Polynucleotides, conformational analysis

Sundaralingam, M. The concept of a conformationally rigid nucleotide and its significance in polynucleotide conformational analysis Sundaralingam, M., Ed. Jerusalem, 1973, pp 417-456. 

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. 

While these "energies" are necessarily approximate, they afford a basis for clear discrimination between sterically allowed and sterically forbidden structures. The "energy" approach also offers a means to extrapolate experimental studies (nmr, X-ray, etc.) on the conformation of small model compounds to the polynucleotide level and to test the relevance of the data in a helical complex. In addition, the method provides a starting point for a refined potential energy analysis of double helical conformation and stability. 

The analysis obtained with classical polarographic methods corresponds roughly with those reached by the pulse-polarographic technique, but the sensitivity is much lower. The difference between the polarographic behaviour of single-stranded and double-helical form of polynucleotides makes possible the study of the conformation of nucleic acids [81,82,108-113]. Polarography can be utilized also in the study of structural changes of polynucleotides under the influence of the temperature [112,114,115] or irradiation [116]. The photodynamic destabilisation of DNA has been described [117]. 

Second, in small molecules, the NOE builds up slowly and attains a theoretical maximum of only 50%, as noted earlier in the ID context. (See Section 5-4 and Appendix 5.) Because a single proton may be relaxed by several neighboring protons, the actual maximum normally is much less than 50%. (Of course, the same problem exists in the ID NOE experiment.) Moreover, as the molecular size increases and behavior departs from the extreme narrowing limit, the maximum NOE decreases to zero and becomes negative. Thus, particularly for medium-sized molecules, the NOESY experiment may fail. For larger molecules, whose relaxation is dominated by the Wq term, not only is the maximum NOE —100% rather than +50%, but also the NOE buildup occurs more rapidly. The NOESY experiment thus has been of particular utility in the analysis of the structure and conformation of large molecules such as proteins and polynucleotides. 

The preceding considerations, together with others drawn from the results of model building studies and from an analysis of the substrate specificity of pancreatic RNase (v. infra) are discussed more fully elsewhere all are consistent with the following formulations in contrast to normal nucleotides (1) formycin residues in polynucleotides are subject to conformational transitions which tcike place at the glycosyl bond. (2) The formycin nucleotides are (a) anti in ordered double-stranded structures of the Watson-Crick type (b) syn in neutral poly F and (c) probably a mixture of syn and anti in single stranded copolymers. 

The strongest evidence that the proposed conformational abnormalities actually occur in the polynucleotide analogues considered here emerges from the stereochemical analysis of the catalytic specificity of pancreatic RNase. 

Scope of data. This chapter covers metal ion interactions with DNA, RNA and polynucleotides. A few related data involving oligonucleotides are included when necessary and appropriate. Oligomers when crystallized for X-ray analysis resemble polymers and are treated as such. The subject matter is limited to direct effects of metal binding, e.g. metal association constants and binding characteristics, metal binding effects on conformation, and metal-catalyzed depolymerization. There are of course many other phenomena that could be included, but are deemed unsuitable for tabulation. The effects of metal binding to DNA and RNA that involve interaction with proteins are covered only when the primary effect is on the nucleic acid moiety. 

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