Stability of the ;-; stacking interactions in the substituted-coronene||cyclooctatetraene complexes wasstudied using the computational quantum chemistry methods (where || denotes ;–; stackinginteraction, and substituted-coronene is coronene which substituted with four similar X groups; X =OH, SH, H, F, CN, and NO). There are meaningful correlations between changes of geometricalparameters and t...

Complementary to our first paper on the origin of threefold contrast on SiC high resolution transmission electron microscopy (HRTEM) images, we now provide an example of threefold contrast produced by a stacking layer sequence which corresponds to one unit cell of the 9R polytype.

T30177 is a G-rich oligonucleotide with the sequence (GTGGTGGGTGGGTGGGT) which inhibits the HIV-1 integrase activity at nanomolar concentrations. Here we show that this DNA sequence forms in K(+) solution a dimeric G-quadruplex structure comprising a total of six G-tetrad layers through the stacking of two propeller-type parallel-stranded G-quadruplex subunits at their 5'-end. All twelve guanin...

1 2004 (1) References [1] M. Cho and S. Y. Rhee. Optimization of laminates with free edges under bounded uncertainty subject to extension, bending and twisting. International Journal of Solids and Structures, 41:227–245, 2004. [2] C. Lin and Y. Lee. Stacking sequence optimization of laminated composite structures using genetic algorithm with local improvement. Composite Structures, 63:339–345, ...

It is shown that distributed chaos, generated by Hamiltonian DNA dynamics with spontaneously broken time translational symmetry, imprints itself on the DNA sequence of Arabidopsis thaliana (a model plant for genetic sequencing and mapping) and of the NRXN1 and BRCA2 human genes (as an example). The base-stacking interactions in the DNA duplex and degenerate codon groups have been discussed in t...

We show that the origin of the universal optical conductivity in a normal N-layer graphene multilayer is an emergent chiral symmetry which guarantees that sigma(omega) = Nsigma_{uni} in both low and high-frequency limits. [sigma_{uni} = (pi/2)e;{2}/h]. We use this physics to relate intermediate frequency conductivity trends to qualitative characteristics of the multilayer stacking sequence.

We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate perpendicular to the sequence axis. We show, through molecular dynamics simulations, that the model has the correct behaviour at the denaturation transition.

Stability of duplex DNA with respect to separation of complementary strands is crucial for DNA executing its major functions in the cell and it also plays a central role in major biotechnology applications of DNA: DNA sequencing, polymerase chain reaction, and DNA microarrays. Two types of interaction are well known to contribute to DNA stability: stacking between adjacent base-pairs and pairin...

Loops which are linkers connecting G-strands and supporting the G-tetrad core in G-quadruplex are important for biological roles of G-quadruplexes. TTA loop is a common sequence which mainly resides in human telomeric DNA (hTel) G-quadruplex. A series of molecular dynamics (MD) simulations were carried out to investigate the structural dynamics of TTA loops. We found that (1) the TA base pair f...

The aggregation of polypeptides into amyloid fibrils is associated with a number of human diseases. Because these fibrils--or intermediates on the aggregation pathway--play important roles in the etiology of disease, considerable effort has been expended to understand which features of the amino acid sequence promote aggregation. One feature suspected to direct aggregation is the π-stacking of ...