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Replication and expansion of simple DNA repeats.
Uncontrollable expansions of trinucleotide repeats lead
to more than a dozen human neurological disorders, including
Fragile X mental retardation, Huntington’s disease,
myotonic dystrophy, and Friedreich’s ataxia. It has
been hypothesized that these expansions are caused by
replication errors. Using model bacterial and yeast
experimental systems, we have obtained the first direct
evidence that the replication fork progression through
various repeated runs is indeed abnormal. Further, the
frequency of the expansion of repeats in those systems
is drastically affected by mutations in the replication
apparatus. We are currently extending these observations
into mammalian cell systems. Our working hypothesis
is that the replication fork stalls at a trinucleotide
repeat due to the formation of a very stable secondary
structure in a lagging strand template. Extra copies
of repeats are then added when the replication fork
tries to bypass this roadblock.
(2) Transcriptionally-dependent rearrangements in DNA.
The relationship between RNA polymerase and the DNA
template is a two-way avenue. Transcription is believed
to change DNA structure both upstream and downstream
of the promoter. At the same time, both initiation and
elongation of transcription dramatically depend on the
structure of a DNA template. We concentrate on several
specific aspects of these relations in living cells.
They include transcription-induced DNA supercoiling,
the domain structure of transcribed DNAs, the formation
of unusual DNA structures within and near transcription
units, and the instability of repeated DNA mediated
by transcription. We also study the influence of transcriptionally
driven changes in DNA on genetic recombination.
(3) Triplex DNA structures. Since our discovery
of three-stranded H-DNA more than a decade ago, triplex
DNA has attracted very broad attention from a structural
viewpoint, as a potential regulator of genetic processes
and as a promising therapeutic. We have found that DNA
triplexes present a steady barrier for different DNA
and RNA polymerases, and we are studying the mechanisms
of this phenomenon. Considerable efforts are also being
devoted to detecting DNA triplexes inside living cells
and elucidating their biological roles.
Selected Publications:
Pelletier,
R., Krasilnikova, M.M., Samadashwily, G.M., Lahue, R.,
Mirkin. SM. (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)
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)
Siyanova,
E.Y., Mirkin, S.M. (2001) Expansion of trinucleotide
repeats. Mol. Biol. 35, 168-182. (pdf)
Mirkin,
S.M. (2001) DNA topology: fundamentals. In: Encyclopedia
of Life Sciences, Macmillan Publishers Ltd.
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)
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)
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.
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., and Mirkin, S.M. (1997). Trinucleotide
repeats affect DNA replication in vivo. Nature Genet. 17, 298-304.
Cox, R., Mirkin, S.M. (1997) Characteristic enrichment of DNA
repeats in different genomes. Proc. Natl. Acad. Sci. USA 94, 5237-5242. (pdf)
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