Search Results (5 total)

Transcription-factor proteins bind to specific DNA sequences to regulate gene expression in cells. DNA-binding sites are often identified using weight matrices calculated from multiple known binding sites. However, in many cases the number of examples is limited. Here, we report on an atomistic method that starts from an x-ray co-crystal structure of the protein bound to one particular DNA sequence, and infers other binding sites, which are used to construct a weight matrix. The emphasis of the paper is on using the Wang-Landau Monte Carlo algorithm to efficiently sample high-affinity binding sites, which demonstrates that sampling can produce accurate weight matrices in analogy to bioinformatics approaches. For cases of low complexity, we compare to the exhaustive (but slow) dead-end elimination algorithm. To recover crystal binding sites, it is important to include bound water in the protein-DNA interface. Our approach can, in principle, even be applied when no native protein-DNA co-crystal structure is available, only the structure of a closely related homologous protein whose amino-acid sequence is changed to the protein of interest.

Motivated by recent experiments, we study the optical conductivity of DNA in its natural environment containing water molecules and counterions. Our density functional theory calculations (using Siesta) for four base pair B-DNA with order 250 surrounding water molecules suggest a thermally activated doping of the DNA by water states which generically leads to an electronic contribution to low-frequency absorption. The main contributions to the doping result from water near DNA ends, breaks, or nicks and are thus potentially associated with temporal or structural defects in the DNA.

The DNA molecule, well known from biology for containing the genetic code of all living species, has recently caught the attention of chemists and physicists. A major reason for this interest is DNA’s potential use in nanoelectronic devices, both as a template for assembling nanocircuits and as an element of such circuits. Without question, a truly conducting form of DNA would have a major impact on developments in nanotechnology. It has also been suggested that extended electronic states of DNA could play an important role in biology, e.g., through the processes of DNA damage sensing or repair or through long-range charge transfer. However, the electronic properties of DNA remain very controversial. Charge-transfer reactions and conductivity measurements show a large variety of possible electronic behavior, ranging from Anderson and band-gap insulators to effective molecular wires and induced superconductors. Indeed, understanding the conductance of a complicated polyelectrolytic aperiodic system is by itself a major scientific problem. In this Colloquium, the authors summarize the wide-ranging experimental and theoretical results and look for any consistencies between them. They also pose simple questions regarding the electronic states of DNA within the framework of generalized Hückel and Slater-Koster theories. The Colloquium provides a quantitative overview of DNA’s electronic states as obtained from density-functional theory, focusing on dependence on structure, on molecular stretching and twisting, and on water and counterions. While there is no clear theoretical basis for truly metallic DNA, situations are discussed in which very small energy gaps might arise in the overall DNA/water/counterion complex, leading to thermally activated conduction at room temperature.

We present a theory of nonequilibrium long range charge transfer between donor and acceptor centers in a model polymer mediated by magnetic exciton (Kondo) bound states. Our model produces electron tunneling lengths easily exceeding 10 Å, as observed recently in DNA and organic charge transfer systems. This long ranged tunneling is effective for weak to intermediate donor-bridge coupling, and is enhanced both by weak to intermediate strength Coulomb hole-electron attraction (through the orthogonality catastrophe) and by coupling to local vibrational modes.

The ratio of the electric and magnetic form factors of the proton G_Ep/G_Mp, which is an image of its charge and magnetization distributions, was measured at the Thomas Jefferson National Accelerator Facility (JLab) using the recoil polarization technique. The ratio of the form factors is directly proportional to the ratio of the transverse to longitudinal components of the polarization of the recoil proton in the elastic e→p→ep→ reaction. The new data presented span the range 3.5<Q²<5.6 GeV² and are well described by a linear Q² fit. Also, the ratio sqrt[Q²] F_2p/F_1p reaches a constant value above Q²  =  2 GeV².