Faculty Appointments
Professor of Chemistry
Professor of Biochemistry
Education
Ph.D., Physical Chemistry, University of California, Irvine, CaliforniaB.S., Chemistry, University of California, Davis, California
Office Address
VU Station B 351822
7332 Stevenson Center
TN
7332 Stevenson Center
TN
Research Description
My expertise is in chemistry and biology of DNA damage. My laboratory is recognized for expertise with aflatoxin-DNA damage. With Prof. Harris, we synthesized aflatoxin B1 (AFB1) epoxide, the intermediate involved in AFB1 genotoxicity. We showed that AFB1 intercalates above the 5'-face of the nucleobase, explaining the regiochemistry and sequence-specificity of DNA adduction by this agent. We elucidated the chemistry of the AFB1-induced N7-dG formamidopyrmimidine (Fapy-dG) lesion, showing that the ¿¿deoxyribose anomer destabilized DNA whereas the ¿¿anomer stabilized DNA. We showed that when bypassed by the Y-family Sulfolobus solfataricus P2 DNA Polymerase IV (Dpo4), the AFB1-induced Fapy-dG lesion induces G¿T mutations characteristic of AFB1-induced genotoxicity, whereas bypass of the initially formed N7-dG lesion is error-free. Most recently we have worked on the chemistry and biology of additional Fapy-dG lesions and AP site chemistry and biology. With Prof. Lawrence J. Marnett, we reported that DNA facilitates re-arrangement of the malondialdehyde-induced lesion M1dG to its ring-opened OpdG aldehydic rearrangement product, potentially leading to DNA interstrand cross-links. M1dG may also be oxidized to 6-oxo-M1dG, the chemistry and biology of which we now propose to examine further. With Profs. Harris, Rizzo, and Lloyd, we worked out the chemistry and structural biology of interstrand cross-linking by ¿¿¿-unsaturated aldehydes, including acrolein, crotonaldehyde, and trans-4-hydroxynonenal, all of which are produced as intracellular byproducts of lipid peroxidation. We have also examined the chemistry and structural biology of DNA damage induced by mutagenic and carcinogenic polycyclic aromatic hydrocarbons (PAH), styrene and butadiene, aryl amines produced during cooking of meats, and thymine glycol.
Research Keywords
structural biology, NMR, crystallography, DNA, biophysical chemistry, nucleic acid chemistry, DNA damage
Publications
Kellum AH, Pallan PS, Nilforoushan A, Sturla SJ, Stone MP, Egli M. Conformation and Pairing Properties of an O6-Methyl-2'-deoxyguanosine-Directed Benzimidazole Nucleoside Analog in Duplex DNA. Chem Res Toxicol [print-electronic]. 2022 Oct 10/17/2022; 35(10): 1903-13. PMID: 35973057, DOI: 10.1021/acs.chemrestox.2c00165, ISSN: 1520-5010.
Tomar R, Minko IG, Kellum AH, Voehler MW, Stone MP, McCullough AK, Lloyd RS. DNA Sequence Modulates the Efficiency of NEIL1-Catalyzed Excision of the Aflatoxin B1-Induced Formamidopyrimidine Guanine Adduct. Chem Res Toxicol [print-electronic]. 2021 Mar 3/15/2021; 34(3): 901-11. PMID: 33595290, PMCID: PMC8727046, DOI: 10.1021/acs.chemrestox.0c00517, ISSN: 1520-5010.
Kellum AH, Qiu DY, Voehler MW, Martin W, Gates KS, Stone MP. Structure of a Stable Interstrand DNA Cross-Link Involving a ß-N-Glycosyl Linkage Between an N6-dA Amino Group and an Abasic Site. Biochemistry [print-electronic]. 2021 Jan 1/12/2021; 60(1): 41-52. PMID: 33382597, PMCID: PMC7952047, DOI: 10.1021/acs.biochem.0c00596, ISSN: 1520-4995.
Minko IG, Vartanian VL, Tozaki NN, Coskun E, Coskun SH, Jaruga P, Yeo J, David SS, Stone MP, Egli M, Dizdaroglu M, McCullough AK, Lloyd RS. Recognition of DNA adducts by edited and unedited forms of DNA glycosylase NEIL1. DNA Repair (Amst) [print-electronic]. 2020 Jan; 85: 102741. PMID: 31733589, PMCID: PMC7069121, PII: S1568-7864(19)30281-2, DOI: 10.1016/j.dnarep.2019.102741, ISSN: 1568-7856.
Minko IG, Vartanian VL, Tozaki NN, Linde OK, Jaruga P, Coskun SH, Coskun E, Qu C, He H, Xu C, Chen T, Song Q, Jiao Y, Stone MP, Egli M, Dizdaroglu M, McCullough AK, Lloyd RS. Characterization of rare NEIL1 variants found in East Asian populations. DNA Repair (Amst) [print-electronic]. 2019 Jul; 79: 32-9. PMID: 31100703, PMCID: PMC6677271, PII: S1568-7864(19)30117-X, DOI: 10.1016/j.dnarep.2019.05.001, ISSN: 1568-7856.
Minko IG, Christov PP, Li L, Stone MP, McCullough AK, Lloyd RS. Processing of N5-substituted formamidopyrimidine DNA adducts by DNA glycosylases NEIL1 and NEIL3. DNA Repair (Amst) [print-electronic]. 2019 Jan; 73: 49-54. PMID: 30448017, PMCID: PMC6588396, PII: S1568-7864(18)30233-7, DOI: 10.1016/j.dnarep.2018.11.001, ISSN: 1568-7856.
