Furanose rings, conformational flexibility

The furanose rings of the deoxyribose units of DNA are conformationally labile. All flexible forms of cyclopentane and related rings are of nearly constant strain and pseudorotations take place by a fast wave-like motion around the ring The flexibility of the furanose rings (M, Levitt, 1978) is presumably responsible for the partial unraveling of the DNA double helix in biological processes. 

Finally, the effect of neomycin-B flexibility on its enzymatic inactivation by Enterococcus faecalis APH(3 ) was tested. This enzyme catalyzes the transfer of a phosphate group from ATP to position 4 of ring I. In this case, the X-ray structure of the enzyme in complex with neomycin-B shows that the antibiotic structure recognized by the enzyme and the target RNA are remarkably similar (see Fig. 7) [40]. In fact, they mainly differ in the conformation adopted by the furanose ring of III (C3-endo and close to C2-endo for the RNA- and enzyme-bound conformations respectively). 

The furanose ring of ribose or deoxyribose is flexible and can be interconverted smoothly among an infinite number of envelope (E) and skew or twist (T) conformations. See Chapter 4, Section A,2. However, there are limits set by steric and anomeric effects.27 62-64 Conformations are often described as in Fig. 5-10 by stating which atom in an envelope conformation lies mostly out of the plane of the other four atoms. If this atom lies above the ring, i.e., toward the base, the ring... 

The second difficulty peculiar to carbohydrates is the allowance for conformational flexibility in the pyranose and furanose rings, which is not easily accounted for by the comparatively simple computer program described above. 

In summary it may be said that AnEryt has a special position compared to the other polyols. The fact that AnEryt models a furanoside and not a pyranoside is of particular importance for dealing with small central atoms. Because of the smaller O-C-C-0 torsion angle in the range from 0 to approximately 40°, the steric demand is smaller than that of pyranoses as could be shown for cobalt(III) complexes [80]. A cA-furanoidic diol thus appears to be a better choice than open-chain diols and, particularly, pyranoidic diol functions. The reason for the conformational flexibility of a furanose ring is its balance of strain. While open-chain diols experience Pitzer strain when twisted into an eclipsed conformation, and pyranoses are burdened with ring strain on being twisted towards 0° torsion, a furanose is characterized by a balance of the various types of strain over a pronounced range of torsions. 

The cyclohexene ring, known to be less rigid than the cyclohexane ring, displays flexibility and conformation similar to those of a furanose ring. This... 

There are many examples of 2H lineshape analyses in the review period, but one of particular interest is the work by Drobny et al.37 This study examines the conformational flexibility of the furanose ring, which is of particular importance in the functioning of DNA. They examined the nucleoside [2 -2H]-2 -deoxycytidine deuterated at the C3 position (Fig. 26(a)) and contained in the sequence [d(CGCGAATTCGCG)]2. The furanose ring... 

The structure discovered by Watson and Crick, referred to as B-DNA, represents the sodium salt of DNA under highly humid conditions. DNA can assume different conformations because deoxyribose is flexible and the C -N-glyco-sidic linkage rotates. (Recall that furanose rings have a puckered conformation.)... 

Furanose rings possess considerable conformational flexibility. The configurations assumed by the rings are important stereochemical characteristics of the three-dimensional structure of DNA and RN A molecules. Statistical analysis of x-ray data has determined the probabilities of alternative conformations of the furanose ring in nucleosides and nucleotides and the free-energy difference <87AX(C)275). However, steric effects alone cannot entirely account for the conformational behavior of various furanose moieties in (modified) nucleosides, and the gauche and anomeric effects are... 

N.m.r. experiments in DjO and DMSO-<4 and molecular mechanics calculations have shown that di-<3-deoxy-3-D-gi ero-pentulose) l,2 2,r- dianhydride (8) is asymmetric with a marked difference in the flexibility of the two furanose rings. Selective deuteration provided efficient markers in the conformational analysis of 2 -deoxyuridine and its 3, 5 -0-Tips derivative H-am.r.-, F.t.i.r.-, and Rarhan-spectroscopy. ... 

Biological CBHs are usually pentoses (five carbon units) or hexoses (six carbon units) which can be found either in linear forms or as cyclic five-membered (furanose) or six-membered (pyranose) rings. Pyranoses have a relatively rigid chair skeleton with dominant C4 or conformations connected by ring inversion. On the other hand, furanoses are more flexible because of the possibility of... 

Any one of the five atoms of the ring can be either above or below the plane defined by the other four in the envelope conformation. The energy barriers separating them are very low, and in cyclopentane or in proline all of the envelope conformations are freely interconvertible through intermediate skew forms.32 Furanose sugar rings are very flexible but the presence of the bulky substituents reduces the number of possible conformations.33-363 See Chapter 5 for further discussion. 

Levitt and Warshel, 1978)or3-5kcal/mol(Kollmanefa/., 1981). This low barrier implies that there may be considerable flexibility in the sugar ring of nucleic acids, with the transient existence of many puckered conformations in the furanose or deoxyfuranose rings in the nucleic add backbone. 

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