. Epub 2015 Jul 2. PubMed PMID: 26145172; PubMed Central PMCID: PMC4517859.

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Yoon JH, Acharya N, Park J, Basu D, Prakash S, Prakash L. Identification of two functional PCNA-binding domains in human DNA polymerase κ. Genes Cells. 2014 Jul;19(7):594-601. doi: 10.1111/gtc.12156. Epub 2014 May 22. PubMed PMID: 24848457; PubMed Central PMCID: PMC4074225.

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Yoon JH, Roy Choudhury J, Park J, Prakash S, Prakash L. A role for DNA polymerase θ in promoting replication through oxidative DNA lesion, thymine glycol, in human cells. J Biol Chem. 2014 May 9;289(19):13177-85. doi: 10.1074/jbc.M114.556977. Epub 2014 Mar 19. PubMed PMID: 24648516; PubMed Central PMCID: PMC4036329.

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Jain R, Rajashankar KR, Buku A, Johnson RE, Prakash L, Prakash S, Aggarwal AK. Crystal structure of yeast DNA polymerase ε catalytic domain. PLoS One. 2014;9(4):e94835. doi: 10.1371/journal.pone.0094835. eCollection 2014. PubMed PMID: 24733111; PubMed Central PMCID: PMC3986358.

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Jain R, Vanamee ES, Dzikovski BG, Buku A, Johnson RE, Prakash L, Prakash S, Aggarwal AK. An iron-sulfur cluster in the polymerase domain of yeast DNA polymerase ε. J Mol Biol. 2014 Jan 23;426(2):301-8. doi: 10.1016/j.jmb.2013.10.015. Epub 2013 Oct 19. PubMed PMID: 24144619; PubMed Central PMCID: PMC4061903.

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Gómez-Llorente Y, Malik R, Jain R, Choudhury JR, Johnson RE, Prakash L, Prakash S, Ubarretxena-Belandia I, Aggarwal AK. The architecture of yeast DNA polymerase ζ. Cell Rep. 2013 Oct 17;5(1):79-86. doi: 10.1016/j.celrep.2013.08.046. Epub 2013 Oct 10. PubMed PMID: 24120860; PubMed Central PMCID: PMC3883112.

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Yoon JH, Prakash S, Prakash L. Genetic control of translesion synthesis on leading and lagging DNA strands in plasmids derived from Epstein-Barr virus in human cells. mBio. 2012;3(5):e00271-12. doi: 10.1128/mBio.00271-12. Print 2012. PubMed PMID: 22967980; PubMed Central PMCID: PMC3448166.

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Johnson RE, Prakash L, Prakash S. Pol31 and Pol32 subunits of yeast DNA polymerase δ are also essential subunits of DNA polymerase ζ. Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12455-60. doi: 10.1073/pnas.1206052109. Epub 2012 Jun 18. PubMed PMID: 22711820; PubMed Central PMCID: PMC3411960.

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Yoon JH, Prakash S, Prakash L. Requirement of Rad18 protein for replication through DNA lesions in mouse and human cells. Proc Natl Acad Sci U S A. 2012 May 15;109(20):7799-804. doi: 10.1073/pnas.1204105109. Epub 2012 Apr 30. PubMed PMID: 22547805; PubMed Central PMCID: PMC3356619.

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Ummat A, Rechkoblit O, Jain R, Roy Choudhury J, Johnson RE, Silverstein TD, Buku A, Lone S, Prakash L, Prakash S, Aggarwal AK. Structural basis for cisplatin DNA damage tolerance by human polymerase η during cancer chemotherapy. Nat Struct Mol Biol. 2012 May 6;19(6):628-32. doi: 10.1038/nsmb.2295. PubMed PMID: 22562137; PubMed Central PMCID: PMC3502009.

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Ummat A, Silverstein TD, Jain R, Buku A, Johnson RE, Prakash L, Prakash S, Aggarwal AK. Human DNA polymerase η is pre-aligned for dNTP binding and catalysis. J Mol Biol. 2012 Jan 27;415(4):627-34. doi: 10.1016/j.jmb.2011.11.038. Epub 2011 Nov 29. PubMed PMID: 22154937; PubMed Central PMCID: PMC3265613.

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Acharya N, Klassen R, Johnson RE, Prakash L, Prakash S. PCNA binding domains in all three subunits of yeast DNA polymerase δ modulate its function in DNA replication. Proc Natl Acad Sci U S A. 2011 Nov 1;108(44):17927-32. doi: 10.1073/pnas.1109981108. Epub 2011 Oct 14. PubMed PMID: 22003126; PubMed Central PMCID: PMC3207673.

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Ai Y, Wang J, Johnson RE, Haracska L, Prakash L, Zhuang Z. A novel ubiquitin binding mode in the S. cerevisiae translesion synthesis DNA polymerase η. Mol Biosyst. 2011 Jun;7(6):1874-82. doi: 10.1039/c0mb00355g. Epub 2011 Apr 11. PubMed PMID: 21483899; PubMed Central PMCID: PMC3228521.

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Gangavarapu V, Santa Maria SR, Prakash S, Prakash L. Requirement of replication checkpoint protein kinases Mec1/Rad53 for postreplication repair in yeast. mBio. 2011;2(3):e00079-11. doi: 10.1128/mBio.00079-11. Print 2011. PubMed PMID: 21586645; PubMed Central PMCID: PMC3101783.

