Role of loops in the guanine quadruplex formation by DNA/RNA hybrid analogs of G 4T 4G 4

Abstract

CD spectroscopy, gel electrophoresis and absorption-based thermal stability were used to analyze quadruplex formation of RNA and RNA/DNA hybrid analogs of the deoxyoligonucleotide G 4T 4G 4, which forms a well-characterized basket-type quadruplex. All RNA-containing dodecamers, g 4u 4g 4, G 4u 4G 4 and g 4T 4g 4 (RNA lower-case, DNA capital letters), formed parallel, namely tetramolecular quadruplexes in Na +-containing solutions. The u 4 loop forced DNA tetrads into the same conformation as adopted by g 4u 4g 4. In contrast, the T 4 loop destabilized the RNA tetrads. Potassium ions markedly stabilized parallel quadruplexes of RNA-containing analogs as well as their bimolecular folding. In the presence of K +, g 4T 4g 4 formed exclusively bimolecular quadruplexes of both parallel and antiparallel types as indicated by CD. Thus, the T 4 loop permits RNA strands to adopt an antiparallel arrangement. These findings may be useful for engineering particular quadruplex foldings in different quadruplex-forming sequences.