Bamberger SN, Malik CK, Voehler MW, Brown SK, Pan H, Johnson-Salyard TL, Rizzo CJ, Stone MP. Configurational and Conformational Equilibria of N6-(2-Deoxy-d-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5- N-methylformamidopyrimidine (MeFapy-dG) Lesion in DNA. Chem Res Toxicol [print-electronic]. 2018 Sep 9/17/2018; 31(9): 924-35. PMID: 30169026, PMCID: PMC6352716, DOI: 10.1021/acs.chemrestox.8b00135, ISSN: 1520-5010.
Vartanian V, Minko IG, Chawanthayatham S, Egner PA, Lin YC, Earley LF, Makar R, Eng JR, Camp MT, Li L, Stone MP, Lasarev MR, Groopman JD, Croy RG, Essigmann JM, McCullough AK, Lloyd RS. NEIL1 protects against aflatoxin-induced hepatocellular carcinoma in mice. Proc Natl Acad Sci U S A [print-electronic]. 2017 Apr 4/18/2017; 114(16): 4207-12. PMID: 28373545, PMCID: PMC5402411, PII: 1620932114, DOI: 10.1073/pnas.1620932114, ISSN: 1091-6490.
Lin YC, Owen N, Minko IG, Lange SS, Tomida J, Li L, Stone MP, Wood RD, McCullough AK, Lloyd RS. DNA polymerase ¿ limits chromosomal damage and promotes cell survival following aflatoxin exposure. Proc Natl Acad Sci U S A [print-electronic]. 2016 Nov 11/29/2016; 113(48): 13774-9. PMID: 27849610, PMCID: PMC5137696, PII: 1609024113, DOI: 10.1073/pnas.1609024113, ISSN: 1091-6490.
Patra A, Politica DA, Chatterjee A, Tokarsky EJ, Suo Z, Basu AK, Stone MP, Egli M. Mechanism of Error-Free Bypass of the Environmental Carcinogen N-(2'-Deoxyguanosin-8-yl)-3-aminobenzanthrone Adduct by Human DNA Polymerase ¿. Chembiochem [print-electronic]. 2016 Nov 11/3/2016; 17(21): 2033-7. PMID: 27556902, PMCID: PMC5172388, DOI: 10.1002/cbic.201600420, ISSN: 1439-7633.
Politica DA, Malik CK, Basu AK, Stone MP. Base-Displaced Intercalated Structure of the N-(2'-Deoxyguanosin-8-yl)-3-aminobenzanthrone DNA Adduct. Chem Res Toxicol [print-electronic]. 2015 Dec 12/21/2015; 28(12): 2253-66. PMID: 26641105, PMCID: PMC4894058, DOI: 10.1021/acs.chemrestox.5b00277, ISSN: 1520-5010.
Stavros KM, Hawkins EK, Rizzo CJ, Stone MP. Base-Displaced Intercalated Conformation of the 2-Amino-3-methylimidazo[4,5-f]quinoline N(2)-dG DNA Adduct Positioned at the Nonreiterated G(1) in the NarI Restriction Site. Chem Res Toxicol [print-electronic]. 2015 Jul 7/20/2015; 28(7): 1455-68. PMID: 26083477, PMCID: PMC4511292, DOI: 10.1021/acs.chemrestox.5b00140, ISSN: 1520-5010.
Patra A, Banerjee S, Johnson Salyard TL, Malik CK, Christov PP, Rizzo CJ, Stone MP, Egli M. Structural Basis for Error-Free Bypass of the 5-N-Methylformamidopyrimidine-dG Lesion by Human DNA Polymerase ¿ and Sulfolobus solfataricus P2 Polymerase IV. J Am Chem Soc [print-electronic]. 2015 Jun 6/10/2015; 137(22): 7011-4. PMID: 25988947, PMCID: PMC4545269, DOI: 10.1021/jacs.5b02701, ISSN: 1520-5126.
Szulik MW, Pallan PS, Nocek B, Voehler M, Banerjee S, Brooks S, Joachimiak A, Egli M, Eichman BF, Stone MP. Differential stabilities and sequence-dependent base pair opening dynamics of Watson-Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine. Biochemistry [print-electronic]. 2015 Feb 2/10/2015; 54(5): 1294-305. PMID: 25632825, PMCID: PMC4325598, DOI: 10.1021/bi501534x, ISSN: 1520-4995.
Szulik MW, Voehler M, Stone MP. NMR analysis of base-pair opening kinetics in DNA. Curr Protoc Nucleic Acid Chem. 2014 Dec 12/12/2014; 59: 7.20.1-18. PMID: 25501592, PMCID: PMC4274747, DOI: 10.1002/0471142700.nc0720s59, ISSN: 1934-9289.
Kowal EA, Wickramaratne S, Kotapati S, Turo M, Tretyakova N, Stone MP. Major groove orientation of the (2S)-N(6)-(2-hydroxy-3-buten-1-yl)-2'-deoxyadenosine DNA adduct induced by 1,2-epoxy-3-butene. Chem Res Toxicol [print-electronic]. 2014 Oct 10/20/2014; 27(10): 1675-86. PMID: 25238403, PMCID: PMC4203389, DOI: 10.1021/tx500159w, ISSN: 1520-5010.
Lin YC, Li L, Makarova AV, Burgers PM, Stone MP, Lloyd RS. Molecular basis of aflatoxin-induced mutagenesis-role of the aflatoxin B1-formamidopyrimidine adduct. Carcinogenesis [print-electronic]. 2014 Jul; 35(7): 1461-8. PMID: 24398669, PMCID: PMC4076807, PII: bgu003, DOI: 10.1093/carcin/bgu003, ISSN: 1460-2180.
