Ribofuranose, conformation

Gautier A. Phosphate mimic of nucleotides, conformational influences on the ribofuranose conformations. Heterocycles 2006 67 823-837. 

Hydantocidin. Hydantocidin (182), C2H2QN2O3, is elaborated by S. hygroscopicus (278). It is unique in that the anomeric carbon of the ribosyl moiety forms the spHo bond of hydantoin (279). The ribofuranose moiety which has been reported to be in a Q -endo conformation (279) has been synthesized (280,281). Hydantocidin is a herbicidal nucleoside with activity against monocotyledenous and dicotyledenous plants. 

P2j Z = 2 Dx = 1.33 R = 0.09 for 792 intensities. The molecule is tricyclic, with a five-membered and a seven-membered ring fused to the ribofuranose ring. Both five-membered rings have an envelope conformation. The seven-membered ring has the same conformation as is found in 2,5-arabinosylcytidine monophosphate.79 ... 

The conformational properties of furanose rings have received considerable attention in recent years because of the impact these properties may have in mediating biological processes . Most notable in this respect are the p-D-ribofuranose 1 and 2-deoxy-p-D-erythro-pentose 2 (Scheme 1) components of ribo- (RNA) and deoxyribonucleic (DNA) acids. It is well known that the furanose ring adopts specific shapes depending on its local structural environment in a biopolymer. For example, in tRNA, the... 

Vitamin Bi2 is a D-ribofuranose derivative, and the structure of vitamin B12 5 -phosphate, a precursoi 11 of vitamin B12, has been determined. The a-D-glycosidic bond lies 16° (0.51 A) out of the plane of the 5,6-dimethylbenzimidazole ring, because of steric or nonbonded interactions. The D-ribofuranose moiety has that envelope conformation having C-2 exo (0.77 A exoplanar) C-3 and C-5 bear phosphate groups. 

Relatively small differences in the puckering of the ribofuranose ring are amplified in the orientation of the 0(30 and 0(5 ) atoms to which, in the nucleic acids, the phosphate groups are bound. For this reason, extensive analyses have been made of the relationship between ring conformation and the overall stereochemistry of the nucleic acid molecules. 

Fressigne C, Piettre SR, Condamine E, Altona C, Gautier A. A C3 modified nucleotide. The difluorophosphonate function, a phosphate mimic, governs the conformational behaviour of the ribofuranose. Tetrahedron 2005 61 4769-4777. 

Nucleosides with a bicyclic sugar ring are often called conformationaly restricted or looked. The two major conformations of natural nucleosides are C-3 -endo and C-2 -endo. The formation of a second ring induces a restriction of the pseudorotational cycle of the ribofuranose puekering. The application of bicyclic nucleosides goes from the synthesis of modified oligonueleotides to enzyme inhibitors. 

Twist conformations have been assigned to 2,3-O-isopropylidene-D-ribofuranose,18 but, strangely, the n.m.r. data for 2,3-O-isopro-pylidene-L-rhamnofuranose derivatives were not evaluated.101... 

The early development of the Karplus relationship has been outlined in Section 1.4 (see p. 60). The significance of this method was soon realized by Jardetzky and by Lemieux, who applied it to the determination of the conformation of the o-ribofuranose and 2-deoxy-D-eri/first time, that furanoid rings are nonplanar in solution. However, it was not realized at that time that the Karplus parameters are subject to a substituent effect, so the original parameters were used hence, the particular values obtained in these investigations may require some slight modification. All of the following empirical modifications of the Karplus parameters were based on the intuitive assumption that allowance must be made for a substituent effect, and this step has only recently been justified by Williamson, and by Laszlo and Schleyer. ... 

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. 

The operation of the anomeric effect in furanosyl derivatives is less clear. A vast amount of data has been accumulated on nucleotides and deoxy nucleotides, but the bulky substituents at C4 and Cl of the ribofuranose ring ensure that the conformational choice for these compounds is between N (VI) and S (VII), in both of which the aglycone is eclipsing one lone pair on oxygen (regarding them as equivalent) [24]. 

Figure 1.71 Main conformational preferences of 2 -deoxy-p-D-ribofuranose rings in polydeoxynucleotides (right). Cartoon illustration of these main envelope conformations (left) (illustrations from Sinden, 1994, Fig. 1.4).

Other than B-form DNA, there are other forms of DNA that are more distorted from Watson and Crick ideality. These include A-form, C-form, D-form and T-form DNA. Of these, A-form DNA is the most similar to B-form DNA (Figure 1.73). The only major difference is that the 2 -deoxy-/3-D-ribofuranose rings of A-form DNA exist in an alternative C -endo twist conformation (Figures 1.71 and 1.73). Consequently, the helix diameter is wider and there are 11 base pair residues per turn (Table 1.2). A-form DNA also possesses shallow major and minor grooves. Z-form DNA, by contrast, is radically different from B-form... 

DNA (Table 1.2) (Figure 1.74). The helbc sense of Z-form DNA is now left handed and the backbones of the two poly deoxynucleotide chains map out a zigzag spiral path. This results from the tendency of deoxyguanosine nucleotide residues to distort so that their 2 -deoxy-/3-D-ribofuranose rings adopt a C -endo instead of C -endo twist conformation (Figure 1.71). However, in addition, the guanine bases move to a syn conformation (positioned over the top of their attached furanose rings), instead of the more usual anti conformation... 

---