DNA phosphodiesters

DNA (phosphodiester) hydrolysis has also been examined with [Co(cyclen)(OH2)(OH)]2+ as the active species.1239,1246 Significant rate enhancement of linear1247 and supercoiled1248 double-stranded polydeoxyribonucleotide hydrolysis is observed by immobilizing the Co complex on a polystyrene support. Wider exploration of reactions with DNA follow. 

Now that we have the monomers, which are pretty complex in this case, it remains to define how they are joined together to create the polymer. The amino acids in proteins are linked by peptide bonds. The nucleotides in nucleic acids are linked by phosphodiester bonds, as is shown in figure 12.2. These DNA phosphodiester bonds are very stable. Indeed, samples of largely intact DNA can be recovered from organisms that have been extinct for thousands of years. This remarkable stability should not come as a surprise the central importance of DNA in all forms of life requires that it be stable to various sorts of insults. 

Fig. 12. Asymmetry of the DNA phosphodiester backbone trace as seen in the Oak Ridge NCP structural model (PDB access code lEQZ). No attempt has been made to regularize the geometry of the DNA positions of phosphates are based solely on the experimental electron density. Here the two DNA gyres are overlaid, with the 72 bp ventral gyre in red and the 73 bp dorsal gyre in blue. The minor groove positions facing the histone core are numbered sequentially from the dyad axis. The most pronounced asymmetry is seen in position 2 (10 o clock).

Figure 9.33. Hydrolysis of a Phosphodiester Bond. All restriction enzymes catalyze the hydrolysis of DNA phosphodiester bonds, leaving a phosphoryl group attached to the 5 end. The bond that is cleaved is shown in red.

C) The abihty to form multiple hydrogen bonds between the protein peptide backbone and the DNA phosphodiester backbone... 

Fig. 8.4. First-generation generalized structures of natural DNA (phosphodiester) and three antisense oligonucleotide derivatives tested as antisense drugs. (Adapted from Agrawal S, Iyer RP. Perspectives in antisense therapeutics. Pharmacol Ther 1997 76 151-160 with permission.)...

Coumarin derivatives also act on type II topoisomerases, which are enzymes that break and re-legate DNA phosphodiester bonds while crossing over DNA strands and altering DNA topology. Therefore, they can interfere with the spatial organization of chromatin and are involved in several crucial biological functions, such as DNA replication and transcription, and chromosome segregation [166]. 

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