Polynucleotides interaction with nucleotides

Rosenberg, M., Wiebers, J.L., and Gilham, P.T. (1972) Interactions of nucleotides, polynucleotides, and nucleic acids with dihydroxyboryl-subsdtuted celluloses. Biochemistry 11, 3623-3628. 

Fig. 8 Model for the response of polynucleotide-sensitive copolymers of NIPAM and derivatives of phenylboronic acid and phenylthiourea on silicon surfaces. Interaction with the nucleotide is supposed to result in unwinding of the polymer structure, causing decrease in contact angle by exposure of hydrophilic moieties. Reprinted, with permission, from [83]. Copyright (2009) American Chemical Society...

Cibacron blue Nucleotide-requiring enzymes, enzymes that interact with oligonucleotides and polynucleotides... 

Polynucleotides such as DNA and RNA are linear sequences of nucleotides linked by 3 - to 5 -phosphodiester bonds between the sugars (Fig. 12.1). The bases of the nucleotides can interact with other bases or with proteins. 

More than 100 enzymes are Involved in the biosynthesis,modification,polymerisation, or degradation of nucleosides and nucleotides, many more act upon the polynucleotides, I A and RNA, or they require nucleotide coenzymes and nucleotides like ATP as cosubstrates or allosteric effectors. Besides their specific catalytic functions all these proteins should exhibit certain common modes of protein - nucleotide Interactions because the amino, Imlno, carbonyl, hydroxyl, and phosphate groups of nucleotides represent but a limited array of substituents capable to Interact with protein residues (Figure 1). There are, however, surprisingly few systematic studies on the structural origins of nucleotide specificity. 

M. Rosenberg, J. L. Wiebers and P. T. Gilham, Studies on the interactions of nucleotides, polynucleotides, and nucleic acids with dihydroxy-boryl-substituted celluloses. Biochemistry, 1972,11(19), 3623-3628. 

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 ... 

Interaction of Polynucleotides with Nucleosides, Nucleotides, and Purines... 

DNA hybridization Chemical interaction of DNA based on the ability of ssDNA to form a helix, dsDNA with a counterpart exhibiting nucleotide sequence complementarity. A process of the formation of dsDNA from ss polynucleotide chains based on complementary base pairing. 

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