Narrow Results

The Polymerase Chain Reaction (PCR) allows for highly sensitive and specific amplification of DNA. It is the backbone of many genetic experiments and tests. Recently, three labs independently uncovered a novel and simple way to perform a PCR reaction. Instead of repetitive heating and cooling, a temperature gradient across the reaction vessel drives thermal convection. By convection, the reaction liquid circulates between hot and cold regions of the chamber. The convection triggers DNA amplification as the DNA melts into two single strands in the hot region and replicates into twice the amount in the cold region. The amplification progresses exponentially as the convection moves on. We review the characteristics of the different approaches and show the benefits and prospects of the method.

A detailed semiempirical quantum-chemical study is reported on homogeneous adenosine-thymidine and guanosine-cytidine base pair steps, both pure ones and their complexes with oxygen molecules. The results of this study help gain detailed insight into physico-chemical mechanisms of electrical conduction control in DNA molecules when doping them with molecular oxygen or related molecules.

Electron spectra of DNA model compounds, adenosine-thymidine and guanosine-cytidine nucleoside base pairs, as well as the relevant homogeneous stacked base pair steps in A-DNA and B-DNA conformations, were investigated using ZINDO semiempirical quantum-chemical method. This work confirms that, in DNA with intact Watson–Crick hydrogen bonding and base stacking, the highest occupied molecular orbitals (HOMO) are residing on purine base residues, whereas the lowest unoccupied molecular orbitals (LUMO) — on pyrimidine base residues. In general, the present results are satisfactorily comparable with the available experimental data. The role of charge transfer excitations in the polymer DNA 260 nm spectral band is discussed.

A detailed study of charge transport properties of synthetic and genomic DNA sequences is reported. Genomic sequences of the Chromosome 22, λ-bacteriophage, and D1s80 genes of Human and Pygmy chimpanzee are considered in this work, and compared with both periodic and quasiperiodic (Fibonacci) sequences of nucleotides. Charge transfer efficiency is compared for all these different sequences, and large variations in charge transfer efficiency, stemming from sequence-dependent effects, are reported. In addition, basic characteristics of tunneling currents, including contact effects, are described. Finally, the thermoelectric power of nucleobases connected in between metallic contacts at different temperatures is presented.

Recent papers have considered moving breathers (MB) in DNA models including long range interaction due to the dipole moments of the hydrogen bonds. We have recalculated the value of the charge transfer when hydrogen bonds stretch using quantum chemical methods which takes into account the whole nucleoside pairs. We explore the consequences of this value on the properties of MBs, including the range of frequencies for which they exist and their effective masses. They are able to travel through bending points with fairly large curvatures, provided that their kinetic energy is larger than a minimum energy which depends on the curvature. These energies and the corresponding velocities are also calculated in function of the curvature.

In this paper, we consider the transformation of a breather type soliton in DNA into its demodulated version due to the strong impact of proteins associated with some sequences of DNA chain. These proteins are, for example, RNA polymerase responsible for the formation of m-RNA or initiation protein complex indispensable for chromosome replication.

In this paper, a double helix model of charge transport in a DNA molecule is presented, and the transmission spectra and I–V curves of four kinds of periodic sequences DNA are obtained. The results show that the transmission characteristics of DNA are not only related to the longitudinal transport but also to the transverse transport of the molecule. The more the composition of bases, the bigger the percent of θ-direction, and the conductive ability reduces. For a different sequence with same composition, the less the number of consecutive appearance of the same base is, the lower the conductive ability.

The shapes of DNA, carbon nanotube (CNT) and vesicle are determined by the minimum of their elastic energy. Two central results about the low-dimensional elastic structure are reported here. Firstly, if the energy density of a one-dimensional structure is only related to its curvature, we generally find that a helix solution with the helix angle θ = ±π/4 will have zero total energy. Secondly, with the fixed length and radii, the helical multi-walled carbon nanotubes (MWNTs) and DNA will have the lowest energy when the helix angle θ = ±π/3.

Using the simple EPB model¹ of DNA (the combined model of the pendulum model of Englander,² and Peyrard–Bishop microscopic model³), we propose a bio (DNA) time measured by EPB pendulum. We have shown that the effective bio time has a thermodynamic origin which equals the ordinary (real) time in the range of room-body temperature. Furthermore, it flows slower at low temperature and much faster near the DNA melting phase transition temperature than real time.

The helix-coil transition in a double-stranded homopolynucleotide is considered. The new approach to the melted loops account is proposed. The relative distance between the corresponding monomers of two polymer chains is modeled by the two-dimensional random walk on the square lattice. Returns of the random walk to the origin describe the formation of hydrogen bonds between complementary units. To take into account the interaction of monomers inside the chains, we consider various regimes of return to the origin. One of them involves two competing interactions and demonstrates a nontrivial sharp denaturation transition. The rich phase behavior of the double-stranded homopolynucleotide is discussed in terms of the proposed approach.

According to $p{K}_a$ measurements, it has been predicted that proton transfer would not occur in the radical cation of adenine–thymine (A:T). However, recent theoretical calculations indicate that proton transfer takes place in the base pair in water below the room temperature. We have performed simulations of proton transfer in the cation of B-DNA stack composed of 10 A:T base pairs in water from 20 K to 300 K. Proton transfer occurs below the room temperature, meanwhile it could also be observed at the room temperature under the external electric field. Another case that interests us is that proton transfer bounces back after $\sim$300 fs from the appearance of proton transfer at low temperatures.

In this paper, we present a coupled sine-Gordon (CSG) system, which describes the dynamics of two deoxyribonucleic acid (DNA) twisting strands in open configuration. We investigate the associated linear eigenvalue problem of the CSG system and obtain generalized formulae for multiple soliton solutions by employing the Darboux transformation (DT). Explicit expressions of one- and two-kink and line soliton solutions, single breather and first-order degenerate solutions are obtained by using particular solutions to the associated linear eigenvalue problem. We also present the dynamics of the different solutions.