Simple model to account for the deoxy-versus ribodimer stacking quotient data. Estimation of apparent and intrinsic equilibrium quotients for intramolecular stacking association of purine deoxy- and ribodinucleoside monophosphates

Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment

We report the results of a series of 1-μs-long explicit-solvent molecular dynamics (MD) simulations performed to compare the free energies of stacking (ΔGstack) of all possible combinations of DNA and RNA nucleoside (NS) pairs and dinucleoside-monophosphates (DNMPs). For both NS pairs and DNMPs, we show that the computed stacking free energies are in reasonable qualitative agreement with experimental measurements and appear to provide the closest correspondence with experimental data yet found among computational studies; in all cases, however, the computed stacking free energies are too favorable relative to experimental data. Comparisons of NS-pair systems indicate that stacking interactions are very similar in RNA and DNA systems except when a thymine or uracil base is involved: the presence of a thymine base favors stacking by ∼0.3 kcal/mol relative to a uracil base. One exception is found in the self-stacking of cytidines, which are found to be significantly more favorable for the DNA form; an analysis of the rotational orientations sampled during stacking events suggests that this is likely to be due to more favorable sugar-sugar interactions in stacked complexes of deoxycytidines. Comparisons of the DNMP systems indicate that stacking interactions are more favorable in RNA than in DNA except, again, when thymine or uracil bases are involved. Finally, additional simulations performed using a previous generation of the AMBER force field-in which the description of glycosidic bond rotations was less than optimal-produce computed stacking free energies that are in poorer agreement with experimental data. Overall, the simulations provide a comprehensive view of stacking thermodynamics in NS pairs and in DNMPs as predicted by a state-of-the-art MD force field.

Acid-base and metal ion binding properties of guanylyl(3'-->5')guanosine (GpG-) and 2'-deoxyguanylyl(3'-->5')-2'-deoxyguanosine [d(GpG)-] in aqueous solution

The acidity constants of guanylyl(3'-->5')guanosine (GpG(-)) and 2'-deoxyguanylyl(3'-->5')-2'-deoxyguanosine [d(GpG)(-)] for the deprotonation of their (N1)H sites were measured by potentiometric pH titrations in aqueous solution (25 degrees C; I = 0.1 M, NaNO(3)). The same method was used for the determination of the stability constants of the 1:1 complexes formed between Mg(2+), Ni(2+), or Cd(2+) (= M(2+)) and (GG-H)(2-), and in the case of Mg(2+) also of (GG-2H)(3-), where GG(-) = GpG(-) or d(GpG)(-). The stability constants of the M(GG)(+) complexes were estimated. The acidity constants of the H(dGuo)(+) and dGuo species (dGuo = 2'-deoxyguanosine) and the stability constants of the corresponding M(dGuo)(2+) and M(dGuo-H)(+) complexes were also measured. Comparison of these and related data allows the conclusion that N7 of the 5'G unit in GG(-) is somewhat more basic than the one in the 3'G moiety; the same holds for the (N1)(-) sites. On the basis of comparisons with the stability constants measured for the dGuo complexes, it is concluded that M(2+) binding of the GG dinucleoside monophosphates occurs predominantly in a mono-site fashion, meaning that macrochelate formation is not very pronounced. Indeed, it was a surprise to find that the stabilities of the complexes of dGuo or (dGuo-H)(-) and the corresponding ones derived from GG(-) are so similar. Consequently, it is suggested that in the M(GG)(+) and M(GG-H) complexes the metal ion is mainly located at N7 of the 5'G unit since this is the more basic site allowing also an outer-sphere interaction with the C6 carbonyl oxygen and because this coordination mode is also favorable for an electrostatic interaction with the negatively charged phosphodiester bridge. It is further suggested that Mg(2+) binding (which is rather weak compared to that of Ni(2+) and Cd(2+)) occurs mainly in an outer-sphere mode, and on the basis of the so-called Stability Ruler it is concluded that the binding properties of Zn(2+) to the GG species are similar to those of Ni(2+) and Cd(2+).

N4-Methoxydeoxycytidine triphosphate is in the imino tautomeric form and substitutes for deoxythymidine triphosphate in primed poly d[A-T] synthesis with E. coli DNA polymerase I

N4- Methoxydeoxycytidine triphosphate ( mo4dCTP ) substitutes for dTTP in poly d[A-T] synthesis with E. coli DNA polymerase I (Pol I). In parallel experiments using as template-primer, poly d[G-C], no incorporation of [14C] mo4dC was detected. This indicates that this deoxy derivative acts as the imino tautomer, as previously found for the riboderivative . Nearest neighbor analysis of transcripts of poly d[A-T] containing mo4dC shows that the derivative substitutes for only one base. In replication, singlestranded mo4dC -containing polymers gave little misincorporation, including that of dATP which can hydrogen-bond to mo4dC in the imino form, if the methoxy group is anti to the N-3. It is therefore assumed that the methoxy group is constrained anti in a polymer such as d[A-T], but can be in the syn form in singlestranded polymers and not recognized by DNA polymerase. mo4dC destabilizes the poly d[A-T] helix, as indicated by a lowered and less cooperative melting. Steric factors such as adjacent base displacement were invoked for similar findings with the doublestranded r( U61 , mo4C39 ) X r(A).

Intramolecular stacking association and conformation properties of a 'cap' structure, m7G5'pppUm, and the related model compounds

The stacking equilibrium quotient of the m7G5'pppUm unit, which occurs as the 5'-terminal "cap" of certain eukaryotic mRNA's, was determined by temperature-dependent difference spectrophotometry as Kstack = 1.82 at 25 degrees and pH 5. In order to evaluate the contribution of different structural modifications to the net stabilization of the cap structures of mRNA, a variety of compounds related to m7G5'pppUm were synthesized and their stacking properties were studied by the same method and compared. The results are summarized as: (1) Introduction of a methyl group into N-7 of G residue results in an increase in base stacking. (2) Methylation at 2'-OH of U residue also stabilizes the stacked structure of G-containing dimers, but it does not influence stacking interaction in m7G-containing dimers. (3) The effect of different types of internucleotide linkages on the order of stacking tendencies is: N5'ppN' greater than N5'pppN' greater than NpN'. UV hypochromicity and CD spectral measurements of the relevant dimers were also conducted, and the hypochromicity values and CD spectra of dimers in their stacked conformation were estimated by making use of the determined Kstack values. The results indicate that, while 2'-O-methylation exerts very little effect on the stacked conformation of the dimers, methylation at N-7 and the nature of the internucleotide linkage strongly influence the stacked conformation, thereby forming unusual left-handed conformations in m7G5'pppU(m), m7G5'ppU(m), and G5'ppU(m).