Book of Abstracts: Albany 2003

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Conversation 13
Abstract Book
June 17-21 2003

Intramolecular Py·Pu·Py Triplex in the (GAA)n·(TTC)n Repeats Flanked by the Human Genomic Sequences is Stable at Neutral pH

More than 15 human genetic diseases have been associated with the expansion of DNA repeats, presumably via the formation of non-duplex DNA structures. Biological processes that require temporary strand separation may lead to the slipped-strand nucleation of the duplex DNA within the GC-rich trinucleotide repeats thereby triggering events that result in the changes of repeat length. Such a mechanism is not possible for the AT-rich (GAA)n·(TTC)n repeats because the correct reassociation of separated strands starts in the more GC-rich flanking sequences. Using two-dimensional agarose gels, chemical probing and atomic force microscopy, we studied the structural properties of (GAA)n·(TTC)n repeats that were cloned together with their flanking genomic sequences into supercoiled plasmids. At the normal genomic length of the repeats (n=9) our data are consistent with the formation of a very stable protonated Py·Pu·Py intramolecular triplex (H-DNA). Its stability at pH 7.4 is likely due to the high proportion of the T·A·T triads which form within the repeats as well as in the flanking AT-rich sequences. At increasing repeat lengths (n=23, 42) and higher supercoiling, the formation of a single H-DNA structure becomes less favorable and the experimental data are more consistent with the formation of a bi-triplex structure.

V. N. Potaman1,*
E. A. Oussatcheva1
Y. L. Lyubchenko2,3
L. S. Shlyakhtenko3
R. R. Sinden1

1Institute of Biosciences and Technology
Texas A&M University Health Sciences Center
2121 W. Holcombe
Houston, TX 77030
Departments of
Arizona State University
Tempe, AZ 85287
*Phone: (713) 677-7675
Fax: (713) 677-7689