Study of polynucleotide conformation by resolution-enhanced ultraviolet spectroscopy poly(rC) and poly(dC)

Structural transitions in poly(A), poly(C), poly(U), and poly(G) and their possible biological roles

The homopolynucleotide (homo-oligonucleotide) tracts function as regulatory elements at various stages of mRNAs life cycle. Numerous cellular proteins specifically bind to these tracts. Among them are the different poly(A)-binding proteins, poly(C)-binding proteins, multifunctional fragile X mental retardation protein which binds specifically both to poly(G) and poly(U) and others. Molecular mechanisms of regulation of gene expression mediated by homopolynucleotide tracts in RNAs are not fully understood and the structural diversity of these tracts can contribute substantially to this regulation. This review summarizes current knowledge on different forms of homoribopolynucleotides, in particular, neutral and acidic forms of poly(A) and poly(C), and also biological relevance of homoribopolynucleotide (homoribo-oligonucleotide) tracts is discussed. Under physiological conditions, the acidic forms of poly(A) and poly(C) can be induced by proton transfer from acidic amino acids of proteins to adenine and cytosine bases. Finally, we present potential mechanisms for the regulation of some biological processes through the formation of intramolecular poly(A) duplexes.

Ultrafast IR spectroscopy of polymeric cytosine nucleic acids reveal the long-lived species is due to a localised state

The decay pathways of UV-excited cytosine polymers are investigated using picosecond time-resolved infrared spectroscopy. Similar yields of a non-emissive (1)nπ* state are found in the single-stranded dC(30) polymer as in the dCMP monomer, but with a longer lifetime in the polymer (80 ps vs. 39 ps). A longer lifetime is also found in the d(CpC) dinucleotide. No evidence of excimer states is observed, suggesting that localised (1)nπ* excited states are the most significant intermediates present on the picosecond timescale.

Binding of eukaryotic initiation factor 3 to ribosomal 40S subunits and its role in ribosomal dissociation and anti-association

The multisubunit eukaryotic initiation factor (eIF) 3 plays various roles in translation initiation that all involve interaction with 40S ribosomal subunits. eIF3 can be purified in two forms: with or without the loosely associated eIF3j subunit (eIF3j+ and eIF3j-, respectively). Although unlike eIF3j+, eIF3j- does not bind 40S subunits stably enough to withstand sucrose density gradient centrifugation, we found that in addition to the known stabilization of the eIF3/40S subunit interaction by the eIF2*GTP*Met-tRNA(i)Met ternary complex, eIF3j-/40S subunit complexes were also stabilized by single-stranded RNA or DNA cofactors that were at least 25 nt long and could be flanked by stable hairpins. Of all homopolymers, oligo(rU), oligo(dT), and oligo(dC) stimulated the eIF3/40S subunit interaction, whereas oligo(rA), oligo(rG), oligo(rC), oligo(dA), and oligo(dG) did not. Oligo(U) or oligo(dT) sequences interspersed by other bases also promoted this interaction. The ability of oligonucleotides to stimulate eIF3/40S subunit association correlated with their ability to bind to the 40S subunit, most likely to its mRNA-binding cleft. Although eIF3j+ could bind directly to 40S subunits, neither eIF3j- nor eIF3j+ alone was able to dissociate 80S ribosomes or protect 40S and 60S subunits from reassociation. Significantly, the dissociation/anti-association activities of both forms of eIF3 became apparent in the presence of either eIF2-ternary complexes or any oligonucleotide cofactor that promoted eIF3/40S subunit interaction. Ribosomal dissociation and anti-association activities of eIF3 were strongly enhanced by eIF1. The potential biological role of stimulation of eIF3/40S subunit interaction by an RNA cofactor in the absence of eIF2-ternary complex is discussed.

