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J. Biol. Chem., Vol. 277, Issue 42, 39228-39234, October 18, 2002
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From the Center for Genome Research, Institute of Biosciences and
Technology, Texas A&M University, Texas Medical Center,
Houston, Texas 77030-3303
The polypurine·polypyrimidine
sequence requirements for the formation of sticky DNA were evaluated in
Escherichia coli plasmid systems to determine the potential
occurrence of this conformation throughout biological systems. A mirror
repeat, dinucleotide tract of (GA·TC)37, which is
ubiquitous in eukaryotes, formed sticky DNA, but shorter sequences of
10 or 20 repeats were inert. (GGA·TCC)n inserts (where n = 126, 159, and 222 bp) also formed
sticky DNA. As shown previously, the control sequence
(GAA·TTC)150 (450 bp) readily adopted the X-shaped sticky
structure; however, this structure has never been found for the
nonpathogenic (GAAGGA·TCCTTC)65 of the same
approximate length (390 bp). A sequence that is replete with
polypurine·polypyrimidine tracts that can form triplexes and slipped
structures but lacks long repeating motifs (the 2.5-kbp intron 21 sequence from the polycystic kidney disease gene 1) 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. The stabilities of the triple base (Watson-Crick and
Hoogsteen) interactions in the DNA/DNA associated triplex region of the
sticky conformations account for these observations. Our results have
significant chemical and biological implications for the structure and
function of this unusual DNA conformation in Friedreich's ataxia.
To whom correspondence should be addressed: Center for Genome
Research, Institute of Biosciences and Technology, Texas A&M University, Texas Medical Center, 2121 W. Holcombe Blvd., Houston, TX
77030-3303. Tel.: 713-677-7651; Fax: 713-677-7689; E-mail: rwells@ibt.tamu.edu.
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