Lin YC, Li L, Makarova AV, Burgers PM, Stone MP, Lloyd RS. Error-prone replication bypass of the primary aflatoxin B1 DNA adduct, AFB1-N7-Gua. J Biol Chem [print-electronic]. 2014 Jun 6/27/2014; 289(26): 18497-506. PMID: 24838242, PMCID: PMC4140297, PII: S0021-9258(20)40555-1, DOI: 10.1074/jbc.M114.561563, ISSN: 1083-351X.
Kowal EA, Seneviratne U, Wickramaratne S, Doherty KE, Cao X, Tretyakova N, Stone MP. Structures of exocyclic R,R- and S,S-N(6),N(6)-(2,3-dihydroxybutan-1,4-diyl)-2'-deoxyadenosine adducts induced by 1,2,3,4-diepoxybutane. Chem Res Toxicol [print-electronic]. 2014 May 5/19/2014; 27(5): 805-17. PMID: 24741991, PMCID: PMC4027948, DOI: 10.1021/tx400472p, ISSN: 1520-5010.
Stavros KM, Hawkins EK, Rizzo CJ, Stone MP. Base-displaced intercalation of the 2-amino-3-methylimidazo[4,5-f]quinolone N2-dG adduct in the NarI DNA recognition sequence. Nucleic Acids Res [print-electronic]. 2014 Mar; 42(5): 3450-63. PMID: 24366876, PMCID: PMC3950664, PII: gkt1109, DOI: 10.1093/nar/gkt1109, ISSN: 1362-4962.
Szulik MW, Voehler MW, Ganguly M, Gold B, Stone MP. Site-specific stabilization of DNA by a tethered major groove amine, 7-aminomethyl-7-deaza-2'-deoxyguanosine. Biochemistry [print-electronic]. 2013 Oct 10/29/2013; 52(43): 7659-68. PMID: 24131376, PMCID: PMC3812902, DOI: 10.1021/bi400695r, ISSN: 1520-4995.
Shanmugam G, Minko IG, Banerjee S, Christov PP, Kozekov ID, Rizzo CJ, Lloyd RS, Egli M, Stone MP. Ring-opening of the ¿-OH-PdG adduct promotes error-free bypass by the Sulfolobus solfataricus DNA polymerase Dpo4. Chem Res Toxicol [print-electronic]. 2013 Sep 9/16/2013; 26(9): 1348-60. PMID: 23947567, PMCID: PMC3775444, DOI: 10.1021/tx400200b, ISSN: 1520-5010.
Kowal EA, Lad RR, Pallan PS, Dhummakupt E, Wawrzak Z, Egli M, Sturla SJ, Stone MP. Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction. Nucleic Acids Res [print-electronic]. 2013 Aug; 41(15): 7566-76. PMID: 23748954, PMCID: PMC3753623, PII: gkt488, DOI: 10.1093/nar/gkt488, ISSN: 1362-4962.
Banerjee S, Christov PP, Kozekova A, Rizzo CJ, Egli M, Stone MP. Replication bypass of the trans-4-Hydroxynonenal-derived (6S,8R,11S)-1,N(2)-deoxyguanosine DNA adduct by the sulfolobus solfataricus DNA polymerase IV. Chem. Res. Toxicol [print-electronic]. 2012 Feb 2/20/2012; 25(2): 422-35. PMID: 22313351, PMCID: PMC3285121, DOI: 10.1021/tx200460j, ISSN: 1520-5010.
Huang H, Das RS, Basu AK, Stone MP. Structures of (5'S)-8,5'-Cyclo-2'-deoxyguanosine Mismatched with dA or dT. Chem. Res. Toxicol [print-electronic]. 2012 Feb 2/20/2012; 25(2): 478-90. PMID: 22309170, PMCID: PMC3285119, DOI: 10.1021/tx2005053, ISSN: 1520-5010.
Huang H, Das RS, Basu AK, Stone MP. Structure of (5'S)-8,5'-cyclo-2'-deoxyguanosine in DNA. J. Am. Chem. Soc [print-electronic]. 2011 Dec 12/21/2011; 133(50): 20357-68. PMID: 22103478, PMCID: PMC3279155, DOI: 10.1021/ja207407n, ISSN: 1520-5126.
Kowal EA, Ganguly M, Pallan PS, Marky LA, Gold B, Egli M, Stone MP. Altering the electrostatic potential in the major groove: thermodynamic and structural characterization of 7-deaza-2'-deoxyadenosine:dT base pairing in DNA. J Phys Chem B [print-electronic]. 2011 Dec 12/1/2011; 115(47): 13925-34. PMID: 22059929, PMCID: PMC3225014, DOI: 10.1021/jp207104w, ISSN: 1520-5207.
Huang H, Wang H, Kozekova A, Rizzo CJ, Stone MP. Formation of a N2-dG:N2-dG carbinolamine DNA cross-link by the trans-4-hydroxynonenal-derived (6S,8R,11S) 1,N2-dG adduct. J. Am. Chem. Soc [print-electronic]. 2011 Oct 10/12/2011; 133(40): 16101-10. PMID: 21916419, PMCID: PMC3187658, DOI: 10.1021/ja205145q, ISSN: 1520-5126.
Stone MP, Huang H, Brown KL, Shanmugam G. Chemistry and structural biology of DNA damage and biological consequences. Chem. Biodivers. 2011 Sep; 8(9): 1571-615. PMID: 21922653, PMCID: PMC3714022, DOI: 10.1002/cbdv.201100033, ISSN: 1612-1880.
