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Albany 2001

category image Biomolecular
Stereodynamics
SUNY at Albany
June 19-23, 2001

Slipped-strand DNA in trinucleotide repeat sequences may be stabilized by inter-loop interactions.

Misalignment in directly repeated DNA sequences (micro- and minisatellites) results in a slipped-strand structure (S-DNA) that has been suggested to mediate satellite instability. A recent example is the length expansion of trinucleotide repeats (TNR) leading to several human diseases. Although double-stranded DNA can locally melt between the two loop-outs to allow S-DNA re-annealing into a fully double-stranded form, the current data indicate a significant stability of S-DNA. We have designed experimental models for S-DNA where looped-out TNR are separated by 30 bp of non-repeating sequence. The molecular shapes implied from polyacrylamide gel migration are different for S-DNA models in which the inter-loop base pairing is and is not possible. Chemical probing shows that the central bases in a single 23 TNR loop are unpaired, but they become base paired when a complementary loop can make the inter-loop contacts. Atomic force microscopy images show different molecular shapes for S-DNA models that may or may not have inter-loop base pairing. We suggest that tertiary interactions involving base pairing between complementary loops of the slipped-out strands may stabilize S-DNA and prevent its re-arrangement into a perfect duplex.

V.N.Potaman (1)*, E.A.Oussatcheva (1), L.S.Shlyakhtenko (2), Y.L.Lyubchenko (2), and R.R.Sinden (1).

Institute of Biosciences and Technology (1), Texas A&M University Health Science Center, 2121 W. Holcombe, Houston, TX 77030; Department of Microbiology (2), Arizona State University, Tempe, AZ 85287
Phone: 713-677-7675; Fax: 713-677-7689; E-mail: vpotaman@ibt.tamu.edu