作者: Gautam Prakash , Eric T. Kool
DOI: 10.1021/JA00035A056
关键词: Oligonucleotide 、 DNA binding site 、 Base pair 、 Sequence (biology) 、 Molecular biology 、 Ligand (biochemistry) 、 Crystallography 、 Chemistry 、 DNA 、 DNA clamp 、 HMG-box
摘要: It was recently reported that certain pyrimidine-rich circular DNA oligomers can bind strongly and specifically to purine-rich or RNA strands by forming bimolecular triple helical complexes.1-3 In this study are investigated the effects of structural variations on strength binding for new class nucleotide-binding ligand. The number loop nucleotides (nt) which is optimum bridging two domains a circle examined. Comparing sizes 3, 4, 5, 6, 10 nt, in found be five sequences studied. order test method construction ability these compounds sites varied length, we attempted synthesize circles size. Circles over size range 24-46 nt were successfully constructed. Varying target site length shows four, eight, twelve, eighteen complexed circles, with melting temperatures (Tm) 17° >33 °C higher at pH 7.0 than corresponding Watson-Crick duplexes same length. Also studied effect covalently closed structure comparison linear having sequence; it shown has considerably affinity do three different "nicked" (linear oligomers) contain bases. high affinities thus attributed entropic benefit preorganization. Finally, such complementary within longer oligomers, ends must pass beyond loops circle, confirmed studies synthetic 36 bases