Banerjee S, Brown KL, Egli M, Stone MP. Bypass of aflatoxin B1 adducts by the Sulfolobus solfataricus DNA polymerase IV. J. Am. Chem. Soc [print-electronic]. 2011 Aug 8/17/2011; 133(32): 12556-68. PMID: 21790157, PMCID: PMC3154525, DOI: 10.1021/ja2015668, ISSN: 1520-5126.
Shanmugam G, Kozekov ID, Guengerich FP, Rizzo CJ, Stone MP. 1,N2-Etheno-2'-deoxyguanosine adopts the syn conformation about the glycosyl bond when mismatched with deoxyadenosine. Chem. Res. Toxicol [print-electronic]. 2011 Jul 7/18/2011; 24(7): 1071-9. PMID: 21675798, PMCID: PMC3138413, DOI: 10.1021/tx200089v, ISSN: 1520-5010.
Huang H, Wang H, Voehler MW, Kozekova A, Rizzo CJ, McCullough AK, Lloyd RS, Stone MP. ¿-Hydroxy-1,N2-propano-2'-deoxyguanosine DNA adduct conjugates the N-terminal amine of the KWKK peptide via a carbinolamine linkage. Chem. Res. Toxicol [print-electronic]. 2011 Jul 7/18/2011; 24(7): 1123-33. PMID: 21561113, PMCID: PMC3138414, DOI: 10.1021/tx200113n, ISSN: 1520-5010.
Christov PP, Petrova KV, Shanmugam G, Kozekov ID, Kozekova A, Guengerich FP, Stone MP, Rizzo CJ. Comparison of the in vitro replication of the 7-(2-oxoheptyl)-1,N2-etheno-2'-deoxyguanosine and 1,N2-etheno-2'-deoxyguanosine lesions by Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4). Chem. Res. Toxicol. 2010 Aug 8/16/2010; 23(8): 1330-41. PMID: 20578729, PMCID: PMC2922457, DOI: 10.1021/tx100082e, ISSN: 1520-5010.
Huang H, Kozekov ID, Kozekova A, Rizzo CJ, McCullough AK, Lloyd RS, Stone MP. Minor groove orientation of the KWKK peptide tethered via the N-terminal amine to the acrolein-derived 1,N2-gamma-hydroxypropanodeoxyguanosine lesion with a trimethylene linkage. Biochemistry. 2010 Jul 7/27/2010; 49(29): 6155-64. PMID: 20604523, PMCID: PMC2907095, DOI: 10.1021/bi100364f, ISSN: 1520-4995.
Huang H, Kozekov ID, Kozekova A, Wang H, Lloyd RS, Rizzo CJ, Stone MP. DNA cross-link induced by trans-4-hydroxynonenal. Environ. Mol. Mutagen. 2010 Jul; 51(6): 625-34. PMID: 20577992, PMCID: PMC3140422, DOI: 10.1002/em.20599, ISSN: 1098-2280.
Christov PP, Chowdhury G, Garmendia CA, Wang F, Stover JS, Elmquist CE, Kozekova A, Angel KC, Turesky RJ, Stone MP, Guengerich FP, Rizzo CJ. The C8-2'-deoxyguanosine adduct of 2-amino-3-methylimidazo[1,2-d]naphthalene, a carbocyclic analogue of the potent mutagen 2-amino-3-methylimidazo[4,5-f]quinoline, is a block to replication in vitro. Chem. Res. Toxicol. 2010 Jun 6/21/2010; 23(6): 1076-88. PMID: 20377178, PMCID: PMC2891123, DOI: 10.1021/tx100053n, ISSN: 1520-5010.
Shanmugam G, Kozekov ID, Guengerich FP, Rizzo CJ, Stone MP. Structure of the 1,N(2)-etheno-2'-deoxyguanosine lesion in the 3'-G(epsilon dG)T-5' sequence opposite a one-base deletion. Biochemistry. 2010 Mar 3/30/2010; 49(12): 2615-26. PMID: 20201499, PMCID: PMC2844103, DOI: 10.1021/bi901516d, ISSN: 1520-4995.
Christov PP, Banerjee S, Stone MP, Rizzo CJ. Selective Incision of the alpha-N-Methyl-Formamidopyrimidine Anomer by Escherichia coli Endonuclease IV. J Nucleic Acids. 2010; 2010: PMID: 20798848, PMCID: PMC2925382, DOI: 10.4061/2010/850234, ISSN: 2090-021X.
Brown KL, Roginskaya M, Zou Y, Altamirano A, Basu AK, Stone MP. Binding of the human nucleotide excision repair proteins XPA and XPC/HR23B to the 5R-thymine glycol lesion and structure of the cis-(5R,6S) thymine glycol epimer in the 5'-GTgG-3' sequence: destabilization of two base pairs at the lesion site. Nucleic Acids Res [print-electronic]. 2010 Jan; 38(2): 428-40. PMID: 19892827, PMCID: PMC2811006, PII: gkp844, DOI: 10.1093/nar/gkp844, ISSN: 1362-4962.
Brown KL, Voehler MW, Magee SM, Harris CM, Harris TM, Stone MP. Structural perturbations induced by the alpha-anomer of the aflatoxin B(1) formamidopyrimidine adduct in duplex and single-strand DNA. J. Am. Chem. Soc. 2009 Nov 11/11/2009; 131(44): 16096-107. PMID: 19831353, PMCID: PMC2773149, DOI: 10.1021/ja902052v, ISSN: 1520-5126.
