cgNA plus web : A Visual Interface to the cgNA plus Sequence-dependent Statistical Mechanics Model of Double-stranded Nucleic Acids
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π−π interactions in heteroaromatic systems are ubiquitous in biological systems. In the present study, stabilization energies of stacked and hydrogen-bonded dimers of N-heteroaromatic systems (pyridine, pyrazine, sym-triazine, and sym-tetrazine) have been ...
It is well recognized that base sequence exerts a significant influence on the properties of DNA and plays a significant role in protein-DNA interactions vital for cellular processes. Understanding and predicting base sequence effects requires an extensive ...
This thesis explores different aspects of DNA topology through experimental and numerical techniques. Topology is a vast mathematical field, that deals with the spatial properties of objects undergoing continuous deformations, but here it is restricted to ...
Nucleic acid-templated reactions leading to a fluorescent product represent an attractive strategy for the detection and imaging of cellular nucleic acids. Herein we report the use of a Staudinger reaction to promote the reduction of profluorescent azidorh ...
The invention relates to methods of generating templates for a nucleic acid sequencing reaction which comprise: providing at least one double-stranded nucleic acid molecule, wherein both strands of the double-stranded nucleic acid molecule are attached to ...
A method is described to extract a complete set of sequence-dependent material parameters for rigid base and basepair models of DNA in solution from atomistic molecular dynamics simulations. The method is properly consistent with equilibrium statistical me ...
The thesis presents the development of a custom made atomic force microscope (AFM) conceived to image biological molecules at low temperatures in ultrahigh vacuum conditions, and its application to DNA single molecule studies. Starting from a first prototy ...
The design, synthesis, and base-pairing properties of bicyclo[3.2.1]amide-DNA (bca-DNA), a novel phosphodiester-based DNA analog, are reported. This analog consists of a conformationally constrained backbone entity, which emulates a B-DNA geometry, to whic ...
Critiquing-based recommender systems provide an efficient way for users to navigate through complex product spaces even if they are not familiar with the domain details in e-commerce environments. While recent research has mainly concentrated on methods fo ...
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In this letter, we show the results achieved using a hydrogenated amorphous silicon photosensor for a "label-free" deoxyribonucleic acid (DNA) analysis based on the measurements of the absorbance in the ultraviolet range. The optimization of the sensor str ...