Ribose puckering

The differing conformations of the ribose have been named with respect to that ring atom which puckers out of the plane given by the other ring atoms. The most prominent conformations are Cy-endo in B-helices and Cy-endo in A-helices. At room temperature both conformers are in a dynamic equilibrium. Intermediates between Cy-endo and Cy-endo are found in several (time-averaged) structures obtained from X-ray crystallography or NMR. When changing the pucker phase... 

Fig. 16.7 Theoretical curves of the CCR rate as a function of the ribose pseudorotation phase angle P for three different pucker amplitudes (i/m = 30, 35 and 40°. A rotational correlation time of 1.5 ns and a C-H distance of 1.07 A has been used for the calculation.

Nucleic acids have two kinds of pentoses. The recurring deoxyribonucleotide units of DNA contain 2 -deoxy-D-ribose, and the ribonucleotide units of RNA contain D-ribose. In nucleotides, both types of pentoses are in their j3-furanose (closed five-membered ring) form. As Figure 8-3 shows, the pentose ring is not planar but occurs in one of a variety of conformations generally described as puckered. ... 

RGURE 8-18 Structural variation in DNA. (a) The conformation of a nucleotide in DNA is affected by rotation about seven different bonds. Sx of the bonds rotate freely. The limited rotation about bond 4 gives rise to ring pucker, in which one of the atoms in the five-membered furanose ring is out of the plane described by the other four. This conformation is endo or exo, depending on whether the atom is displaced to the same side of the plane as C-5 or to the opposite side (see Fig. 8-3b). (b) For purine bases in nucleotides, only two conformations with respect to the attached ribose units are sterically permitted, anti or syn. Fyrimidines generally occur in the anti conformation. 

Lanthanide shift and relaxation probes have been used to show that the family of conformations of 5 -AMP in solution which most closely fits the NMR data is very similar to that of the crystal structure of AMP. This work (758) includes a description of the computer program used for the conformational searches. A subsequent study of cyclic 3, 5 -AMP (762) (Fig. 14) produced families of solution conformations with the pucker of the phosphate and ribose rings similar to that in an approximate X-ray study of the nucleotide. The solution conformation of 5 -CMP is found (763) to be similar to that of 5 -AMP. 

Furanose rings, like pyranose rings, are not planar. They can be puckered so that four atoms are nearly coplanar and the fifth is about 0.5 A away from this plane (Figure 11.8). This conformation is called an envelope form because the structure resembles an opened envelope with the back flap raised. In the ribose moiety of most biomolecules, either C-2 or C-3 is out of the plane on the same side as C-5. These conformations are called C2-endo and C3-endo, respectively. 

Many of the structural differences between B-DNA and A-DNA arise from different puckerings of their ribose units... 

Figure 27.5. Sugar Puckers. In A-form DNA, the C-3 carbon atom lies above the approximate plane defined by the four other sugar nonhydrogen atoms (called C-3 endo). In B-form DNA, each ribose is in a C-2 -endo conformation. 

Oligonucleotides containing 2 -deoxy-2 -fluoro-D-arabinose or -D-ribose form stable, triple-heUcal complexes stabilized by the intermolecular 2 -OH phosphate contacts and sugar puckering these derivatives have promoted interest in relation to compounds synthesized for DNA targeting in vivo Fig. 6 [31]. 

Many of the structural differences between B-DNA and A-DNA arise from different puckcrings of their ribose units (Figure 28,4). In A-DNA, C-3 lies out of the plane (a conformation referred to as C-3 endo) formed by the other four atoms of the furanose ring in B- DNA, C-2 lies out of the plane (a conformation called C-2 endo). The C-3 -endo puckering in A-DNA leads to an 11 -degree tilting of the base pairs away from the normal to the helix. The phosphates and other groups in the A helix bind fewer H>0 molecules than do those in B-DNA. Hence, dehydration favors the A form. 

NMR structure of a 2 -deoxy-2 -fluoro-D-arabinose (aF) nucleic acid duplex has been reported. The structure is a hybrid hairpin duplex containing a ribose-aF stem duplex and a four-residue DNA loop (177). The RNA strand adopted the classical A-form structure with endo sugar puckers, whilst the aF strand contained O -endo puckers and was intermediate between A- and B-form, similar to that found in DNA-RNA structures. 

In the case of furanosides, especially nucleosides, Altona and Sundara-lingam s original symbols for the pseudorotational angle P and pucker (or sometimes (p are used P = is defined as the T2 conformation. Figure 2.4 shows the pseudorotational itinerary, with a nucleoside (sugar D-ribose) as an example. Nucleoside chemists refer to conformations with 0 < P < 36° as N ... 

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