Huang H, Dooley PA, Harris CM, Harris TM, Stone MP. Differential base stacking interactions induced by trimethylene interstrand DNA cross-links in the 5'-CpG-3' and 5'-GpC-3' sequence contexts. Chem. Res. Toxicol. 2009 Nov; 22(11): 1810-6. PMID: 19916525, PMCID: PMC2778138, DOI: 10.1021/tx900225c, ISSN: 1520-5010.
Brown KL, Basu AK, Stone MP. The cis-(5R,6S)-thymine glycol lesion occupies the wobble position when mismatched with deoxyguanosine in DNA. Biochemistry. 2009 Oct 10/20/2009; 48(41): 9722-33. PMID: 19772348, PMCID: PMC2761728, DOI: 10.1021/bi900695e, ISSN: 1520-4995.
Huang H, Kim HY, Kozekov ID, Cho YJ, Wang H, Kozekova A, Harris TM, Rizzo CJ, Stone MP. Stereospecific formation of the (R)-gamma-hydroxytrimethylene interstrand N2-dG:N2-dG cross-link arising from the gamma-OH-1,N2-propano-2'-deoxyguanosine adduct in the 5'-CpG-3' DNA sequence. J. Am. Chem. Soc. 2009 Jun 6/24/2009; 131(24): 8416-24. PMID: 19530727, PMCID: PMC2753404, DOI: 10.1021/ja809543j, ISSN: 1520-5126.
Tomar R, Minko IG, Kellum AH, Voehler MW, Stone MP, McCullough AK, Lloyd RS. DNA Sequence Modulates the Efficiency of NEIL1-Catalyzed Excision of the Aflatoxin B1-Induced Formamidopyrimidine Guanine Adduct. Chem Res Toxicol [print-electronic]. 2021 Mar 3/15/2021; 34(3): 901-11. PMID: 33595290, PMCID: PMC8727046, DOI: 10.1021/acs.chemrestox.0c00517, ISSN: 1520-5010.
Kellum AH, Qiu DY, Voehler MW, Martin W, Gates KS, Stone MP. Structure of a Stable Interstrand DNA Cross-Link Involving a ß-N-Glycosyl Linkage Between an N6-dA Amino Group and an Abasic Site. Biochemistry [print-electronic]. 2021 Jan 1/12/2021; 60(1): 41-52. PMID: 33382597, PMCID: PMC7952047, DOI: 10.1021/acs.biochem.0c00596, ISSN: 1520-4995.
Minko IG, Vartanian VL, Tozaki NN, Coskun E, Coskun SH, Jaruga P, Yeo J, David SS, Stone MP, Egli M, Dizdaroglu M, McCullough AK, Lloyd RS. Recognition of DNA adducts by edited and unedited forms of DNA glycosylase NEIL1. DNA Repair (Amst) [print-electronic]. 2020 Jan; 85: 102741. PMID: 31733589, PMCID: PMC7069121, PII: S1568-7864(19)30281-2, DOI: 10.1016/j.dnarep.2019.102741, ISSN: 1568-7856.
Minko IG, Vartanian VL, Tozaki NN, Linde OK, Jaruga P, Coskun SH, Coskun E, Qu C, He H, Xu C, Chen T, Song Q, Jiao Y, Stone MP, Egli M, Dizdaroglu M, McCullough AK, Lloyd RS. Characterization of rare NEIL1 variants found in East Asian populations. DNA Repair (Amst) [print-electronic]. 2019 Jul; 79: 32-9. PMID: 31100703, PMCID: PMC6677271, PII: S1568-7864(19)30117-X, DOI: 10.1016/j.dnarep.2019.05.001, ISSN: 1568-7856.
Minko IG, Christov PP, Li L, Stone MP, McCullough AK, Lloyd RS. Processing of N5-substituted formamidopyrimidine DNA adducts by DNA glycosylases NEIL1 and NEIL3. DNA Repair (Amst) [print-electronic]. 2019 Jan; 73: 49-54. PMID: 30448017, PMCID: PMC6588396, PII: S1568-7864(18)30233-7, DOI: 10.1016/j.dnarep.2018.11.001, ISSN: 1568-7856.
Bamberger SN, Malik CK, Voehler MW, Brown SK, Pan H, Johnson-Salyard TL, Rizzo CJ, Stone MP. Configurational and Conformational Equilibria of N6-(2-Deoxy-d-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5- N-methylformamidopyrimidine (MeFapy-dG) Lesion in DNA. Chem Res Toxicol [print-electronic]. 2018 Sep 9/17/2018; 31(9): 924-35. PMID: 30169026, PMCID: PMC6352716, DOI: 10.1021/acs.chemrestox.8b00135, ISSN: 1520-5010.
Vartanian V, Minko IG, Chawanthayatham S, Egner PA, Lin YC, Earley LF, Makar R, Eng JR, Camp MT, Li L, Stone MP, Lasarev MR, Groopman JD, Croy RG, Essigmann JM, McCullough AK, Lloyd RS. NEIL1 protects against aflatoxin-induced hepatocellular carcinoma in mice. Proc Natl Acad Sci U S A [print-electronic]. 2017 Apr 4/18/2017; 114(16): 4207-12. PMID: 28373545, PMCID: PMC5402411, PII: 1620932114, DOI: 10.1073/pnas.1620932114, ISSN: 1091-6490.
