Conformational flexibility in the right-handed and in the left-handed double helices of Na+-d(m5C-G-T-A-m5C-G) studied by IR spectroscopy

Abstract

The X ray diffraction study of a d(m5C-G-A-T-m5C-G) crystals has shown the existence of a 2 conformation while the Raman spectroscopy study of the same fragment in solution showed that then the oligonucleotide adopted a B geometry. Infrared spectroscopy has allowed us to study this sequence in films in a wide range of hydrations and to vary the water content of the sample at different rates. We have thus obtained four I.R. spectra, of the B and 2 conformations respectively at 100% and 98% relative humidities, of another 2 form with a different geometry of the phosphate groups at relative humidities below 98% and in addition a fourth spectrum recorded after a rapid dehydration of the sample which is then blocked in a right-handed form at low R.H. In this case the structure of the phosphodiester chain may be not uniform. The results are discussed by comparison with previously obtained I.R. spectra of poly d(G-C), poly d(A-C). d(G-T), d'm5C-G-A-m5C-G-T-G-C-G) d(m5C-G-C-G-m5C-G) and d(C-G-m5C-G).