Sugar puckers parameters

CPMAS solid-state NMR has been used to investigate the dependence of sugar chemical shifts on specific conformational parameters of a variety of ribonucleotides and ribonucleosides. The distinct effects of sugar puckering on the Cl, C4, and C5 resonances of Cj endo (S type) and C3 endo (N type) furanoid conformations allow us to separate them into two groups. 

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. 

Molecular dynamics simulations performed on the NP-modified sequence starting in A and B form also lead to structures which are rather close to each other (within 1.9 A for all atom, or 1.5 A for the central 8 residues) and belong to the A family. These structures are also 1.7-2.3 A (or 1.4-2.0 A for the 8 cpre residues) fi-om canonical A DNA and are 6.4-7.0 A (3.0-5.0 A) fix)m canonical B DNA. Examining the structural parametars we could also demonstrate that the % angle, sugar pucker, x-displacement and twist are much closer to those characteristic of A than B structures, alfiiough the standard deviations for those parameters are higho than for the normal... 

The free energy of the sugar moieties of deoxyrlbonucleosides was calculated for a wide range of puckering parameters using different force fields. The resulting data were compared with 224 structures from DNA sin e crystal X-ray data. A modified Weiner s force field yielded excellent a eement.i79... 

Another important parameter is the sugar puckering mode which is strongly dominated by the C3 - and C2 -endo conformations, as found respectively in the A- and B-form... 

There are many homonuclear and heteronuclear couplings that are sensitive to the conformation, that is, pucker, of the five-membered sugar ring. The parameters for generalized Karplus equations for 3J7hh couplings have been given,214,215 and parameters for 3/H3 Ci, l H2 C4, 2/h2 CiS 2/h3 C2, 2/h2 C3, and 2.7h3 C4 have been reported.213... 

There are two preferred orientation anti and syn) of the base with respect to the sugar, as determined by steric restrictions during the torsion (%) about the CT—N glyco-syl bond. The sugar is nonplanar, and two of its common puckering modes are C2 -endo (S-type) and C3 -endo (A-type). The secondary stracture of DNA can be described by a number of parameters that define the helix (Dickerson et al 1989) ... 

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