Nucleic acids modeling

The chemistry of nucleic acid analogs has received much attention in recent years, and a series of nucleic acid models has been designed and widely prepared, in order to estimate and utilize their functionalities in relation to the specific basepairing properties ( J., i, ). These monomers and polymers, particularly those containing purines, pyrimidines, nucleosides, and nucleotides, are not only of interest to the field of heterocyclic organic chemistry, but also to that of biomimetic macro-molecular chemistry as synthetic analogs of the nucleic acids. 

This chapter will address software systems to interactively fit molecular models to electron density maps and to analyse the resulting models. This chapter is heavily biased toward proteins, but the programs can also build nucleic acid models. First a brief review of molecular modelling and graphics is presented. Next, the best current and freely available programs are discussed with respect to their performance on common tasks. Finally, some views on the future of such software are given. 

Most of the nucleic acid model compound prepared so far are water insoluble however, when the analogs are water soluble, they may not permeate into the hydrophobic cell membranes. Recently, an improved drug delivery system for water soluble drugs using polysaccharide-coated liposomes [68] was developed. 

The probably most delicate aspect of nucleic-acid modeling is the treatment of long-range interactions. The particle-mesh Ewald method, introduced by Darden et al. [109] [110] has yielded very promising results in a number of recent molecular-dynamics simulations of oligonucleotides... 

Nucleic Acid Model Building Multiple Conformations of E. coli tip Operator DNA. ... 

Nucleic acids, models and analogues of 79ZC241 76KGS27. 

Smith, J. R. 1996. Nucleic acid models. Prog. Polym. Sci. 21 209-253. 

The fourth summation corresponds to an energy function for all atoms j not directly bonded to atom /, and represented by a van der Waals attractive and repulsive energy term. This term is essential for nucleic acid model building in order to maintain a reasonable base stacking such that the stacked base planes are approximately parallel and separated by about 3.4 A. In addition to this, the fourth summation is used to constrain certain specified pairs of atoms at hydrogen bond distances. Thus, we initially specified in the refinement the base-paired secondary structure as well as the tertiary structure hydrogen bonds which could be seen in the MIR and partial group structure Fourier maps. 

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