Hydrated water molecules of pyrimidine/purine/pyrimidine DNA triple helices as revealed by FT-IR spectroscopy: a role of cytosine methylation.

Hydrated water molecules of pyrimidine/purine/pyrimidine DNA hairpin tripler was studied by a comparison of tripler (CC . AG6) formed by a host oligodeoxypyrimidine of 5'-d(TC)(3)T-4(CT)(3) (CC) with a target hexadeoxypurine 5'-d(AG)(3) (AG6) strand and by triplexes (MM . AG6, MC . AG6, and CM . AG6) formed by oligonucleotides with the exact sequences as above except 5-methylcytosine replaced all (MM), 5' end half(MC), and 3' end half (CM) cytosine bases in CC via FT-IR spectroscopy in hydrated film. Results revealed that: (i) all these triplexes have a similar hydration pattern, in which water molecules probably bound in the N-7 sites of adenines and guanines in the Crick-Hoogsteen groove, and to the methyl group of thymidines in the Watson-Hoogsteen groove. There are also some bound water molecules found at the O-2 sites of thymines in both Watson-Crick and Crick-Hoogsteen grooves. (ii) In the CC AG6 tripler the S-type sugars are always dominant in all hydrated states, whereas in MM . AG6 tripler the relative population of the N-type sugars is very close to that of the S-type between 86% and 66% of humidity. Furthermore, the sugar conformation in two partially modified triplexes (CM . AG6, and MC . AG6) are dominant by the N-type at lower humidity. This phenomenon might reflect that the degree of bound water varies among the binding sites of bases. (iii) The effect of introducing a methyl group on cytosine is to generate a spine of hydrophobic region in MM (MC and MC). The enlarging hydrophobic area not only increase the stability in solution, and also the stability in sodium hydrated films of the pyrimidine/purine/pyrimidine hairpin triplexes.