Lin YC, Owen N, Minko IG, Lange SS, Tomida J, Li L, Stone MP, Wood RD, McCullough AK, Lloyd RS. DNA polymerase ¿ limits chromosomal damage and promotes cell survival following aflatoxin exposure. Proc Natl Acad Sci U S A [print-electronic]. 2016 Nov 11/29/2016; 113(48): 13774-9. PMID: 27849610, PMCID: PMC5137696, PII: 1609024113, DOI: 10.1073/pnas.1609024113, ISSN: 1091-6490.
Patra A, Politica DA, Chatterjee A, Tokarsky EJ, Suo Z, Basu AK, Stone MP, Egli M. Mechanism of Error-Free Bypass of the Environmental Carcinogen N-(2'-Deoxyguanosin-8-yl)-3-aminobenzanthrone Adduct by Human DNA Polymerase ¿. Chembiochem [print-electronic]. 2016 Nov 11/3/2016; 17(21): 2033-7. PMID: 27556902, PMCID: PMC5172388, DOI: 10.1002/cbic.201600420, ISSN: 1439-7633.
Politica DA, Malik CK, Basu AK, Stone MP. Base-Displaced Intercalated Structure of the N-(2'-Deoxyguanosin-8-yl)-3-aminobenzanthrone DNA Adduct. Chem Res Toxicol [print-electronic]. 2015 Dec 12/21/2015; 28(12): 2253-66. PMID: 26641105, PMCID: PMC4894058, DOI: 10.1021/acs.chemrestox.5b00277, ISSN: 1520-5010.
Stavros KM, Hawkins EK, Rizzo CJ, Stone MP. Base-Displaced Intercalated Conformation of the 2-Amino-3-methylimidazo[4,5-f]quinoline N(2)-dG DNA Adduct Positioned at the Nonreiterated G(1) in the NarI Restriction Site. Chem Res Toxicol [print-electronic]. 2015 Jul 7/20/2015; 28(7): 1455-68. PMID: 26083477, PMCID: PMC4511292, DOI: 10.1021/acs.chemrestox.5b00140, ISSN: 1520-5010.
Patra A, Banerjee S, Johnson Salyard TL, Malik CK, Christov PP, Rizzo CJ, Stone MP, Egli M. Structural Basis for Error-Free Bypass of the 5-N-Methylformamidopyrimidine-dG Lesion by Human DNA Polymerase ¿ and Sulfolobus solfataricus P2 Polymerase IV. J Am Chem Soc [print-electronic]. 2015 Jun 6/10/2015; 137(22): 7011-4. PMID: 25988947, PMCID: PMC4545269, DOI: 10.1021/jacs.5b02701, ISSN: 1520-5126.
Szulik MW, Pallan PS, Nocek B, Voehler M, Banerjee S, Brooks S, Joachimiak A, Egli M, Eichman BF, Stone MP. Differential stabilities and sequence-dependent base pair opening dynamics of Watson-Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine. Biochemistry [print-electronic]. 2015 Feb 2/10/2015; 54(5): 1294-305. PMID: 25632825, PMCID: PMC4325598, DOI: 10.1021/bi501534x, ISSN: 1520-4995.
Szulik MW, Voehler M, Stone MP. NMR analysis of base-pair opening kinetics in DNA. Curr Protoc Nucleic Acid Chem. 2014 Dec 12/12/2014; 59: 7.20.1-18. PMID: 25501592, PMCID: PMC4274747, DOI: 10.1002/0471142700.nc0720s59, ISSN: 1934-9289.
Kowal EA, Wickramaratne S, Kotapati S, Turo M, Tretyakova N, Stone MP. Major groove orientation of the (2S)-N(6)-(2-hydroxy-3-buten-1-yl)-2'-deoxyadenosine DNA adduct induced by 1,2-epoxy-3-butene. Chem Res Toxicol [print-electronic]. 2014 Oct 10/20/2014; 27(10): 1675-86. PMID: 25238403, PMCID: PMC4203389, DOI: 10.1021/tx500159w, ISSN: 1520-5010.
Lin YC, Li L, Makarova AV, Burgers PM, Stone MP, Lloyd RS. Molecular basis of aflatoxin-induced mutagenesis-role of the aflatoxin B1-formamidopyrimidine adduct. Carcinogenesis [print-electronic]. 2014 Jul; 35(7): 1461-8. PMID: 24398669, PMCID: PMC4076807, PII: bgu003, DOI: 10.1093/carcin/bgu003, ISSN: 1460-2180.
Lin YC, Li L, Makarova AV, Burgers PM, Stone MP, Lloyd RS. Error-prone replication bypass of the primary aflatoxin B1 DNA adduct, AFB1-N7-Gua. J Biol Chem [print-electronic]. 2014 Jun 6/27/2014; 289(26): 18497-506. PMID: 24838242, PMCID: PMC4140297, PII: S0021-9258(20)40555-1, DOI: 10.1074/jbc.M114.561563, ISSN: 1083-351X.
Kowal EA, Seneviratne U, Wickramaratne S, Doherty KE, Cao X, Tretyakova N, Stone MP. Structures of exocyclic R,R- and S,S-N(6),N(6)-(2,3-dihydroxybutan-1,4-diyl)-2'-deoxyadenosine adducts induced by 1,2,3,4-diepoxybutane. Chem Res Toxicol [print-electronic]. 2014 May 5/19/2014; 27(5): 805-17. PMID: 24741991, PMCID: PMC4027948, DOI: 10.1021/tx400472p, ISSN: 1520-5010.
Stavros KM, Hawkins EK, Rizzo CJ, Stone MP. Base-displaced intercalation of the 2-amino-3-methylimidazo[4,5-f]quinolone N2-dG adduct in the NarI DNA recognition sequence. Nucleic Acids Res [print-electronic]. 2014 Mar; 42(5): 3450-63. PMID: 24366876, PMCID: PMC3950664, PII: gkt1109, DOI: 10.1093/nar/gkt1109, ISSN: 1362-4962.
