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Publications

Book Chapters:

Mirkin S.M. (2006) "Replication of Expandable Repeats". In: Genetic Instabilities and Neurological Diseases, 2nd ed., R.D. Wells and T. Ashizawa eds., pp. 637-644.
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Krasilnikova, M.M., Mirkin, S.M. (2004) Analysis of triplet repeat replication by 2-dimensional gel-electrophoresis. In: Methods in Molecular Biology, vol. 277: Trinucleotide Repeat Protocols. Edited by: Y. Kohwi © Humana Press Inc., Totowa, NJ, pp.19-28.
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Mirkin, S.M. (2001) DNA topology: Fundamentals. In: Encylopedia of Life Sciences, London: Nature Publishing Group.
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Mirkin, S.M. (1999) Structure and biology of H DNA. In: Triple Helix Forming Oligonucleotides, Kluwer Academic Publishers (Norwell, MA) C. Malvy and A. Harel-Bellan eds., pp. 193-222.
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Articles:

Kim, J.C., Harris, S.T., Dinter. T., Shah, K.A., Mirkin S.M. (2017) The role of break-induced replication in large-scale expansions of (CAG)n/(CTG)n repeats. Nat Struct Mol Biol 24: 55-60.
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Aksenova, A.Y., Han, G., Shishkin, A.A., Volkov, K.V., Mirkin, S.M. (2015) Expansion of interstitial telomeric sequences in yeast. Cell Rep. 13: 1545-1551.
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Kim, J.C., Mirkin, S.M. (2015) Putting the Brakes on Huntington Disease in a Mouse Experimental Model. PLoS Genet. 11: e1005409.
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Pandey, S., Ogloblina, A.M., Belotserkovskii, B.P., Dolinnaya, N.G., Yakubovskaya, M.G., Mirkin, S.M., Hanawalt, P.C. (2015) Transcription blockage by stable H-DNA analogs in vitro. Nucleic Acids Res., in press
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Shah, K.A., Mirkin, S.M. (2015) The hidden side of unstable DNA repeats: Mutagenesis at a distance. DNA Repair 32: 106-112.
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Shah, K.A., McGinty, R.J., Egorova, V.I., Mirkin, S.M. (2014) Coupling transcriptional state to large-scale repeat expansions in yeast. Cell Rep. 9: 1594-1602.
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Mirkin, E.V., Mirkin, S.M. (2014) To switch or not to switch: at the origin of repeat expansion disease. Mol. Cell. 53: 1-3.
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Aksenova, A.Y., Greenwell, P.W., Dominska, M., Shishkin, A.A., Kim, J.C., Petes, T.D., Mirkin, S.M. (2013) Genome rearrangements caused by interstitial telomeric sequences in yeast. Proc Natl Acad Sci USA 110:19866-19871.
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Belotserkovskii, B.P., Mirkin, S.M., Hanawalt, P.C. (2013) DNA sequences that interfere with transcription: implications for genome function and stability. Chem. Rev. 113: 8620-8637.
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Kim, J.C, Mirkin, S.M. (2013) The balancing act of DNA repeat expansions. Curr. Opin. Genet. Dev. 23: 280-288.
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Mirkin, S.M. (2013) DNA replication: driving past four-stranded snags. Nature 497: 449-450.
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Belotserkovskii, B.P., Neil, A.J., Saleh, S.S., Shin, J.H., Mirkin, S.M., Hanawalt, P.C. (2013) Transcription blockage by homopurine DNA sequences: role of sequence composition and single-strand breaks. Nucleic Acids Res. 41: 1817-1828.
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Shah, K.A., Shishkin, A.A., Voineagu, I., Pavlov, Y.I., Shcherbakova, P.V., Mirkin, S.M. (2012) Role of DNA polymerases in repeat-mediated genome instability. Cell Rep. 2: 1088-1095.
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Zhang, Y., Shishkin, A.A., Nishida, Y., Marcinkowski-Desmond, D., Saini, N., Volkov, K.V., Mirkin, S.M., Lobachev, K.S. (2012) Genome-wide screen identifies pathways that govern GAA/TTC repeat fragility and expansions in dividing and nondividing yeast cells. Mol. Cell 48: 254-265.
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Chandok, G.S., Patel, M.P., Mirkin, S.M., Krasilnikova, M.M. (2012) Effects of Friedreich's ataxia GAA repeats on DNA replication in mammalian cells. Nucleic Acids Res. 40:3964-3974. [PDF]

Anand, R.P., Shah, K.A., Niu, H., Sung, P., Mirkin, S.M., Freudenreich, C.H. (2012) Overcoming natural replication barriers: differential helicase requirements. Nucleic Acids Res. 40:1091-1105. [PDF]

