Site-specific labeling of supercoiled DNA

Visualization of site-specific labels in long linear or circular DNA allows unambiguous identification of various local DNA structures. Here we describe a novel and efficient approach to site-specific DNA labeling. The restriction enzyme SfiI binds to DNA but leaves it intact in the presence of calcium and therefore may serve as a protein label of 13 bp recognition sites. Since SfiI requires simultaneous interaction with two DNA recognition sites for stable binding, this requirement is satisfied by providing an isolated recognition site in the DNA target and an additional short DNA duplex also containing the recognition site. The SfiI/DNA complexes were visualized with AFM and the specificity of the labeling was confirmed by the length measurements. Using this approach, two sites in plasmid DNA were labeled in the presence of a large excess of the helper duplex to compete with the formation of looped structures of the intramolecular synaptic complex. We show that the labeling procedure does not interfere with the superhelical tension-driven formation of alternative DNA structures such as cruciforms. The complex is relatively stable at low and high pH (pH 5 and 9) making the developed approach attractive for use at conditions requiring the pH change

Giant suppression of shot noise as signature of coherent transport in double barrier resonant diodes

Shot noise suppression in double barrier resonant tunnelling diodes with a Fano factor well below the value of 0.5 is theoretically predicted. This giant suppression is found to be a signature of the coherent transport regime and can occur near zero temperature as a consequence of the Pauli principle or above about 77 K as a consequence of long range Coulomb interaction. These predictions are validated by experimental data

Coherent approach to transport and noise in double-barrier resonant diodes

We implement a quantum approach which includes long range Coulomb interaction and investigate current voltage characteristics and shot noise in double-barrier resonant diodes. The theory applies to the region of low applied voltages up to the region of the current peak and considers the wide temperature range from zero to room temperature. The shape of the current voltage characteristic is well reproduced and we confirm that even in the presence of Coulomb interaction the shot noise can be suppressed with a Fano factor well below the value of 0.5. This feature can be an indication of coherent tunneling since the standard sequential tunneling predicts in general a Fano factor equal to or greater than the value 0.5. This giant suppression is a consequence of Pauli principle as well as long range Coulomb interaction. The theory generalizes previous findings and is compared with experiments

Giant suppression of shot noise in double barrier resonant diode: a signature of coherent transport

Shot noise suppression in double barrier resonant tunnelling diodes with a Fano factor well below the value of 0.5 is theoretically predicted. This giant suppression is found to be a signature of coherent transport regime and can occur at zero temperature as a consequence of the Pauli principle or at sufficiently high temperatures above 77 K as a consequence of a long-range Coulomb interaction. These predictions are in agreement with experimental data

Superhigh-frequency characteristics of optical modulators on the basis of InGaAlAs resonance-tunnel heterostructures

The impedance of InGaAlAs resonance-tunnel heterostructures used for modulation of optical radiation is experimentally studied in the frequency range from 45 to 18 MHz. The dependence of their equivalent circuit on the bias voltage is determined. The spectrum of the harmonics of the current in the resistive frequency multiplication in such structures is calculated. The results confirm that these structures are promising as applied to the frequency multiplication. The effect of frequency multiplication is demonstrated experimentally at low frequencies

Hereditary breast cancer: present status of problem

The incidence of breast cancer is increasing in most countries every year. The purpose of this literature review is to provide up-to-date information about the causes, mechanisms of development, various methods of prevention, early diagnosis and treatment of hereditary breast cancer. The effectiveness of bilateral preventive mastectomy is discussed

Triplet repeat DNA structures and human genetic disease: dynamic mutations from dynamic DNA.

Fourteen genetic neurodegenerative diseases and three fragile sites have been associated with the expansion of (CTG)n (CAG)n, (CGG)n (CCG)n, or (GAA)n (TTC)n repeat tracts. Different models have been proposed for the expansion of triplet repeats, most of which presume the formation of alternative DNA structures in repeat tracts. One of the most likely structures, slipped strand DNA, may stably and reproducibly form within triplet repeat sequences. The propensity to form slipped strand DNA is proportional to the length and homogeneity of the repeat tract. The remarkable stability of slipped strand DNA may, in part, be due to loop-loop interactions facilitated by the sequence complementarity of the loops and the dynamic structure of three-way junctions formed at the loop-outs

Bubbles, clusters and denaturation in genomic DNA: modeling, parametrization, efficient computation

The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the relevant statistical mechanics. Computed melting profiles of long and short heterogeneous sequences are presented, using a recently introduced reparametrization of the PBD model, and critically discussed. The statistics of extended open bubbles and bound clusters is formulated and results are presented for selected examples.Comment: to appear in a special issue of the Journal of Nonlinear Mathematical Physics (ed. G. Gaeta

Au-Ag template stripped pattern for scanning probe investigations of DNA arrays produced by Dip Pen Nanolithography

We report on DNA arrays produced by Dip Pen Nanolithography (DPN) on a novel Au-Ag micro patterned template stripped surface. DNA arrays have been investigated by atomic force microscopy (AFM) and scanning tunnelling microscopy (STM) showing that the patterned template stripped substrate enables easy retrieval of the DPN-functionalized zone with a standard optical microscope permitting a multi-instrument and multi-technique local detection and analysis. Moreover the smooth surface of the Au squares (abput 5-10 angstrom roughness) allows to be sensitive to the hybridization of the oligonucleotide array with label-free target DNA. Our Au-Ag substrates, combining the retrieving capabilities of the patterned surface with the smoothness of the template stripped technique, are candidates for the investigation of DPN nanostructures and for the development of label free detection methods for DNA nanoarrays based on the use of scanning probes.Comment: Langmuir (accepted