Role of loops in the guanine quadruplex formation by DNA/RNA hybrid analogs of G4T4G4

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 G4T4G4, which forms a well-characterized basket-type quadruplex. All RNA-containing dodecamers, g4u4g4, G4u4G4 and g4T4g4 (RNA lower-case, DNA capital letters), formed parallel, namely tetramolecular quadruplexes in Na+-containing solutions. The u4 loop forced DNA tetrads into the same conformation as adopted by g4u4g4. In contrast, the T4 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+, g4T4g4 formed exclusively bimolecular quadruplexes of both parallel and antiparallel types as indicated by CD. Thus, the T4 loop permits RNA strands to adopt an antiparallel arrangement. These findings may be useful for engineering particular quadruplex foldings in different quadruplex-forming sequences.