Thermodynamic and structural properties of r(ACC) as revealed by ultraviolet electronic absorption, circular dichroism, 1H-NMR spectroscopy and Monte Carlo simulations

Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopy

We rank the reactivity of the adenyl residues (A) of model DNA and RNA molecules with electropositive subnano size [Ag]n+ sites as a function of nucleic acid primary sequences and secondary structures and in the presence of biological amounts of Cl- and Na+ or Mg2+ ions. In these conditions A is markedly more reactive than any other nucleic acid bases. A reactivity is higher in ribo (r) than in deoxyribo (d) species [pA>pdA and (pA)n>>(pdA)n]. Base pairing decreases A reactivity in corresponding duplexes but much less in r than in d. In linear single and paired dCAG or dGAC loci, base stacking inhibits A reactivity even if A is bulged or mispaired (A.A). dA tracts are highly reactive only when dilution prevents self-association and duplex structures. In d hairpins the solvent-exposed A residues are reactive in CAG and GAC triloops and even more in ATC loops. Among the eight rG1N2R3A4 loops, those bearing a single A (A4) are the least reactive. The solvent-exposed A2 is reactive, but synergistic structural transitions make the initially stacked A residues of any rGNAA loop much more reactive. Mg2+ cross-bridging single strands via phosphates may screen A reactivity. In contrast d duplexes cross-bridging enables "A flipping" much more in rA.U pairs than in dA.T. Mg2+ promotes A reactivity in unpaired strands. For hairpins Mg2+ binding stabilizes the stems, but according to A position in the loops, A reactivity may be abolished, reduced, or enhanced. It is emphasized that not only accessibility but also local flexibility, concerted docking, and cation and anion binding control A reactivity.

Conformational flexibility of two RNA trimers explored by computational tools and database search

Two RNA sequences, AAA and AUG, were studied by the conformational search program CICADA and by molecular dynamics (MD) in the framework of the AMBER force field, and also via thorough PDB database search. CICADA was used to provide detailed information about conformers and conformational interconversions on the energy surfaces of the above molecules. Several conformational families were found for both sequences. Analysis of the results shows differences, especially between the energy of the single families, and also in flexibility and concerted conformational movement. Therefore, several MD trajectories (altogether 16 ns) were run to obtain more details about both the stability of conformers belonging to different conformational families and about the dynamics of the two systems. Results show that the trajectories strongly depend on the starting structure. When the MD start from the global minimum found by CICADA, they provide a stable run, while MD starting from another conformational family generates a trajectory where several different conformational families are visited. The results obtained by theoretical methods are compared with the thorough database search data. It is concluded that all except for the highest energy conformational families found in theoretical result also appear in experimental data. Registry numbers: adenylyl-(3' --> 5')-adenylyl-(3' --> 5')-adenosine [917-44-2] adenylyl-(3' --> 5')-uridylyl-(3' --> 5')-guanosine [3494-35-7].

Differences in conformational behavior of ATA and TAT sequences in single strand DNA trimer

The conformational behavior of single strand (ss) TAT and ATA trimers of DNA have been studied by computational chemistry tools including CICADA software interfaced with AMBER molecular mechanics and dynamics. The Single-Coordinate-Driving (SCD) method has been used in conjunction with molecular dynamics simulated annealing. It has been revealed that the conformational flexibility of each sequence differs substantially from the other one. Four common conformational families have been found for both trimers. These are: helical, reverse-stacked (base 3), half-stacked (base 3), reverse-stacked (base 1). However, the energies of conformers representing the families are different for both the studied systems. An additional conformational family, bulged, has been found for ss(ATA), while ss(TAT) has been found also in half-stacked (base 1) conformation. In general, ss(TAT) exhibits a higher number of low energy conformations while ss(ATA) shows one interesting low energy conformational interconversion between reverse-stacked (A3) family and half-stacked (A3) family. The high conformational variability of the trimers has been confirmed by flexibility analysis and by molecular dynamics simulations, which have also shown the conformational stability of single conformational families. It has been concluded that the methodology used is able to provide a very detailed picture of the conformational space of these molecules.

Structural features of the UCCG and UGCG tetraloops in very short hairpins as evidenced by optical spectroscopy

Structures of the UCCG and UGCG tetraloops formed in octamer ribonucleotidic hairpin sequences, i.e., 5'-r[GC(UCCG)GC]-3' and 5'-r[GC(UGCG)GC]-3', have been studied in aqueous solution by methods of optical spectroscopy. UV absorption melting profiles of these short hairpins, containing only two closing GC base pairs in the stem, are consistent with a monophasic, completely reversible order-to-disorder transition and clearly confirm their unusual structural stability (with Tm congruent with 50 degrees C). To establish structural characteristics of these tetraloops, Raman and FTIR spectroscopies have been used and vibrational conformation markers arising from the phosphate backbone and various nucleosides have been analyzed. They have been assigned on the basis of known unambiguous vibrational markers established for DNA and RNA chains. Surprisingly, they are easily transferable to short oligonucleotidic sequences. Intensities and wavenumbers of these conformation markers have been monitored in the 0-70 degrees C temperature range, i.e., in going from an ordered to a disordered structure. The main structural features of the UCCG and UGCG tetraloops are similar to those previously found in the UUCG and UACG tetraloops by means of NMR and vibrational spectroscopies, except those of the second nucleosides of the tetraloops (rC and rG, respectively) which adopt a 3'-endo/anti rather than a 2'-endo/anti conformation.

Common structural features of UUCG and UACG tetraloops in very short hairpins determined by UV absorption, Raman, IR and NMR spectroscopies

Thermodynamic and structural properties of two UNCG tetraloops in very short hairpin octamers, 5'-r(GCUUCGGC)-3' and 5'-r(GCUACGGC)-3', have been studied by means of various physical techniques. Melting profiles of both octamers, obtained from UV absorption spectra taken as a function of temperature, are consistent with a monophasic, progressive and completely reversible order-to-disorder transition and confirm their unusual structural stability (Tm > 51 degrees C). The 1H, 13C and 31P NMR chemical shifts and coupling constants of the UACG loop nucleotides are comparable with those reported previously for UUCG loops, i.e. 2'-endo/anti conformation of the second and third nucleotide of the loop as well as the syn orientation of the ultimate guanine base and the A-type double helical conformation of the hairpin stem. Simulation of quantitative NOESY volumes shows that the UACG octamer adopts a very rigid compact structure which is well represented by an average order parameter of 0.9. Three base-pairs and four additional strong hydrogen bonds are undoubtedly responsible for such limited flexibility. Raman and infrared spectra as a function of temperature reflect the order-to-disorder transition, as well. Vibrational conformational markers in low temperature spectra of both octamers indicate the hairpin structure as the major conformer in aqueous phase. These spectra further support the structural features of most of the nucleotides involved in the tetraloops and clearly demonstrate the structural similarities of the phosphodiester backbone in both hairpins. Consequently, on the basis of all present results, one can deduce that the conformational features of the UUCG and UACG tetraloops seem to be inherent to the UNCG type tetraloops, regardless of either the nature of the tetraloop second base or the stem length.