Cherng, N., Shishkin, A.A., Schlager, L.I., Tuck, R.H., Sloan, L., Matera, R., Sarkar, P.S., Ashizawa, T., Freudenreich, C.H., Mirkin, S.M. (2011) Expansions, contractions, and fragility of the spinocerebellar ataxia type 10 pentanucleotide repeat in yeast. Proc. Natl. Acad. Sci. USA 108: 2843-2848. [PDF]

Tang, W., Dominska, M., Greenwell, P.W., Harvanek, Z., Lobachev, K.S., Kim, H.M., Narayanan, V., Mirkin, S.M., Petes, T.D. (2011) Friedreich's ataxia (GAA)n•(TTC)n repeats strongly stimulate mitotic crossovers in Saccharomyces cerevisae. PLoS Genet. 7: e1001270. [PDF]

Belotserkovskii, B.P., Liu, R., Tornaletti, S., Krasilnikova, M.M., Mirkin, S.M., Hanawalt, P.C. (2010) Mechanims and implications of transcription blockage by guanine-rich DNA sequences. Proc. Natl. Acad. Sci. USA, 107,12816-12821. [PDF]

Mirkin, S.M. (2010) Getting to the core of repeat expansions by cell reprogramming. Cell Stem Cell 7: 545- 546. [PDF]

Shishkin, A.A., Voineagu, I., Matera, R., Cherng, N., Chernet, B.T., Krasilnikova, M.M., Narayanan, V., Lobachev, K.S., Mirkin, S.M. (2009) Large-scale expansions of Friedreich's ataxia GAA repeats in yeast. Mol Cell 35: 82-92. [PDF]

Voineagu, I., Freudenreich, C.F., Mirkin, S.M. (2009) Checkpoint Responses to Unusual Structures Formed by DNA Repeats. Mol. Carcinogen. 48: 309-318. [PDF]

Stamatoyannopoulos, J.A., Adzhubei, I., Thurman, R.E., Kryukov, G.V. Mirkin, S.M., Sunyaev, S.R. (2009) Time of human DNA replication predicts mutation rate. Nat. Genet., 41: 393-395. [PDF]

Voineagu, I., Surka, C.F., Shishkin, A.A., Krasilnikova, M.M., Mirkin, S.M. (2009) Replisome stalling and stabilization at CGG repeats, which are responsible for chromosomal fragility. Nat Struct Mol Biol 16: 226-228. [PDF]

Kim, H.M., Narayanan, V., Mieczkowski, P.A., Petes, T.D., Krasilnikova, M.M., Mirkin, S.M., Lobachev, K.S. (2008) Chromosome fragility at GAA tracts in yeast depends on repeat orientation and requires mismatch repair. EMBO J. 27: [PDF]

Voineagu, I., Narayanan V., Lobachev, K.S., Mirkin, S.M. (2008) Replication stalling at unstable inverted repeats: Interplay between DNA hairpins and fork stabilizing proteins. Proc. Natl. Acad. Sci. USA, 105: 9936-41. [PDF]

Mirkin S.M. (2008) Discovery of alternative DNA structures: a heroic decade (1979-1989). Front Biosci 13, 1064-1071. [PDF]

Mirkin S.M. (2007) Expandable DNA repeats and human disease. Nature 447, 932-940. [PDF]

Mirkin, E.V., Mirkin, S.M. (2007) Replication fork stalling and natural impediments. Microbiol Mol Biol Rev. 71, 13-35. [PDF]

Krasilnikova, M.M., Kireeva, M.L., Petrovic, V., Knijnikova, N., Kashlev, M., Mirkin, S.M. (2007) Effects of Friedreich’s ataxia (GAA)n.(TTC)n repeats on RNA synthesis and stability. Nucleic Acids Res. 35, 1075-1084. [PDF]

Mirkin, S.M. (2006) DNA structures, repeat expansions and human hereditary disorders. Curr. Opin. Struct. Biol. 16, 1-8. [PDF]

Mirkin, E. V., Castro Roa D., Nudler E., Mirkin, S.M. (2006) Transcription regulatory elements are punctuation marks for DNA replication. Proc. Natl. Acad. Sci. USA 103, 7276-7281. [PDF]

Mirkin, S.M. (2005) Toward a unified theory for repeat expansions. Nature Struct. Mol. Biol. 12, 635-637. [PDF]

Mirkin, E. V., Mirkin, S.M. (2005) Mechanisms of transcription-replication collisions in bacteria. Mol. Cell. Biol. 25, 888-895. [PDF]

Krasilnikova, M.M., Mirkin, S.M. (2004) Replication stalling at Friedreich's ataxia (GAA)n repeats in vivo. Mol. Cell. Biol. 24, 2286-2295. [PDF]

Mirkin, S.M. (2004) Molecular models for repeat expansions. Chemtracts - Biochem. Mol. Biol.17, 639-662. [PDF]

Bondar, T., Mirkin, E.V., Ucker, D.S., Walden, W.E., Mirkin, S.M., Raychaudhuri, P. (2003) S. pombe Ddb1 is functionally linked to the replication checkpoint pathway. J. Biol. Chem. 278, 37006-37014. [PDF]

