Raman pH profiles for nucleic acid constituents I. Cytidine and uridine ribonucleosides

Robust IR-based detection of stable and fractionally populated G-C+ and A-T Hoogsteen base pairs in duplex DNA

Noncanonical G-C+ and A-T Hoogsteen base pairs can form in duplex DNA and play roles in recognition, damage repair, and replication. Identifying Hoogsteen base pairs in DNA duplexes remains challenging due to difficulties in resolving syn versus antipurine bases with X-ray crystallography; and size limitations and line broadening can make them difficult to characterize by NMR spectroscopy. Here, we show how infrared (IR) spectroscopy can identify G-C+ and A-T Hoogsteen base pairs in duplex DNA across a range of different structural contexts. The utility of IR-based detection of Hoogsteen base pairs is demonstrated by characterizing the first example of adjacent A-T and G-C+ Hoogsteen base pairs in a DNA duplex where severe broadening complicates detection with NMR.

Structures, ionization equilibria, and tautomerism of 6-oxopurines in solution

6-Oxopurine and its analogues form an important class of biological molecules that include nucleobases and their precursors and are substrates of a wide range of enzymes. Solution structures of purines have been debated in the literature because of the many possible tautomers and protonation states in which they can exist in solution. Substitutions on the pyrimidine and imidazole rings alter tautomerization and protonation equilibria, and as a consequence, the solution compositions and structures of closely related analogues can be significantly different. We have obtained resonance Raman spectra of 6-oxopurines: hypoxanthine, xanthine, their riboside phosphates, guanine monophosphate in the protonated and deprotonated forms with UV excitation at 260 nm. The species present in solution under different pH conditions were identified by isotopic labeling with deuterium as well as by comparison with extensive density functional theoretical calculations. At physiological pH, while N7H and N9H tautomeric forms of hypoxanthine exist in equilibrium, in xanthine, the additional carbonyl group at C2 shifts the equilibrium in favor of the N7H tautomer. The corresponding nucleotide of xanthine, xanthosine monophosphate, on the other hand, is in the anionic form (pK(a) 5.5). We find that Raman spectra show systematic shifts with change in the protonation state and substitution on the ring. In general, deprotonation of the neutral molecule is marked by a downshift in the observed Raman wavenumbers, and protonation is accompanied by an upshift.

The pH-dependent structure of calf thymus DNA studied by Raman spectroscopy

The pH-dependent structure of calf thymus DNA is analyzed using Raman spectroscopy. The Raman spectra in the acidic region demonstrate that denaturation occurs in several steps. The binding of H+ to adenine and cytosine residues is accompanied by a decrease in the percentage of DNA in the B-conformation and a concurrent increase in a conformation most probably related to the C-form. The denaturation of DNA is observed at pH 3.3 and parallels the protonation of guanine bases. The Raman spectra of calf thymus DNA in the basic region (above pH 10) show that guanine residues are deprotonated at lower pH value than are thymine residues. In addition, Raman spectra in the basic region detect conformational changes of the phosphate backbone different from those found in the acidic region.

Laser raman spectroscopy of a complementary base pair in the Hoogsteen configuration

Cocrystallization of m9Ade and m1Thy from water yielded crystals of te Hoogsteen base pair, m9Ade x m1Thy, as demonstrated by X-ray diffraction data. The Raman spectrum of the Hoogsteen base pair in the crystalline state was obtained and compared to the crystals of the individual monomers. Frequency changes between the heterobase dimer and both m9Ade and m1Thy are indicative of the base pairing interaction. Utilizing previously reported vibrational analyses for m9Ade, the frequency changes are clearly associated with modes involving the internal coordinates most sensitive to a Hoogsteen hydrogen bonding interaction. The spectrum of an equimolar mixture of e9Ade and ch1Ura in CHCl3 was also compared to the spectrum of the separate monomers in solution. The numerous frequency shifts and band intensity changes observed in the mixture from that of the individual monomers suggest a cyclic dimer is formed although the nature of the base pairing interaction is not clear.

Raman ph profiles for nucleic acid constituents. II. 5'-AMP and 5'-GMP ribonucleotides

Raman spectra of aqueous solutions of 5'-AMP and 5'-GMP have been recorded as a function of pH. Band intensities and frequencies have been monitored to determine bands which may be considered as diagnostic for the concentration and the pK of the solution species. Quantitative band intensity measurements indicate only a selected number of bands can be considered as diagnostic of the base or the secondary phosphate proton dissociation. The utility of the pH profiles derived from specific band intensity variations for 5'-AMP is discussed in terms of the effect of acidification on solution characteristics of polyadenylic acid.