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A more recent version of this article appeared on October 11, 2002
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M205210200v1
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Papers In Press, published online ahead of print August 2, 2002
J. Biol. Chem, 10.1074/jbc.M205210200
Submitted on May 28, 2002
Revised on July 31, 2002
Accepted on August 1, 2002

Sticky DNA: Effect of poly purine5pyrimidine (R5Y) sequence

Alexandre A. Vetcher, Marek Napierala, and Robert D. Wells

Center for Genome Research, Institute of Biosciences & Technology, Houston, TX 77030

Corresponding Author: rwells{at}ibt.tamu.edu

The poly R•Y sequence requirements for the formation of sticky DNA were evaluated in Escherichia coli plasmid systems. A mirror repeat, dinucleotide tract of (GA•TC)37 formed sticky DNA but shorter sequences of 20 or 40 bp were inert. (GGA•TCC) inserts of 126, 159, and 222 bp also formed sticky DNA but shorter repeats of 48 and 90 bp did not. As shown previously, the control sequence (GAA•TTC)150 (450 bp) readily adopted the X-shaped sticky structure; however, the non-pathogenic (GAAGGA•TCCTTC)65 of the same approximate length (390 bp) did not. The 2.5 Kbp intron 21 sequence from the polycystic kidney disease gene 1, which is replete with R•Y tracts that can form triplexes and slipped structures, was also inert. Interestingly, tracts of (GAA•TTC)n (where n=176 or 80) readily formed sticky DNA with (GAAGGA•TCCTTC)65 cloned into the same plasmid when the pair of inserts was in the direct, but not in the indirect (inverted), orientation. These results are explained on the basis of the stabilities of the triple-base interactions in the DNA:DNA associated triplex region of the sticky conformations. These data have significant chemical and biological implications for the structure and function of this unusual DNA conformation in Friedreich’s ataxia.


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