Pelletier, R., Krasilnikova, M.M., Samadashwily, G.M., Lahue, R., Mirkin. S.M. (2003) Replication and expansion of trinucleotide repeats in yeast. Mol. Cell. Biol., 23, 1349-1357. [PDF]

Mirkin, S.M., Smirnova, E.V. (2002) Positioned to expand. Nature Genet., 31, 5-6. [PDF]

Mirkin, S.M. (2002) Thinking of R. B. Khesin. Mol. Biol. (Mosk.) 36, 347-360. [PDF]
[PDF in Russian]

Siyanova, E. Y., Mirkin, S.M. (2001) Expansion of trinucleotide repeats. Mol. Biol (Mosk.) 35, 168-182. [PDF]  [PDF in Russian]

Krasilnikova, M.M., Smirnova, E.V., Krasilnikov, A.S., Mirkin, S.M. (2001) A new trick for an old dog: TraY binding to a homopurine-homopyrimidine run attenuates replication. J. Mol. Biol. 313, 271-282. [PDF]

Raca, G, Siyanova, E.Y., McMurray, C.T., Mirkin, S.M. (2000) Expansion of the (CTG)n repeat in the 5'-UTR of a reporter gene impedes translation. Nucleic Acids Res. 28, 3943-3949. [PDF]

Krasilnikova, M.M., Samadashwily, G.M., Mirkin, S.M. (1999) Replication of simple DNA repeats. Gene Ther. Mol. Biol. 3, 397-412.

Krasilnikov, A.S., Podtelezhnikov, A., Vologodskii, A., Mirkin, S.M. (1999) Large-scale effects of transcriptional DNA supercoiling in vivo. J Mol. Biol. 292, 1149-1160. [PDF]

Krasilnikova, M.M., Samadashwily, G.M., Krasilnikov, A.S., Mirkin. S.M. (1998) Transcription through a simple DNA repeat blocks replication elongation. EMBO J., 17, 5095-5102. [PDF]

Samadashwily, G.M., Raca, G., Mirkin, S.M. (1997) Trinucleotide repeats affect DNA replication in vivo. Nature Genet., 17, 298-304. [PDF]

Mirkin, S.M. (1997) Everything you always wanted to know about triplexes (but were afraid to ask). J. Am. Chem. Soc. 119, 6692.

Cox, R., Mirkin, S.M. (1997) Characteristic enrichment of DNA repeats in different genomes. Proc. Natl. Acad. Sci. USA 94, 5237-5242. [PDF]

Krasilnikov, A.S., Panyutin, I.G., Samadashwily, G.M., Cox, R., Lazurkin, Yu.S., Mirkin, S.M. (1997) Mechanisms of triplex-caused polymerization arrest. Nucleic Acids Res. 25, 1339-1346. [PDF]

Frank-Kamenetskii, M.D., Mirkin, S.M. (1995) Triplex DNA structures. Annu. Rev. Biochem. 64, 65-95. [PDF]

Samadashwily, G.M., Mirkin, S.M. (1994) Trapping DNA polymerases using triplex-forming oligodeoxyribonucleotides. Gene 149, 127-136. [PDF]

Raghu G., Tevosian, S., Anant, S., Subramanian, K.N., George, D.L, Mirkin, S.M. (1994) Transcriptional activity of the homopurine-homopyrimidine repeat of the c-Ki-ras promoter is independent of its H-forming potential. Nucleic Acids Res. 22, 3271-3279. [PDF]

Mirkin, S.M., Frank-Kamenetskii, M.D. (1994) H-DNA and related structures. Annu. Rev. Biophys. Biomol. Struct. 23, 541-576. [PDF]

Samadashwily, G.M., Dayn, A., Mirkin, S.M. (1993) Suicidal nucleotide sequences for DNA polymerization. EMBO J. 12, 4975-4983. [PDF]

Dayn, A., Samadashwily, G.M., Mirkin, S.M. (1992) Intramolecular DNA triplexes: Novel sequence requirements and influence on DNA polymerization. Proc. Natl. Acad Sci. USA 89, 11406-11410. [PDF]

Dayn, A., Malkhosyan, S., Mirkin, S.M. (1992) Transcriptionally driven cruciform formation in vivo. Nucleic Acids Res. 20, 5991-5997. [PDF]

Pestov, D.G., Dayn, A., Siyanova, E.Yu., George, D.L., Mirkin, S.M. (1991) H-DNA and Z-DNA in the mouse c-Ki-ras promoter. Nucleic Acids Res. 19, 6527-6532. [PDF]

Dayn, A., Malkhosyan, S.R., Duzhii, D.I., Lyamichev, V.I., Panchenko, Y.A., Mirkin, S.M. (1991) Formation of (dA-dT)n cruciforms in Escherichia coli cells under different environmental conditions. J. Bacteriol. 173, 2658-2664. [PDF]