The structure of the guanine-rich polypurine:polypyrimidine sequence at the right end of the rat L1 (LINE) element.
We report here that the 64-base pair (bp) guanine-rich polypurine:polypyrimidine tract derived from the right end of the rat long interspersed DNA element is reactive in a supercoil-dependent manner with a variety of chemical probes of non-B DNA structure. At pH 5.0 in the presence of Mg2+, part of the sequence (position 10-40) forms the following two types of triplexes: a G.G.C triplex, and an unusual C.G.C triplex. The latter structure is much more prevalent than the former and is unusual in that the resultant free purine strand forms a hairpin loop. In the absence of Mg2+ the G.G.C triplex disappears and the amount of C.G.C triplex is diminished, and at pH 7.5 in the presence or absence of Mg2+, little or no triplex is observed. Deletion of the 24-bp region just 3' of the triplex-forming region greatly reduces the amount of triplex formed. In this region, which includes an 18-bp polypurine:polypyrimidine sequence, both strands exhibit a moderate symmetric reactivity with the chemical probes tested, independent of pH and Mg2+. The implications of this structurally complex region for the properties of the rat L1 element are discussed.
Section on Genomic Structure and Function, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892.
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D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D004278:DNA, Superhelical; D006147:Guanine; D007202:Indicators and Reagents; D008969:Molecular Sequence Data; D010957:Plasmids; D051381:Rats; D012091:Repetitive Sequences, Nucleic Acid
D004278:DNA, Superhelical; D007202:Indicators and Reagents; D006147:Guanine