Ribose conformational equilibria

In summary, these peracylated derivatives lead to conformational equilibria, except in the case where the issue is particularly obvious a-D-xylo, Ci -D-arabino, C4 configurations). The free pentoses in aqueous solution still remain to be seen. The diaxial interactions are stronger than with the acetates and the anomeric effect is weaker. Out of the eight D-pentose configurations, four of them (jS-D-arabinose, a-D-lyxose, a-D-ribose, and jS-D-ribose) lead to a conformational equilibrium. 

The conformational equilibrium of the central pento-furanoae ring, N s S, or 3 2 -endo [17] is frequently coupled with the position of the aglycone [18] but at least in e case of xinsubstltuted ribose this is thought a consequence, not a cause of the observed anti/gg-nreference and will not be discussed here. 

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... 

FIGURE 8-3 Conformations of ribose. (a) In solution, the straight-chain (aldehyde) and ring (/3-furanose) forms of free ribose are in equilibrium. RNA contains only the ring form, /3-D-ribofuranose. Deoxy-ribose undergoes a similar interconversion in solution, but in DNA exists solely as /3-2 -deoxy-o-ribofuranose. (b) Ribofuranose rings in nucleotides can exist in four different puckered conformations. In all cases, four of the five atoms are in a single plane. The fifth atom (C-2 or C-3 j is on either the same (endo) or the opposite (exo) side of the plane relative to the C-5 atom. 

Among the analogs presented in table II 2 amA and 3 amA are a pair of compounds with a high conformational purl d and their ectra are sufficiently resolved to allow the determination of nuclear Overhauser enhancements and longitudinal relaxation rates for the single ribose protons. These two compounds were therefore chosen for a critical check of a previously proposed correlation between the conformational states of the ribose and the syn anti equilibrium (3 6 7) proton relaxation data of the common purine(p)ribosides A G I and X can be quantitative reproduced a correlation between N and anti and S and Bjo. (3 6). Since the four nucleosides represented mixtures of comparable concentrations of the B and S state it ap-... 

An incorporation of nucleotides into different types of DNA results in considerable changes of ribose corrformation (Tables 5.9-5.11). Comparison of the values of pseudo rotation angles in equilibrium and DNA-like conformations demonstrates that these values in B-forms of DNA are systematically lower (AP=36.9°) as compared to the equilibriitm conformation. At the same time we observe noticeable changes of the values of pseudo rotation angles among different nucleotides in similar form of DNA, and for one nucleotide in different types of DNA. These data... 

Fig. 15. Temperature dependence of the equilibrium composition of D-ribose in aqueous (D O) solution p and f signify py-ranose and furanose, and Cl and 1C refer to pyranose ring conformations see Fig. 14.

For a nucleoside in solution, despite the fact that the entire pseudorotation cycle would appear to be accessible, experimental evidence seems to indicate that both preferred regions identified in the solid structures are accessible in solution and that both coexist in a dynamic N / S equilibrium. This equilibrium is defined by the relative amounts of these two populated domains in which each N and S conformation is, respectively, a blend of near neighbors of a P = 0° conformer and a P = 180° conformer. In general terms, the N and S conformations are described as C-Y-endo and C-2 -endo, respectively. Endo (up) and exo (down) indicate the direction of displacement (puckering) of a specific atom in relation to the plane of the other atoms in the ribose ring. For the various twist (T) and envelope (E) forms this is described with numbers in the form of superscripts endo) and subscripts (exo) that indicate the atom being displaced above or below the plane (Figure 2). Finally, for the C-4 —C-5 torsion... 

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