Nucleic base pair step

Hill, J. G., Platts, J. A. (2008). Calculating stacking interactions in nucleic acid base-pair steps using spin-component scaling and local second order Moller-Plesset perturbation theory. Physical Chemistry Chemical Physics, 10, 2785-2791. 

Ion-exchange HPLC can also be useful in the separation of larger nucleic acid molecules. One such application is as an alternative to CsCl density gradient centrifugation in the preparation of plasmids. Plasmid molecules typically consist of between 1000 and 10 000 base pairs. The plasmid is first isolated from the bacterial cell by alkaline lysis and pure plasmid obtained from this crude extract by a one-step chromatographic separation. 

Tn orcTer to extend these conformational energy studies to the analysis of multi-stranded nucleic acid systems, it is necessary to devise a procedure to identify the arrangements of the polynucleotide backbone that can acconmodate double, triple, and higher order helix formation. As a first step to this end, a computational scheme is offered here to identify the double helical structures compatible with given base pairing schemes. 

I. Dqbkowska, H.V. Gonzales, P. Jurecka, P. Hobza, Stabilization energies of the hydrogen-bonded and stacked stmctures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5,-d(GCGAAGC)-3 hairpin Complete basis set calculations at the MP2 and CCSD(T) levels. J. Phys. Chem. A 109, 1131-1136 (2005)... 

Since the structure of DNA was first revealed by Watson and Crick in 1953, the formation of the double helix of nucleic acids by a self-directing, co-operative process has fascinated several generations of scientists. In general terms, DNA may be seen to self-assemble by a process in which two long chain polytopic receptors interact with the base pairs in such a way that each association step sets the stage for the one that follows. 

Yet another effect of the action of Ag" has been described, namely, its interaction with nucleic acids [112]. The Ag" ion interacts preferentially with the bases found in DNA rather than with the phosphate group [113-118]. The reaction between Ag and a GC (guanine-cytosine) base pair proceeds via two steps, whereas that between Ag" and an AT (adenine-thymine) base pair requires only one step [116], Ag appears to be attached to the N atom... 

The biosynthetic mechanisms mentioned differ from all others in being guided by a template molecule that dictates which building block is to be added at each step. Tliis template molecule is invariably a nucleic acid, and the mechanism by which it exerts its control relies universally on base pairing, the phenomenon whereby adenine joins specifically with thymine or with uracil, and guanine joins likewise with cytosine. These relationships are summarized by the following cardinal relationships ... 

Step 1. Unwinding of the double helix Replication begins when the enzyme helicase catalyzes the separation and unwinding of the nucleic acid strands at a specific point along the DNA helix. In this process, hydrogen bonds between complementary base pairs are broken, and the bases that were formerly in the center of the helix are exposed. The point where this unwinding takes place is called a replication fork (see I Figure 11.11). 

---