Nucleotides: Rigid or flexible?

Contribution of the intrinsic mechanical energy of the phosphodiester linkage to the relative stability of the A, BI, and BII forms of duplex DNA

Canonical forms of duplex DNA are known to sample well-defined regions of the alpha, beta, gamma, epsilon, and zeta dihedral angles that define the conformation of the phosphodiester linkage in the backbone of oligonucleotides. While extensive studies of base composition and base sequence dependent effects on the sampling of the A, B1, and BII canonical forms of duplex DNA have been presented, our understanding of the intrinsic contribution of the five dihedral degrees of freedom associated with the phosphodiester linkage to the conformational properties of duplex DNA is still limited. To better understand this contribution, ab initio quantum mechanical (QM) calculations were performed on a model compound representative of the phosphodiester backbone to systematically sample the energetics about the alpha, beta, gamma, epsilon, and zeta dihedral angles relevant to the conformational properties of duplex DNA. Low-energy regions of dihedral potential energy surfaces are shown to correlate with the regions of dihedral space sampled in experimental crystal structures of the canonical forms of DNA, validating the utility of the model compound and emphasizing the contribution of the intrinsic mechanical properties of the phosphodiester backbone to the conformational properties of duplex DNA. Those contributions include the relative stability of the A, BI, and BII conformations of duplex DNA, where the gas-phase energetics favor the BI form over the A and BII forms. In addition, subtle features of the potential energy surfaces mimic changes in the probability distributions of alpha, beta, gamma, epsilon, and zeta dihedral angles in A, BI, and BII forms of DNA as well as with conformations sampled in single-stranded DNA. These results show that the intrinsic mechanical properties of the phosphodiester backbone make a significant contribution to conformational properties of duplex DNA observed in the condensed phase and allow for the prediction that single-stranded DNA primarily samples folded conformations thereby possibly lowering the entropic barrier to the formation of duplex DNA.

Ab initio conformational analysis of nucleic acid components: intrinsic energetic contributions to nucleic acid structure and dynamics

In recent years, the use of high-level ab initio calculations has allowed for the intrinsic conformational properties of nucleic acid building blocks to be revisited. This has provided new insights into the intrinsic conformational energetics of these compounds and its relationship to nucleic acids structure and dynamics. In this article we review recent developments and present new results. New data include comparison of various levels of theory on conformational properties of nucleic acid building blocks, calculations on the abasic sugar, known to occur in vivo in DNA, on the TA conformation of DNA observed in the complex with the TATA box binding protein, and on inosine. Tests of the Hartree-Fock (HF), second-order Møller-Plesset (MP2), and Density Functional Theory/Becke3, Lee, Yang and Par (DFT/B3LYP) levels of theory show the overall shape of backbone torsional energy profiles (for gamma, epsilon, and chi) to be similar for the different levels, though some systematic differences are identified between the MP2 and DFT/B3LYP profiles. The east pseudorotation energy barrier in deoxyribonucleosides is also sensitive to the level of theory, with the HF and DFT/B3LYP east barriers being significantly lower (approximately 2.5 kcal/mol) than the MP2 counterpart (approximately 4.0 kcal/mol). Additional calculations at various levels of theory suggest that the east barrier in deoxyribonucleosides is between 3.0 and 4.0 kcal/mol. In the abasic sugar, the west pseudorotation energy barrier is found to be slightly lower than the east barrier and the south pucker is favored more than in standard nucleosides. Results on the TA conformation suggest that, at the nucleoside level, this conformation is significantly destabilized relative to the global energy minimum, or relative to the A- and B-DNA conformations. Deoxyribocytosine would destabilize the TA conformation more than other bases relative to the A-DNA conformation, but not relative to the B-DNA conformation.

Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study

The glycosyl torsion (chi) in nucleic acids has long been recognized to be a major determinant of their conformational properties. chi torsional energetics were systematically mapped in deoxyribonucleosides using high-level quantum mechanical methods, for north and south sugar puckers and with gamma in the g(+) and trans conformations. In all cases, the syn conformation is found higher in energy than the anti. When gamma is changed from g(+) to trans, the anti orientation of the base is strongly destabilized, and the energy difference and barrier between anti and syn are significantly decreased. The barrier between anti and syn in deoxyribonucleosides is found to be less than 10 kcal/mol and tends to be lower with purines than with pyrimidines. With gamma = g(+)/chi = anti, a south sugar yields a significantly broader energy well than a north sugar with no energy barrier between chi values typical of A or B DNA. Contrary to the prevailing view, the syn orientation is not more stable with south puckers than with north puckers. The syn conformation is significantly more energetically accessible with guanine than with adenine in 5-nucleotides but not in nucleosides. Analysis of nucleic acid crystal structures shows that gamma = trans/chi = anti is a minor but not negligible conformation. Overall, chi appears to be a very malleable structural parameter with the experimental chi distributions reflecting, to a large extent, the associated intrinsic torsional energetics.

Comparative conformations of uridine and pseudouridine and their derivatives

Stimulated by the suggestion that pseudouridine psi-39 in yeast tRNAPhe could be in a syn conformation [R. E. Hurd and B. R. Reid (1977) Nucleic Acid Research 4, 2747-2755], we have made a comparative study of the solution conformations of psi and U derivatives, using the proton-proton Overhauser effect. Rotation around the glycosidic bond is observed for pseudouridine and 3 psi MP as well as for uridine and 3'UMP. However pseudouridine an 3 psi MP are mostly syn, whereas uridine, 3'-UMP and 5'UMP are mostly anti. There is no evidence for a correlation between sugar conformation and orientation around the glycosidic bond. The results are confirmed by relaxation measurements. They are discussed in the light of earlier studies. They tend to support the suggestion of Hurd and Reid. They raise the question of the orientation of the pseudouridine found elsewhere in tRNA (e.g. in the T psi C loop).

Conformational analysis of nucleoside and nucleotide antibiotics prossessing five-membered base rings. A comparison of the glycosyl barrier for purine, pyrimidine and imidazole rings

The preferred conformations of the nucleosides comprising five-membered base rings viz., ribavirin, tetrazole, showdomycin and pyrazomycin and their 5'-nucleoside monophosphates have been explored by semiempirical potential energy calculations. The nature of the substituents on the five-membered base ring has been found to influence significantly the favoured glycosyl conformation and the hydrogen bonding between the base and the sugar. In the absence of any such hydrogen bonding, the imidazole nucleosides expectedly exhibit nearly 'free' rotation around the glycosyl bond for the commonly found C(3') endo and C(2') endo sugar ring conformations, thus increasing the probability of anti in equilibrium high-anti in equilibrium syn conformational interconversions as compared to common purine and pyrimidine nucleosides. However, the C(2') exo pucker imparts a high-energy barrier to glycosyl rotation, locking the base in the high-anti region. The conformation behaviour is significantly modified in the nucleoside 5'-monophosphates. The additional attractive interactions between the carboxamide and the phosphate groups favour the syn glycosyl conformation in the 5'-monophosphates of ribavirin as well as pyrazomycin smaller to guanosine 5'-monophosphate whereas the anti conformation is strongly favoured for the 5'-nucleotides of tetrazole and showdomycin similar to other common purine and pyrimidine nucleotides. The conformational properties of five-membered base ring nucleosides have a strong resemblance to purine nucleosides. Molecular modelling studies reveal that only the anti or high anti-glycosyl conformations of ribavirin can mimic the inosine base. It is suggested that experiments on the configurational isomers of ribavirin, viz., aravirin and cycloaravirin would conclusively establish the conformational specificity and biological function of ribavirin and analogues.

Nuclear-magnetic-resonance studies of 5'-ribonucleotide and 5'-deoxyribonucleotide conformations in solution using the lanthanide probe method

The conformations of the metal-bound 5'-ribonucleotides and 5'-deoxyribonucleotides in aqueous solution at different pH values have been studied using the lanthanide probe method. The conformational analysis, based on mixing different conformations in fast exchange within the nuclear magnetic resonance time scale, agrees well with the results from coupling constants, nuclear Over-hauser effects and spin-lattice relaxation times, obtained for the metal-fixed systems. The equilibrium between the two basic conformational combinations for the 5'-nucleotides, anti-(N in equalibrium S)-gg-g'g' and syn-(N in equalibrium S)-gt-g'g' depends on the nature of the furanose ring, the base and also on the state of base protonation and phosphate ionization. The effect of base protonation is particularly strong for the guanine nucleotides.

