Use of alternative alkali chlorides in RT and PCR of polynucleotides containing G quadruplex structures.

Several alkali chlorides were compared for their use in reverse transcription (RT) and PCR of different types of nucleic acid templates. On a test region of biological DNA incapable of forming G quadruplex (G4) structures, Taq DNA polymerase showed similar PCR performance with 50 mM KCl, CsCl, LiCl, and NaCl. In contrast, on a synthetic model polydeoxyribonucleotide prone to G4 formation, good PCR amplification was obtained with 50 mM CsCl, but little or none with LiCl or KCl. Similarly, in RT of a G4-prone model polyribonucleotide, MMLV reverse transcriptase produced a good yield with 50 mM CsCl, mediocre yields with LiCl or without added alkali chloride, and a poor yield with 50 mM KCl. The full RT-PCR assay starting from the G4-prone polyribonucleotide, showed good results with CsCl in both stages, poor results with LiCl, and no product formation with KCl. The model polynucleotides showed fast G quadruplex formation under PCR or RT conditions with 50 mM KCl, but not with CsCl or LiCl. The results argue for the use of CsCl instead of KCl for RT and PCR of G4-prone sequences. No advantage was observed when using the 7-deaza type nucleotide analog c7dGTP in PCR amplification of the G4-prone polydeoxyribonucleotide.

Intercalation of fac-[(4,4'-bpy)ReI(CO)3(dppz)]+, dppz = dipyridyl[3,2-a:2'3'-c]phenazine, in polynucleotides. On the UV-vis photophysics of the Re(I) intercalator and the redox reactions with pulse radiolysis-generated radicals.

The intercalation of fac-[(4,4'-bpy)Re(I)(CO)3(dppz)]+ (dppz = dipyridyl[3,2-a:2'3'-c]phenazine) in polynucleotides, poly[dAdT]2 and poly[dGdC]2, where A = adenine, G = guanine, C = cytosine and T = thymine, is a major cause of changes in the absorption and emission spectra of the complex. A strong complex-poly[dAdT]2 interaction drives the intercalation process, which has a binding constant, Kb approximately 1.8 x 10(5) M(-1). Pulse radiolysis was used for a study of the redox reactions of e(-)(aq), C*H(2)OH and N3* radicals with the intercalated complex. These radicals exhibited more affinity for the intercalated complex than for the bases. Ligand-radical complexes, fac-[(4,4'-bpy*)Re(I)(CO)3(dppz)] and fac-[(4,4'-bpy)Re(I)(CO)3(dppz *)], were produced by e(-)(aq) and C*H(2)OH, respectively. A Re(II) species, fac-[(4,4'-bpy)Re(II)(CO)3(dppz)](2+), was produced by N3* radicals. The rate of annihilation of the ligand-radical species was second order on the concentration of ligand-radical while the disappearance of the Re(II) complex induced the oxidative cleavage of the polynucleotide strand.