Examining the Effects of Netropsin on the Curvature of DNA A-Tracts Using Electrophoresis

A-tracts are sequences of repeated adenine bases that, under the proper conditions, are capable of mediating DNA curvature. A-tracts occur naturally in the regulatory regions of many organisms, yet their biological functions are not fully understood. Orienting multiple A-tracts together constructively or destructively in a phase has the potential to create different shapes in the DNA helix axis. One means of detecting these molecular shape differences is from altered DNA mobilities measured using electrophoresis. The small molecule netropsin binds the minor groove of DNA, particularly at AT-rich sequences including A-tracts. Here, we systematically test the hypothesis that netropsin binding eliminates the curvature of A-tracts by measuring the electrophoretic mobilities of seven 98-base pair DNA samples containing different numbers and arrangements of centrally located A-tracts under varying conditions with netropsin. We find that netropsin binding eliminates the mobility difference between the DNA fragments with different A-tract arrangements in a concentration-dependent manner. This work provides evidence for the straightening of A-tracts upon netropsin binding and illustrates an artificial approach to re-sculpt DNA shape.

Volume Phase Transitions of Heliconical Cholesteric Gels under an External Field along the Helix Axis

We present a mean field theory to describe cholesteric elastomers and gels under an external field, such as an electric or a magnetic field, along the helix axis of a cholesteric phase. We study the deformations and volume phase transitions of cholesteric gels as a function of the external field and temperature. Our theory predicts the phase transitions between isotropic (I), nematic (N), and heliconical cholesteric (ChH) phases and the deformations of the elastomers at these phase transition temperatures. We also find volume phase transitions at the I−ChH and the N−ChH phase transitions.

Optical Forces Acting on a Double DNA-Like Helix, Its Unwinding and Strands Rupture

In this paper we study electromagnetic forces induced on DNA and DNA-like helices by external electromagnetic waves. We consider simultaneously occurring forces and torques, interconnected and acting along the double helix axis. Since the DNA molecule has an absorption band in the ultraviolet and visible range near wavelengths λ1res=280 nm and λ2res=500 nm, we expect that it may be possible to selectively apply engineered forces to DNA molecules using appropriate illumination by light in these frequency ranges. The optical forces are simulated for DNA fragments consisting of 20 and 35 turns. Fragments of this length are convenient for direct sequencing and subsequent use in experiments and in practice. It is shown that repulsion forces can arise between the strands of the double DNA-like helix in the field of external electromagnetic waves. Such forces are characteristic of a DNA-like helix with its specific pitch angle and are not inherent in double helices with more straightened or more compressed turns. These repulsion forces, acting along the entire helix, both for electric charges and for electric currents, can lead to damage and rupture of the strands in the double helix. In addition, there can also exist forces and moments of forces directed along the helix axis, which simultaneously stretch and unwind a double helix. The double helix equilibrium under the action of optical forces is also of interest from another point of view, i.e., for optimizing the structure of artificial magnetics and bianisotropic metamaterials for applications in all frequency ranges.

The Field-Induced Stop-Bands and Lasing Modes in CLC Layers with Deformed Lying Helix

Waveguide optical properties of a cholesteric liquid crystal (CLC) layer with a deformed lying helix (DLH) have been studied by numerical simulations using the finite difference time domain method. The DLH structure, when the helix’s axis is oriented in plane of a CLC layer, is induced by an electric field in a virtual CLC cell with periodic (planar/homeotropic) boundary conditions at one of the alignment surfaces. This in-plane helical structure is stable only in a permanently applied electric field providing the helix deformation. In this work the polarized light reflectance spectra have been studied at different electric fields and light impingement into a waveguide formed by the DLH layer. It is found that for light propagating along the helix axis the reflectance spectrum has multiple stop-bands centred at wavelengths , which is different from set of bands located at , and characteristic of CLC spectra for the Grandjean-plane textures subjected to distortion by an electric or magnetic field perpendicular to the helix axis, where j is a natural number, p is the helix pitch and is the average refractive index. Each of the higher order (j > 1) bands consists of three polarization-dependent sub-bands. In the case of an amplifying CLC DLH layer, depending on an extent of the helix deformation, the lasing modes can be excited at different edges of the sub-bands. While at the strongest deformation the lasing is preferable at the edges of the central sub-band; a lower extent of deformation makes favourable conditions for the lasing at edges of the two other sub-bands.

3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.

We present forgi, a Python library to analyze the tertiary structure of RNA secondary structure elements. Our representation of an RNA molecule is centered on secondary structure elements (stems, bulges and loops). By fitting a cylinder to the helix axis, these elements are carried over into a coarse-grained 3D structure representation. Integration with Biopython allows for handling of all-atom 3D information. forgi can deal with a variety of file formats including dotbracket strings, PDB and MMCIF files. We can handle modified residues, missing residues, cofold and multifold structures as well as nucleotide numbers starting at arbitrary positions. We apply this library to the study of stacking helices in junctions and pseudoknots and investigate how far stacking helices in solved experimental structures can divert from coaxial geometries.

The helicoidal modulated nematic phases in a model system of V-shaped molecules

The phase behavior of the melt of the symmetric V-shaped molecules has been inspected within the Landau–de Gennes approach. The arms of V-shaped molecule are modeled by rod-like segments connected at an external angle [Formula: see text]; these segments are assumed to be composed of monomer units. The phase diagram of the system contains regions of stability of the isotropic, homogeneous nematic, and modulated nematic phases: nematic twist bend (N[Formula: see text]) phase that is characterized by the three directors which move on a helix and one of these directors forms a fixed nonzero cone angle with the helix axis, and the N0 modulated phase in which one director is parallel to the helix axis while two others are orthogonal to the helix axis. The characteristic periods of modulated structures were found to be of order a few molecular lengths.