Nucleotide rigidity

It is show that in aqueous solution the backbone conformation of adenosine is as much flexible as that of 3'-AMP, 5'-AMP and 3', 5'-ADP indicating that nucleotides are not any more rigid than nucleosides. The flexible conformation of the monomeric components is conserved in the nucleotidyl units of destacked ApA, ApApA and poly(A), but it is not conserved in base stacked conditions. The findings are extended to guanosine, uridine and cytidine systems. It is projected that in aqueous solution, conformations of the individual nucleotidyl units of yeast tRNAhe are confined to the classically stable domains in the base stacked region and non-rigid flexible structures populate in the unstacked region comprising D16, D17, G20, U47 and A76.

Proton magnetic resonance study of the intramolecular association and conformation of the alpha and beta pyridine mononucleotides and nucleosides

The chemical shifts and coupling constants are reported for the proton nuclear magnetic resonance (NMR) spectra of the alpha and beta anomers of the oxidized and reduced pyridine mononucleotides and nucleosides. The pseudorotational conformational analyses of the ribose coupling constants indicate that the ribose conformation for beta-nicotinamide mononucleotide, beta NMN, can best be described by a 3:1 mixture of interconverting 3'-exo (S) and 2'-exo (N) conformers. Reduction of betaNMN to betaNMNH results in phase angles consistent with interconverting 2'-endo (S) and 3'-endo (N) conformers without changes in the conformer populations. Cleavage of the 5'-phosphate from betaNMN has a significant effect on the phase angles (becoming more like those for betaNMNH), conformer population (the N and S conformers become nearly equal), and the distribution of the rotational isomers around the ribose 4'-5' bond to the exocyclic methylene (the gauche-gauche population decreases by about 25%). In contrast, for betaNMNH these parameters are all insensitive to dephosphorylation. The pseudorotational analysis has been extended to define the conformational parameters of alpha nucleotides. Analysis of the coupling constants for the alpha anomers indicates that the phase angles, conformer populations, and rotational isomers are generally insensitive to dephosphorylation, whereas both the phase angle and conformer populations are strongly dependent on the redox state of the base, alphaNMN being predominantly 2'-endo and alphaNMNH exclusively 2'-exo. The rotational isomers around the 4'-5' and 5'- O bonds are found to be insensitive to.the large changes in ribose conformation in the absence of any interaction with the base. The results are discussed in terms of relative contributions from base-ribose, ribose-side chain, and base-side chain interactions to the general conformational restraints imposed by the cis-2'-3'-hydroxyl interaction in beta nucleotides and the additional cis-2'-hydroxyl-base interaction in alpha nucleotides. The significance of these interactions with respect to the enzymatic and nonenzymatic properties of the pyridine nucleotides is also considered.

A proton-relaxation-time study of the conformation of some purine and pyrimidine 5'-nucleotides in aqueous solution

The measurement of proton relaxation time T1 in a series of purine and pyrimidine 5'-nucleotides has been carried out to investigate their conformation in dilute neutral aqueous solutions. The interpretation of relaxation data has been performed with the help of computer calculations taking into account the different conformers of the ribose ring and of the exocyclic group. It has been found that all nucleotides under study show nearly the same preferential orientations of the base defined by gamma0 = 70 degrees +/- 10 degrees in the syn range. A more elaborate treatment, using an angular distribution derived from calculated potentials on 5" -GMP gives theoretical relaxation times in close agreement with experimental ones.

Conformational energy calculations for dinucleotide molecules. A study of the component mononucleotide adenosine 3'-monophosphate

Semi-empirical conformational energy calculations were performed for the mononucleotides 5'-AMP, NMN+ and 3'-AMP. Only intramolecular forces are considered. Essentially all conformational states were explored to investigate the population distribution likely to be found in a non-crystalline environment. The calculations suggest that 5'-AMP and 3'-AMP are relatively flexible and a mixture of conformational states is expected. In contrast, the results for NMN+ suggest that a strong electrostatic interaction between the positively charged nicotinamide nitrogen atom and negatively charged phosphate oxygen is possible, stabilizing a few specific states. This interaction will be most significant in a solvent-free situation or an apolar environment.