Influence of sodium ions on the dynamics and structure of single-stranded DNA oligomers: a molecular dynamics study

The effects of sodium counterion presence and chain length on the structure and dynamics of single DNA strands of polythymidylate were studied by means of molecular dynamics simulations. The importance of the base-base stacking phenomenon increases with the chain length and partially reduces the flexibility of the strand. Sodium ions directly interact with the phosphate groups and keto oxygens of the thymine bases, complexes showing lifetimes below 400 ps. Simultaneous phosphate and keto complexes were observed for one of the sodium ions with lifetimes around 1 ns. The implications of such complexes in the folding process experienced by the strand are considered. Structurally, cation inner- and outer-sphere complexes were observed in the coordination of phosphate groups. For the inner-sphere complexes, the structural information retrieved from the simulations is in very good agreement with experimental data. The diffusion properties of the sodium ions also reflect both types of coordination modes.

A soft-modeling approach to interpret thermodynamic and conformational transitions of polynucleotides

Multivariate outputs from the experimental monitoring of biochemical processes are usually difficult to interpret applying methods based on a priori chemical models. Curve resolution methods are model-free procedures, generally known as soft-modeling methods, which obtain the concentration profiles and instrumental responses of each individual species involved in a multivariate monitored process without making any kind of external assumption. Of the curve resolution methods available, the alternating least squares (ALS) is proposed here because of its ability to operate on one or on several matrices. Furthermore, ALS allows the introduction of information related to the internal data structure and to the general features of the concentration profiles and instrumental responses through the input of suitable constraints in the iterative resolution procedure. The ALS potential is tested on several data sets coming from the multivariate spectrometric monitoring of polyuridylic (polyU), polycytidylic (polyC), and polyadenylic (polyA) protonation equilibria in dioxane/water 30% (v/v). Information concerning the evolution of the concentration profiles and the spectra of each individual species involved in the acid-base equilibria, the presence and pattern of polyelectrolyte effects, and the presence of conformational transitions associated or not with the proton uptake process is presented.

Three-way curve resolution applied to the study of solvent effect on the thermodynamic and conformational transitions related to the protonation of polycytidylic acid

Solvent effect on the acid-base behavior of polycytidylic acid [poly(C)] is studied by means of potentiometric and spectrometric (UV and CD) procedures. Low-polarity biological environments are mimicked by using a 30% (v/v) dioxane-water mixture. Experiments performed in this medium are compared with previously reported results in aqueous solution in order to determine changes in both thermodynamic and structural aspects associated with modifications of the biomolecular surroundings. Potentiometric and spectrometric studies reveal the presence of a nonlinear polyelectrolytic effect associated with the protonation of poly(C) in the hydroorganic mixture, different from the analogous effect in aqueous solution. The curve resolution method alternating least squares is applied to the poly(C) spectrometric data. Concentration profiles and spectra of both deprotonated poly(C) and half-protonated [poly(C).poly(CH+)] are thus obtained. The fully protonated species poly(CH+) precipitates in the hydroorganic medium at pH values lower than 4. Evidence for the ordered structure of both poly(C) and [poly(C).poly(CH+)] species is seen through the comparison of the macromolecule spectra with those of the cytidine-3',5'-cyclic monophosphate monomer. Polarity decreases around the macromolecule produce significant hypochromicity in the CD spectra and hyperchromicity in the UV spectra, both signs of a disordering effect in the macromolecular structure due to the weakening of base stacking interactions.

An A-form of poly[d(A-C)].poly[d(G-T)] induced by mercury (II) as studied by UV and FTIR spectroscopies

The conformational changes of poly[d(A-C)].poly[d(G-T)] induced by Hg(ClO4)2 in aqueous solution have been studied using UV absorption and fourth derivative spectrophotometries, and FTIR spectroscopy. The UV absorption and fourth derivative spectra reflect changes in the polynucleotide stacking interactions as a result of the metal-polynucleotide interaction. The fourth derivative spectra do not indicate a Z-form either at low or at high metal-to-polynucleotide ratios. Furthermore, the infrared spectrum at high metal-to-polynucleotide ratio (r = 1.2; r = [Hg(ClO4])2/[nucleotide] molar ratio) has the main features of an A-form, in contrast with previous CD studies which proposed that the polynucleotide adopts a Z-form under these conditions. The nature of a different conformation of the polynucleotide induced at low r-ratios (r < or = 0.2) is discussed.