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Vasquez-Del Carpio R, Silverstein TD, Lone S, Johnson RE, Prakash L, Prakash S, Aggarwal AK. Role of human DNA polymerase κ in extension opposite from a cis-syn thymine dimer. J Mol Biol. 2011 Apr 29;408(2):252-61. doi: 10.1016/j.jmb.2011.02.042. Epub 2011 Feb 24. PubMed PMID: 21354175; PubMed Central PMCID: PMC3093752.

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Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK. DNA synthesis across an abasic lesion by yeast REV1 DNA polymerase. J Mol Biol. 2011 Feb 11;406(1):18-28. doi: 10.1016/j.jmb.2010.12.016. Epub 2010 Dec 15. PubMed PMID: 21167175; PubMed Central PMCID: PMC3127253.

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Silverstein TD, Jain R, Johnson RE, Prakash L, Prakash S, Aggarwal AK. Structural basis for error-free replication of oxidatively damaged DNA by yeast DNA polymerase η. Structure. 2010 Nov 10;18(11):1463-70. doi: 10.1016/j.str.2010.08.019. PubMed PMID: 21070945; PubMed Central PMCID: PMC3044447.

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Yoon JH, Bhatia G, Prakash S, Prakash L. Error-free replicative bypass of thymine glycol by the combined action of DNA polymerases kappa and zeta in human cells. Proc Natl Acad Sci U S A. 2010 Aug 10;107(32):14116-21. doi: 10.1073/pnas.1007795107. Epub 2010 Jul 26. PubMed PMID: 20660785; PubMed Central PMCID: PMC2922520.

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Silverstein TD, Johnson RE, Jain R, Prakash L, Prakash S, Aggarwal AK. Structural basis for the suppression of skin cancers by DNA polymerase eta. Nature. 2010 Jun 24;465(7301):1039-43. doi: 10.1038/nature09104. PubMed PMID: 20577207; PubMed Central PMCID: PMC3030469.

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Acharya N, Yoon JH, Hurwitz J, Prakash L, Prakash S. DNA polymerase eta lacking the ubiquitin-binding domain promotes replicative lesion bypass in humans cells. Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10401-5. doi: 10.1073/pnas.1005492107. Epub 2010 May 24. PubMed PMID: 20498091; PubMed Central PMCID: PMC2890850.

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Yoon JH, Prakash L, Prakash S. Error-free replicative bypass of (6-4) photoproducts by DNA polymerase zeta in mouse and human cells. Genes Dev. 2010 Jan 15;24(2):123-8. doi: 10.1101/gad.1872810. PubMed PMID: 20080950; PubMed Central PMCID: PMC2807347.

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Jain R, Hammel M, Johnson RE, Prakash L, Prakash S, Aggarwal AK. Structural insights into yeast DNA polymerase delta by small angle X-ray scattering. J Mol Biol. 2009 Dec 4;394(3):377-82. doi: 10.1016/j.jmb.2009.09.066. Epub 2009 Oct 8. PubMed PMID: 19818796; PubMed Central PMCID: PMC2790408.

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Yoon JH, Prakash L, Prakash S. Highly error-free role of DNA polymerase eta in the replicative bypass of UV-induced pyrimidine dimers in mouse and human cells. Proc Natl Acad Sci U S A. 2009 Oct 27;106(43):18219-24. doi: 10.1073/pnas.0910121106. Epub 2009 Oct 12. PubMed PMID: 19822754; PubMed Central PMCID: PMC2775276.

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Swan MK, Johnson RE, Prakash L, Prakash S, Aggarwal AK. Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase delta. Nat Struct Mol Biol. 2009 Sep;16(9):979-86. doi: 10.1038/nsmb.1663. Epub 2009 Aug 30. PubMed PMID: 19718023; PubMed Central PMCID: PMC3055789.

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Swan MK, Johnson RE, Prakash L, Prakash S, Aggarwal AK. Structure of the human Rev1-DNA-dNTP ternary complex. J Mol Biol. 2009 Jul 24;390(4):699-709. doi: 10.1016/j.jmb.2009.05.026. Epub 2009 May 21. PubMed PMID: 19464298; PubMed Central PMCID: PMC2739620.

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Jain R, Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK. Replication across template T/U by human DNA polymerase-iota. Structure. 2009 Jul 15;17(7):974-80. doi: 10.1016/j.str.2009.04.011. PubMed PMID: 19604477; PubMed Central PMCID: PMC3030472.

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Acharya N, Johnson RE, Pagès V, Prakash L, Prakash S. Yeast Rev1 protein promotes complex formation of DNA polymerase zeta with Pol32 subunit of DNA polymerase delta. Proc Natl Acad Sci U S A. 2009 Jun 16;106(24):9631-6. doi: 10.1073/pnas.0902175106. Epub 2009 Jun 1. PubMed PMID: 19487673; PubMed Central PMCID: PMC2701015.

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Pagès V, Santa Maria SR, Prakash L, Prakash S. Role of DNA damage-induced replication checkpoint in promoting lesion bypass by translesion synthesis in yeast. Genes Dev. 2009 Jun 15;23(12):1438-49. doi: 10.1101/gad.1793409. PubMed PMID: 19528320; PubMed Central PMCID: PMC2701570.