Polynucleotides poly binding

The hydrolysis step is more controversial, but one view (Roberts et al., 1969) is that it occurs by a reversal of the sequences followed during cyclization. Recently, Cozzone and Jardetzky (1977) studied the interaction of the single-stranded synthetic polynucleotide, poly(A), in the presence of RNase. They found that the enzyme can carry out the cyclization step on such polypurine nucleotides, but not the hydrolysis step. They interpreted their data to indicate that this nonoptimal substrate forms an enzyme-substrate complex which allows alignment with only one of the two active-site histidines. This emphasizes two important points for the mechanism of pancreatic RNase and other enzymes (1) binding must be correct to have the energetically optimal interaction with the enzyme that will lead to the formation of the transition state ... 

The study demonstrated that single-stranded polynucleotide, such as poly(A), is more flexible than a generic dsDNA. On mica, the long B-DNA binds to mica at many sites and remains intact during drying, while the short DNA binds at fewer sites and settles to an A-DNA structure during dehydration. 

Figure H shows experiments in which metals bind to phosphates and bases simultaneously—i.e., degradation (at pH 7) of the polynucleotides by zinc in the presence of silver ion. Silver inhibits the degradation of Poly A and Poly C, which do not readily react strongly with silver.

The formation of the polynucleotide structure poly(I) is strikingly cation dependent, and relates to the size of the alkali metal cation in the central cavity. Lithium and cesium cations are too small or too large respectively to bind effectively. Na+ occupies a site that is 2.2 A away from four carbonyl oxygens, while K+ is able to occupy a site 2.8 A away from eight carbonyl oxygens.101... 

For the complexation of double-stranded DNA, a more elaborate polynucleotide morphology has been designed via the introduction of homopolynucleotide sequences on the ends for SPG binding [54]. Poly(dA) 80-mer was introduced at both ends of DNA, forming loops which provide protection from degradation by endonucleases, an approach adopted from viruses. 

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