Hydrogen bonding to DNA

The primary hydration shell is different from bulk water. Of the 20 water molecules per nucleotide, only 11 to 12 are directly bound to DNA. They form a shell which is impermeable to cations [861] and does not freeze into an ice-like state [862], It is these water molecules which are observed in crystal structure analyses and are hydrogen-bonded to DNA oxygen and nitrogen atoms. 

The solution is then cooled to 60°C allowing new hydrogen bonds to form [Fig ure 28 14(c)] However the reaction mixture contains much larger concentrations of two primer molecules than DNA and the new hydrogen bonds are between the separated DNA strands and the primers rather than between the two strands... 

Molecular dynamics simulations have also been used to interpret phase behavior of DNA as a function of temperature. From a series of simulations on a fully solvated DNA hex-amer duplex at temperatures ranging from 20 to 340 K, a glass transition was observed at 220-230 K in the dynamics of the DNA, as reflected in the RMS positional fluctuations of all the DNA atoms [88]. The effect was correlated with the number of hydrogen bonds between DNA and solvent, which had its maximum at the glass transition. Similar transitions have also been found in proteins. 

Like Thr 124 and Thr 215, the Asn 69 and Asn 159 residues occupy equivalent positions in the two homologous motifs of TBP. By analogy with the symmetric binding of a dimeric repressor molecule to a palindromic sequence described in Chapter 8, the two motifs of TBP form symmetric sequence-specific hydrogen bonds to the quasi-palindromic DNA sequence at the center of the TATA box. The consensus TATA-box sequence has an A-T base pair at position 4, but either a T-A or an A-T base pair at the symmetry-related position 5, and the sequence is, therefore, not strictly palindromic. However, the hydrogen bonds in the minor groove can be formed equally well to an A-T base pair or to a T-A base pair, because 02 of thymine and N3 of adenine occupy nearly stereochemically equivalent positions, and it is sufficient, therefore, for the consensus sequence of the TATA box to be quasi-palindromic. 

Molecules of DNA consist of two complementary polynucleotide strands held together by hydrogen bonds between heterocyclic bases on the different strands and coiled into a double helix. Adenine and thymine form hydrogen bonds to each other, as do cytosine and guanine. 

The platinum(IV) compound that has shown most promise is carboplatin (paraplatin), which received FDA approval in 1990. Features to note in its structure are the use of hydroxy and carboxylate groups to improve water solubility. As noted above, the ammine ligand has been found to need at least one hydrogen, possibly for hydrogen-bonding to phosphate groups in the DNA (Figure 3.116). 

The ability of DNA to replicate lies in its double-helical structure. There is a precise correspondence between the bases in the two strands. Adenine in one strand always forms two hydrogen bonds to thymine in the other, and guanine always forms three hydrogen bonds to cytosine so, across the helix, the base pairs are always AT and GC (Fig. 19.29). Any other combination would not be held together as well. During replication of the DNA, the hydrogen bonds, which are... 

In DNA, base pairing occurs between guanine and cytosine in its most stable form [87], as in [92]. However, cytosine in its imino form [91] is able to form a hydrogen bond to adenine as in [93], and such a base pairing could lead to the formation of mutations if it continued in DNA replication. The kinetics of the tautomerisation of purine and pyrimidine bases has been... 

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