To investigate nucleic acid base pairing and stacking via atom-specific mutagenesis and crystallography, we have synthesized for the first time the 6-Se-deoxyguanosine phosphoramidite and incorporated it into DNAs via solid-phase synthesis with a coupling yield over 97%. We found that the UV absorption of the Se-DNAs red-shifts over 100 nm to 360 nm (epsilon = 2.3 x 10(4) M(-1) cm(-1)), the Se-...

Recently, KOD and its related DNA polymerases have been used for preparing various modified nucleic acids, including not only base-modified nucleic acids, but also sugar-modified ones, such as bridged/locked nucleic acid (BNA/LNA) which would be promising candidates for nucleic acid drugs. However, thus far, reasons for the effectiveness of KOD DNA polymerase for such purposes have not been cle...

Computational results are described of interactions between nucleic acid bases and of searching for local minima of the interaction energy. As the bases are the elementary units of genetic material, their interactions are important for understanding the molecular mechanisms of genetic processes. The results allow us to reveal three different types of energy minima, which are responsible for var...

Although the immobilization of oligonucleotides (nucleic acid) on mineral surfaces is at basis different biotechnological applications, an atomistic understanding interaction nucleic acid components with titanium dioxide has not yet been achieved. Here, adsorption phosphate anion, four DNA bases (adenine, guanine, thymine, and cytosine) some entire nucleotides dinucleotides TiO2 anatase (1 0 1)...

MOTIVATION There are many important proteins which bind single-stranded nucleic acids, such as the nucleocapsid protein in HIV and the RecA DNA repair protein in bacteria. The presence of such proteins can strongly alter the secondary structure of the nucleic acid molecules. Therefore, accurate modeling of the interaction between single-stranded nucleic acids and such proteins is essential to f...

Förster resonance energy transfer (FRET) between a donor nucleobase analogue and an acceptor nucleobase analogue, base-base FRET, works as a spectroscopic ruler and protractor. With their firm stacking and ability to replace the natural nucleic acid bases inside the base-stack, base analogue donor and acceptor molecules complement external fluorophores like the Cy-, Alexa- and ATTO-dyes and ena...

Recent advances in nucleic acid sequencing, structural, and computational technologies have resulted in dramatic progress in our understanding of nucleic acid structure and function in the cell. This knowledge, together with the predictable base-pairing of nucleic acids and powerful synthesis and expression capabilities now offers the unique ability to program nucleic acids to form precise 3D a...

Computer study via molecular mechanics and Monte Carlo methods reveals some interesting features of hydration of nucleic acid bases. The calculations of interactions of one water molecule with each of bases allow to find the sites of preferential hydration. The energy of interactions with some sites is changing upon Watson-Crick pair formation. Hydration of all the H-bonded base pairs is less f...

Expansion of the genetic alphabet by unnatural base pair systems is an attractive future biotechnology.1 DNA fragments containing unnatural base pairs function as templates for the site-specific incorporation of extra components into nucleic acids and proteins by biosyntheses, according to the Central Dogma of molecular biology replication, transcription, and translation. Nucleic acids and prot...