Nucleic Acid Structure Investigated by UV Resonance Raman Spectroscopy: Protonation Effects and A-Tract Structure

Abstract

UV resonance Raman (UVRR) spectroscopy has been used to investigate the three purine bases, adenine, guanine and inosine, as a function of pH. Excitation wavelengths of 260 and 210 nm were used to probe the in-plane ring stretching frequencies and the exocyclic functional groups, respectively. These studies are suggestive that tautomeric forms can be stabilized at low and high pH values and these forms can be identified using UVRR spectroscopy. At pH values ≤5.0, a band at 1693 cm −1 is observed in the UVRR spectra of dAMP, which is suggestive of the imino protonated tautomer. At pH values of 10.0 and above both dGMP and IMP show evidence for forming the enolate tautomer, by the loss in intensity of the C=O stretching mode at 1686 cm−1. The protonated forms of dGMP and dAMP exhibit distinct Raman bands at approximately 1460 and 1561 cm−1 and we suggest that these protonated states can be identified using UVRR spectroscopy. Most distinctively, the −NH2 scissors mode of dGMP and dAMP shifts up in frequency and increases in intensity as the pH is decreased. Interestingly, these features are also observed in a comparison of an A-tract containing dodecamer with a non A-tract dodecamer. In particular, a frequency upshift of the -NH2 scissors mode and a mode at 1466 cm−1 is observed. Because of the resonance enhancement and the similarities to the protonated dAMP spectrum, these features are attributed to the dA residues in the A-tract. It is suggested that these spectral features may be characteristic of ‘bent’ DNA.