Polynucleotide backbone

Most reactions of nucleic acid hydrolysis break bonds in the polynucleotide backbone. Such reactions are important because they can be used to manipulate these polymeric molecules. For example, hydrolysis of polynucleotides generates smaller fragments whose nucleotide sequence can be more easily determined. 

The illustration opposite shows selected nucleic acid molecules. Fig. A shows various conformations of DNA, and Fig. B shows the spatial structures of two small RNA molecules. In both, the van der Waals models (see p. 6) are accompanied by ribbon diagrams that make the course of the chains clear. In all of the models, the polynucleotide backbone of the molecule is shown in a darker color, while the bases are lighter. 

The computations described briefly in this paper illustrate the interrelationship between the local structure and macroscopic behavior of the DNA helix. Statistical mechanical studies help to identify the most likely morphological arrangements of the polynucleotide backbone and to understand the macroscopic flexibility of the DNA as a whole. Model building and potential energy calculations uncover the detailed local geometries of the chain and clarify the likely pathways between the multitude of allowed spatial forms. 

Mg2+. They are attracted to the negative charges on the polynucleotide backbone and, although they remain mobile, they tend to occupy a restricted volume.175 177 Some may bind in well-defined locations as in Fig. 5-8. Because of the presence of these positive ions the interactions of nucleic acids with cationic groups of proteins are strongly affected by the salt concentration. 

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. 

An additional practical consideration for measurement of RNA using SAXS is the relatively high scattering contrast of RNA molecules relative to that of proteins as a result of the high density of phosphate moieties in the polynucleotide backbone. This means that shorter exposure times or more dilute samples may be used compared to SAXS measurements for proteins. 

Figure 14.24. Illustration of the expected NOESY correlations along the polynucleotide backbone.

Type I topoisomerases catalyze the relaxation of supercoiled DNA, a thermodynamically favorable process. Type II topoisomerases utilize free energy from ATP hydrolysis to add negative supercoils to DNA. The two types of enzymes have several common features, including the use of key tyrosine residues to form covalent links to the polynucleotide backbone that is transiently broken. 

The strands must be antiparallel (one strand is 3 - 5 while the other is as described in Chapter 28) to maximize hydrogen bonding because the stereo-genic nature of the ribofuranose and deoxyribofuranose units leads to a twist in the polynucleotide backbone. The term stereogenic is described in Chapter 9, Section 9.1. These hydrogen bonding base pairs are called Watson-Crick base pairs the C-G pair is shown in 97 and the A-T base pair is shown in 98. The inherent chirality (see Chapter 9) of the D-ribofuranose and the D-deoxyribofura-nose leads the P-form of DNA to adopt a right-handed helix (see 99). 

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