Rotations about the glycosidic

Figure 11. An externally bound BPDE l(+)-N2(G) adduct, (upper) The pyrene is placed in the major groove after an anti - syn rotation about the glycosidic bond of G by 200° in an otherwise B-DNA conformation. (lower) The pyrene moiety is placed in the minor groove in a DNA conformation with a -70° kink, a(BPDE) = 15° and y(DNA = 35°.

The turning of the key once the complex has formed is a separate issue. In this regard, Lemieux (47) has pointed out that rotation about the glycosidic bond must weaken the exo-anomeric effect and thereby importantly activate the anomeric carbon to nucleophilic attack. Therefore, it seems likely that the role of the key hydroxyl group of the aglycon is to accommodate the rotation prior to the attack by water to form / -D-glucopyranose, which is the first product of the reaction. 

The evaluation of the dipole moment of uridine as a function of the rotation about the glycosidic bond has been carried out by the FOILO method by Weiler-Feilchenfeld et al,237 (for the C -endo gg and CJ-endo gg conformations). The same method has been used by Berthod and Pullman238 to calculate the dipole moments of anti and syn conformers of uridine, C -endo gg (7.0 and 3.4 D, respectively) and those of dcoxyuridinc, Cj-endo gg (4.8 and 4.8 D, respectively). For the -contributions for the dipole moments of uraoils see refs. 174,177,407. 

Dipole moment of cytidine as a function of rotation about the glycosidic bond has been calculated by the ZNDO method by Kang (for the different puckerings of the sugar, o<4 )-o(5 ) = 300°) and by the PCILO method by WeUer-Feilchenfeld et td. (for... 

For some linkages, at least, it is possible to detect a substantial influence on the rotation about the glycosidic bond from the exo anomeric effect this evidence is from coupling constants (74T1933 80CJC631) and... 

Fig. 24. Conformational map for rotation about the glycosidic bond in C(3 )-endo nucleosides of uridine and thymidine...

The 5 -triphosphate deoxynucleoside derivatives of pyrrole-3-carboxamide and pyrrole 3,4-dicarboxamide have been incorporated into DNA with DNA polymerases. They are preferentially incorporated with Klenow fragment where they are incorporated as either dA or dC. The base analogue 1,2,4-triazole-3-carboxamide (124) can exist in four different conformations by rotation about the glycosidic or carboxamide bonds, and thus can in principle behave as a universal base. The analogue has been examined by NMR in duplexes opposite G and T where it is anticipated that it would adopt syn and anti conformations, respectively. NMR showed that in both duplexes, the complementary nucleotide adopted a syn conformation, and the carboxamide group is able to adopt two rotational isomers. 

The exo-anomeric effect is illustrated in Fig. 3, which shows three staggered orientations for rotation about the glycosidic bond in both the a and p anomer of methyl D-glycopyranoside. These are referred to as -I-sc),... 

When NAD+ is bound to GAPDH there is a 180° rotation about the glycosidic bond linking the ribose to the nicotinamide moiety, compared to the conformation of NAD+ in LDH, s-MDH, and by inference in LADH. The effect of this rotation is to change the available side of the nicotinamide ring, one side being blocked by hydrophobic residues on... 

These are the "unperturbed values iil the root-mean-square, end-to-end distance. Calculated aasuming free rotation about the glycosidic bond, from the model of Eliczer and Hayman. ... 

Table 5 contains ribonucleotides with the common amino and carbonyl structures, with extra substituents, and with totally unsubstituted bases like purine or benzimidazole. Apparent values and velocities do not vary more than about tenfold in the presence of specific effector deoxyribonucleotides. Guanine and cytosine nucleotides have usually fastest and compounds with fewer base substituents show decreased reaction rates. Loss of substrate activity is only observed in syn-oriented nucleotides where the nucleobase is rotated about the glycosidic bond like in 8-bromo-ADP or -ATP. Molecular conformation-enzyme activity relationships have been discussed in detail ... 

The rationale for the correct setting of current knowledge about the shape of polysaccharides in solution is based on three factors the correlation between primary structure (i.e., the chemical identity of the carbohydrates polymerized in the chain), intrinsic conformational features dictated by the rotational equilibria (often the major contributions are due to the rotation about the glycosidic linkages) and the interaction with the other mo-... 

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