Szulik MW, Voehler MW, Ganguly M, Gold B, Stone MP. Site-specific stabilization of DNA by a tethered major groove amine, 7-aminomethyl-7-deaza-2'-deoxyguanosine. Biochemistry [print-electronic]. 2013 Oct 10/29/2013; 52(43): 7659-68. PMID: 24131376, PMCID: PMC3812902, DOI: 10.1021/bi400695r, ISSN: 1520-4995.
Shanmugam G, Minko IG, Banerjee S, Christov PP, Kozekov ID, Rizzo CJ, Lloyd RS, Egli M, Stone MP. Ring-opening of the ¿-OH-PdG adduct promotes error-free bypass by the Sulfolobus solfataricus DNA polymerase Dpo4. Chem Res Toxicol [print-electronic]. 2013 Sep 9/16/2013; 26(9): 1348-60. PMID: 23947567, PMCID: PMC3775444, DOI: 10.1021/tx400200b, ISSN: 1520-5010.
Kowal EA, Lad RR, Pallan PS, Dhummakupt E, Wawrzak Z, Egli M, Sturla SJ, Stone MP. Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction. Nucleic Acids Res [print-electronic]. 2013 Aug; 41(15): 7566-76. PMID: 23748954, PMCID: PMC3753623, PII: gkt488, DOI: 10.1093/nar/gkt488, ISSN: 1362-4962.
Banerjee S, Christov PP, Kozekova A, Rizzo CJ, Egli M, Stone MP. Replication bypass of the trans-4-Hydroxynonenal-derived (6S,8R,11S)-1,N(2)-deoxyguanosine DNA adduct by the sulfolobus solfataricus DNA polymerase IV. Chem. Res. Toxicol [print-electronic]. 2012 Feb 2/20/2012; 25(2): 422-35. PMID: 22313351, PMCID: PMC3285121, DOI: 10.1021/tx200460j, ISSN: 1520-5010.
Huang H, Das RS, Basu AK, Stone MP. Structures of (5'S)-8,5'-Cyclo-2'-deoxyguanosine Mismatched with dA or dT. Chem. Res. Toxicol [print-electronic]. 2012 Feb 2/20/2012; 25(2): 478-90. PMID: 22309170, PMCID: PMC3285119, DOI: 10.1021/tx2005053, ISSN: 1520-5010.
Huang H, Das RS, Basu AK, Stone MP. Structure of (5'S)-8,5'-cyclo-2'-deoxyguanosine in DNA. J. Am. Chem. Soc [print-electronic]. 2011 Dec 12/21/2011; 133(50): 20357-68. PMID: 22103478, PMCID: PMC3279155, DOI: 10.1021/ja207407n, ISSN: 1520-5126.
Kowal EA, Ganguly M, Pallan PS, Marky LA, Gold B, Egli M, Stone MP. Altering the electrostatic potential in the major groove: thermodynamic and structural characterization of 7-deaza-2'-deoxyadenosine:dT base pairing in DNA. J Phys Chem B [print-electronic]. 2011 Dec 12/1/2011; 115(47): 13925-34. PMID: 22059929, PMCID: PMC3225014, DOI: 10.1021/jp207104w, ISSN: 1520-5207.
Huang H, Wang H, Kozekova A, Rizzo CJ, Stone MP. Formation of a N2-dG:N2-dG carbinolamine DNA cross-link by the trans-4-hydroxynonenal-derived (6S,8R,11S) 1,N2-dG adduct. J. Am. Chem. Soc [print-electronic]. 2011 Oct 10/12/2011; 133(40): 16101-10. PMID: 21916419, PMCID: PMC3187658, DOI: 10.1021/ja205145q, ISSN: 1520-5126.
Stone MP, Huang H, Brown KL, Shanmugam G. Chemistry and structural biology of DNA damage and biological consequences. Chem. Biodivers. 2011 Sep; 8(9): 1571-615. PMID: 21922653, PMCID: PMC3714022, DOI: 10.1002/cbdv.201100033, ISSN: 1612-1880.
Banerjee S, Brown KL, Egli M, Stone MP. Bypass of aflatoxin B1 adducts by the Sulfolobus solfataricus DNA polymerase IV. J. Am. Chem. Soc [print-electronic]. 2011 Aug 8/17/2011; 133(32): 12556-68. PMID: 21790157, PMCID: PMC3154525, DOI: 10.1021/ja2015668, ISSN: 1520-5126.
Shanmugam G, Kozekov ID, Guengerich FP, Rizzo CJ, Stone MP. 1,N2-Etheno-2'-deoxyguanosine adopts the syn conformation about the glycosyl bond when mismatched with deoxyadenosine. Chem. Res. Toxicol [print-electronic]. 2011 Jul 7/18/2011; 24(7): 1071-9. PMID: 21675798, PMCID: PMC3138413, DOI: 10.1021/tx200089v, ISSN: 1520-5010.
Huang H, Wang H, Voehler MW, Kozekova A, Rizzo CJ, McCullough AK, Lloyd RS, Stone MP. ¿-Hydroxy-1,N2-propano-2'-deoxyguanosine DNA adduct conjugates the N-terminal amine of the KWKK peptide via a carbinolamine linkage. Chem. Res. Toxicol [print-electronic]. 2011 Jul 7/18/2011; 24(7): 1123-33. PMID: 21561113, PMCID: PMC3138414, DOI: 10.1021/tx200113n, ISSN: 1520-5010.
