Reentrant melting of RNA with quenched sequence randomness.

The effect of quenched sequence disorder on the thermodynamics of RNA secondary structure formation is investigated for two- and four-letter alphabet models using the constrained annealing approach, from which the temperature behavior of the free energy, specific heat, and helicity is analytically obtained. For competing base pairing energies, the calculations reveal reentrant melting at low temperatures, in excellent agreement with numerical results. Our results suggest an additional mechanism for the experimental phenomenon of RNA cold denaturation.

Competition for hydrogen-bond formation in the helix-coil transition and protein folding.

The problem of the helix-coil transition of biopolymers in explicit solvents, such as water, with the ability for hydrogen bonding with a solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide Chains. Besides the regular helix-coil transition, an additional coil-helix or reentrant transition is also found at lower temperatures. The reentrant transition arises due to competition between polymer-polymer and polymer-water hydrogen bonds. The balance between the two types of hydrogen bonding can be shifted to either direction through changes not only in temperature, but also by pressure, mechanical force, osmotic stress, or other external influences. Both polypeptides and polynucleotides are considered within a unified formalism. Our approach provides an explanation of the experimental difficulty of observing the reentrant transition with pressure and underscores the advantage of pulling experiments for studies of DNA. Results are discussed and compared with those reported in a number of recent publications with which a significant level of agreement is obtained.

Microscopic formulation of the Zimm-Bragg model for the helix-coil transition.

A microscopic spin model is proposed for the phenomenological Zimm-Bragg model for the helix-coil transition in biopolymers. This model is shown to provide the same thermophysical properties of the original Zimm-Bragg model and it allows a very convenient framework to compute statistical quantities. Physical origins of this spin model are made transparent by an exact mapping into a one-dimensional Ising model with an external field. However, the dependence on temperature of the reduced external field turns out to differ from the standard one-dimensional Ising model and hence it gives rise to different thermophysical properties, despite the exact mapping connecting them. We discuss how this point has been frequently overlooked in the recent literature.

Intersegment interactions and helix-coil transition within the generalized model of polypeptide chains approach.

The generalized model of polypeptide chains is extended to describe the helix-coil transition in a system comprised of two chains interacting side-by-side. The Hamiltonian of the model takes into account four possible types of interactions between repeated units of the two chains, i.e., helix-helix, helix-coil, coil-helix, and coil-coil. Analysis reveals when the energy I(hh)+I(cc) of (h-h, c-c) interactions overwhelms the energy I(hc)+I(ch) of mixed (h-c, c-h) interactions, the correlation length rises substantially, resulting in narrowing of the transition interval. In the opposite case, when I(hh)+I(cc)

Two scale generalized model of polypeptide chains.

The generalized model of polypeptide chains (GMPC) is expanded to simultaneously consider two types of interactions occurring over different scales. This new two scale GMPC is applied in several specific cases to examine: The combined influence of stacking or antistacking and hydrogen bonding, or spatial restrictions on the length of helical segments, on the cooperativity and temperature interval of the helix-coil transition of duplex DNA. For the cases of stacking or antistacking in combination with hydrogen bonding the model reduces to the basic uniscale model with a redefined scaling parameter Delta. Antistacking increases the cooperativity, while stacking decreases it. In each case, explanations are given in terms of different lengths of helical segments. Restrictions on the length of helical regions result in the appearance of antiferromagnetic-type correlations where there is no apparent link between cooperativity and transition interval.

RNA folding in the presence of counterions.

We present a general thermodynamic picture of the folding of RNA-like heteropolymer based on the basic physical principles. The Hamiltonian of the model includes all characteristic interactions explicitly. A particular attention is paid to the electrostatic interactions whose role in the RNA folding is known to be crucial. In this paper we study RNA folding with the full Hamiltonian and describe the spin-glass behavior on the level of tertiary structure. We show that formation of the stable tertiary structure is possible in the random RNA-like molecule. By including into the model the nonspecific interactions of the RNA molecule with counterions, we derive the logarithmic dependencies of the melting and freezing temperatures on the ion concentration, which is consistent with experimental data [R. Shiman and D. E. Draper, J. Mol. Biol. 302, 79 (2000)]. We also infer that the large RNA folds slower than the hierarchical model predicts, which was observed in the experiments.

Stacking heterogeneity: a model for the sequence dependent melting cooperativity of duplex DNA.

