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.
Usdin
K
K
Section on Genomic Structure and Function, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892.
Furano
A V
AV
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