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

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.

Evidence against stabilization of the transition state oxyanion by a pKa-perturbed RNA base in the peptidyl transferase center

The crystal structure of the ribosomal 50S subunit from Haloarcula marismortui in complex with the transition state analog CCdA-phosphate-puromycin (CCdApPmn) led to a mechanistic proposal wherein the universally conversed A2451 in the ribosomal active site acts as an "oxyanion hole" to promote the peptidyl transferase reaction [Nissen, P., Hansen, J., Ban, N., Moore, P.B., and Steitz, T.A. (2000) Science 289, 920-929]. In the model, close proximity (3 A) between the A2451 N3 and the nonbridging phosphoramidate oxygen of CCdApPmn suggested that the carbonyl oxyanion formed during the tetrahedral transition state is stabilized by hydrogen bonding to the protonated A2451 N3, the pKa of which must be perturbed substantially. We characterize the contribution of the putative hydrogen bond between the N3 of A2451 and the nonbridging phosphoramidate oxygen by using chemical protection and peptidyl transfer inhibition assays. If this putative hydrogen bond makes a significant thermodynamic contribution, then CCdApPmn-binding affinity to the 50S ribosomal subunit should be strongly pH-dependent, with affinity increasing as the pH is lowered. We report that CCdApPmn binds 50S ribosomes with essentially equal affinity at all pH values between 5.0 and 8.5. These data argue against a mechanism for peptidyl transfer in which a residue with near neutral pKa stabilizes the transition-state oxyanion, at least to the extent that CCdApPmn accurately mimics the transition state.

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.