Sugar nucleotides conformations

The recognition mechanism suggested appears to require participation of a specific conformer of the sugar nucleotide in interaction with the enzyme. 

Direct experimental evidence for the existence of an ordered conformation of sugar nucleotides in solutions has been reported by Hirano,344 who observed characteristic optical-rotatory changes for a series of these compounds upon transition from water to concentrated urea solutions. The structural requirements for such an ordered conformation are still not clear. However, data at this point, based on indirect kinetic evidence from hydrogenation and hydroxylamin-olysis reactions (see Section IV, p. 360), seem to accord with the hypothetical model just described. Further studies on the conformations of sugar nucleotides in solution are highly desirable. 

A large number of stable conformations of both natural and synthetic DNA have been observed. They may be characterized in terms of gross structural parameters such as N, the number of molecular asymmetric units in K turns of the helix h, the axial rise per residue and r, the axial rotation per residue. Both right- and left-handed helices have been observed [13, 43]. In typical cases the molecular asymmetric unit is a mononucleotide but dinucleotide asymmetric units have been found in molecules in which the chemical repeat consists of two nucleotides [11]. The nucleotide conformations can be related to the different helical parameters both in terms of the backbone and conformational angles and features such as the sugar pucker and the base-pair displacement and orientation with respect to the helix axis. 

A7obs.-AJf2 ee)Hz and sugar ring conformation (Ja u Hz) for purine emd pyrimidine nucleosides and nucleotides. 

A simple metric to measure the distance between two nucleotide conformations is to compute the rms deviation between the heavy atoms in the backbone of the two nucleotides when their nitrogen bases are superimposed. A variant of this metric consists in calculating the distance between the phosphate atoms only. This allows one to avoid the potential counterbalancing effect of the sugar pucker modes and backbone torsion angles. 

The two others, XXX and XXXI, were created from hydrogen bonding theory. All nucleotide conformations in the motif were assigned C2 - and CJ-endo sugar pucker modes and the glycosylic torsion the syn and anti values. 

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