A microscopic Potts-like one-dimensional model with many particle interactions [referred as the generalized model of polypeptide chains (GMPCs)] is developed to investigate cooperativity of DNA sequence dependent melting. For modeling sequence, regular homogeneous sequences were arranged in heterogeneous blocks of various lengths. Within the framework of the GMPC the authors show that the inclusion of stacking interaction heterogeneity relative to homogeneous hydrogen bond interactions leads to an unexpected and quite remarkable increase in melting cooperativity for small blocks. In some cases this tendency persists for long blocks having sharp sequence heterogeneity.

The helix-coil transition in heterogeneous double stranded DNA: microcanonical method.

A microscopic Potts-like one-dimensional model with many-particle interactions is developed to construct a statistical mechanical description of the melting of heterogeneous sequence duplex DNA. For this model, referred as the generalized model of polypeptide chains (GMPC), a closed-form expression for the free energy is derived. The characteristic equation of the model enables estimates on the melting temperature and transition interval, consistent with results obtained from more classical approaches. From the characteristic equation of the model, the temperature-dependent statistical weight parameter for helical states is evaluated. This parameter is shown to change throughout the transition from a harmonic form in early regions of the transition to an arithmetic form in later stages. The GMPC is extended to consider the influence of sequence heterogeneity in the melting of duplex DNA.

[Modification of the DNA spatial structure when complexed with cisplatin]. / Modifikatsiia prostranstvennoi struktury DNK v komplekse s tsis-platinoi.

The experimental and theoretical analyses of the conformational transitions of DNA-cis-platinum complexes have been carried out. It is shown that at low concentrations of the ligand, the thermodynamic parameters of the helix-coil transition of the complexes are not the result of the local B-->A transition.

The helix-coil transition in polypeptides: a microscopic approach. II.

In the framework of an earlier constructed model [N.S. Ananikyan et al. (1990) Biopolymers, Vol. 30, pp. 357-367], some analytical estimates for the correlation length and degree of helicity near the transition point were obtained in the case of an arbitrary topology of hydrogen bond closing (delta). It was shown that the Zimm-Bragg cooperativity parameter sigma is determined by the set of (delta-1) amino acid residues and so is nonlocal. An analytic expression for cooperativity parameters in a heteropolypeptide chain was obtained and numerical calculations showed that in case of heteropolypeptide with random primary structure the nonlocality of cooperativity parameter influenced the temperature dependence of helicity degree.

[The epidemiological characteristics of HIV infection in Ukraine]. / Osobennosti épidemiologii VICh-infektsii v Ukraine.

The paper presents results of screening tests involving different groups of the population in the Ukraine, for antibodies to HIV, findings from epidemiologic investigation into cases with HIV-infection, with a view to outlining epidemiologic situation and assessing effectiveness of antiepidemic measures. HIV-transmission through sexual contacts is the commonest way of HIV-transportation in the Ukraine (66.1% of all cases of infection). An attempt is made of giving a short-term prognosis of epidemic situation in the Ukraine over a period of up to 1995. A conclusion is reached on the necessity of strengthening preventive measures with the view of influencing the unsafe forms of sexual behaviour.

[Helix-coil transitions of a polypeptide in a two-component solvent]. / Perekhod spiral'-klubok polipeptidov v dvukhkomponentnom rastvoritele.

A microscopic model is considered of a helix-coil transition of polypeptides in a two-component solvent one of whose components competes for the formation of hydrogen bonds with the peptide group. It is shown that by a redetermination of the temperature parameter the model is reduced to a polypeptide chain without the solvent. Behavior of the transition parameters is calculated in relation to the solvent concentration competing for the formation of hydrogen bonds at different parameters of polypeptide-solvent interaction.

[Calculation of parameters of the phenomenological theory of helix-coil transition in polypeptides based on a microscopic model]. / Raschet parametrov fenomenologicheskoi teorii perekhoda spiral'-klubok v polipeptidakh na osnove mikroskopicheskoi modeli.

An expression for the partition function of the model including only two parameters-U (energy of hydrogen bond) and Q (the number of conformations of the repeating unit) with Hamiltonian is obtained. This expression has the form of algebraic series with the number of members approximately N3, N being the length of the chain. The results of calculations of the temperature relationship of helicity degree are presented for different values of N. The transition width and the parameter of cooperativity are calculated.