Christov PP, Petrova KV, Shanmugam G, Kozekov ID, Kozekova A, Guengerich FP, Stone MP, Rizzo CJ. Comparison of the in vitro replication of the 7-(2-oxoheptyl)-1,N2-etheno-2'-deoxyguanosine and 1,N2-etheno-2'-deoxyguanosine lesions by Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4). Chem. Res. Toxicol. 2010 Aug 8/16/2010; 23(8): 1330-41. PMID: 20578729, PMCID: PMC2922457, DOI: 10.1021/tx100082e, ISSN: 1520-5010.
Huang H, Kozekov ID, Kozekova A, Rizzo CJ, McCullough AK, Lloyd RS, Stone MP. Minor groove orientation of the KWKK peptide tethered via the N-terminal amine to the acrolein-derived 1,N2-gamma-hydroxypropanodeoxyguanosine lesion with a trimethylene linkage. Biochemistry. 2010 Jul 7/27/2010; 49(29): 6155-64. PMID: 20604523, PMCID: PMC2907095, DOI: 10.1021/bi100364f, ISSN: 1520-4995.
Huang H, Kozekov ID, Kozekova A, Wang H, Lloyd RS, Rizzo CJ, Stone MP. DNA cross-link induced by trans-4-hydroxynonenal. Environ. Mol. Mutagen. 2010 Jul; 51(6): 625-34. PMID: 20577992, PMCID: PMC3140422, DOI: 10.1002/em.20599, ISSN: 1098-2280.
Christov PP, Chowdhury G, Garmendia CA, Wang F, Stover JS, Elmquist CE, Kozekova A, Angel KC, Turesky RJ, Stone MP, Guengerich FP, Rizzo CJ. The C8-2'-deoxyguanosine adduct of 2-amino-3-methylimidazo[1,2-d]naphthalene, a carbocyclic analogue of the potent mutagen 2-amino-3-methylimidazo[4,5-f]quinoline, is a block to replication in vitro. Chem. Res. Toxicol. 2010 Jun 6/21/2010; 23(6): 1076-88. PMID: 20377178, PMCID: PMC2891123, DOI: 10.1021/tx100053n, ISSN: 1520-5010.
Shanmugam G, Kozekov ID, Guengerich FP, Rizzo CJ, Stone MP. Structure of the 1,N(2)-etheno-2'-deoxyguanosine lesion in the 3'-G(epsilon dG)T-5' sequence opposite a one-base deletion. Biochemistry. 2010 Mar 3/30/2010; 49(12): 2615-26. PMID: 20201499, PMCID: PMC2844103, DOI: 10.1021/bi901516d, ISSN: 1520-4995.
Christov PP, Banerjee S, Stone MP, Rizzo CJ. Selective Incision of the alpha-N-Methyl-Formamidopyrimidine Anomer by Escherichia coli Endonuclease IV. J Nucleic Acids. 2010; 2010: PMID: 20798848, PMCID: PMC2925382, DOI: 10.4061/2010/850234, ISSN: 2090-021X.
Brown KL, Roginskaya M, Zou Y, Altamirano A, Basu AK, Stone MP. Binding of the human nucleotide excision repair proteins XPA and XPC/HR23B to the 5R-thymine glycol lesion and structure of the cis-(5R,6S) thymine glycol epimer in the 5'-GTgG-3' sequence: destabilization of two base pairs at the lesion site. Nucleic Acids Res [print-electronic]. 2010 Jan; 38(2): 428-40. PMID: 19892827, PMCID: PMC2811006, PII: gkp844, DOI: 10.1093/nar/gkp844, ISSN: 1362-4962.
Brown KL, Voehler MW, Magee SM, Harris CM, Harris TM, Stone MP. Structural perturbations induced by the alpha-anomer of the aflatoxin B(1) formamidopyrimidine adduct in duplex and single-strand DNA. J. Am. Chem. Soc. 2009 Nov 11/11/2009; 131(44): 16096-107. PMID: 19831353, PMCID: PMC2773149, DOI: 10.1021/ja902052v, ISSN: 1520-5126.
Huang H, Dooley PA, Harris CM, Harris TM, Stone MP. Differential base stacking interactions induced by trimethylene interstrand DNA cross-links in the 5'-CpG-3' and 5'-GpC-3' sequence contexts. Chem. Res. Toxicol. 2009 Nov; 22(11): 1810-6. PMID: 19916525, PMCID: PMC2778138, DOI: 10.1021/tx900225c, ISSN: 1520-5010.
Brown KL, Basu AK, Stone MP. The cis-(5R,6S)-thymine glycol lesion occupies the wobble position when mismatched with deoxyguanosine in DNA. Biochemistry. 2009 Oct 10/20/2009; 48(41): 9722-33. PMID: 19772348, PMCID: PMC2761728, DOI: 10.1021/bi900695e, ISSN: 1520-4995.
Huang H, Kim HY, Kozekov ID, Cho YJ, Wang H, Kozekova A, Harris TM, Rizzo CJ, Stone MP. Stereospecific formation of the (R)-gamma-hydroxytrimethylene interstrand N2-dG:N2-dG cross-link arising from the gamma-OH-1,N2-propano-2'-deoxyguanosine adduct in the 5'-CpG-3' DNA sequence. J. Am. Chem. Soc. 2009 Jun 6/24/2009; 131(24): 8416-24. PMID: 19530727, PMCID: PMC2753404, DOI: 10.1021/ja809543j, ISSN: 1520-5126.