Puckering furanose ring

Energy profiles in Figure 14 also reveal that planar furanose forms are often of lower energy than puckered conformers. For example, relative conformational energies determined for 7 with the 3-21G basis set indicate that the planar conformer is more stable than the Eq conformer in 8, the planar conformer is calculated to be more stable than. These observations suggest that the conformational dynamics of some furanose rings may not be completely described by pseudorotation in these cases,conformer interconversion may occur by both inversion and pseudorotational pathways, with the latter being the more preferred route. 

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. 

The conformational effects arising from the endoanomeric effect are for furanoses much less profound and as a result relatively little research has been performed in this area. The puckering of the furanose ring of an a and a P anomer usually adjusts the anomeric substituent in a quasi-axial orientation and hence both anomers experience a similar stereoelectronic effect. On the other hand, the conformational preference of the exocyclic C—O bond is controlled by the exoanomeric effect in the usual way. 

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 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. 

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.)... 

Fig. 9.13. Polar diagram of the puckering phase 0 (°) vs. the puckering amplitude (A) of 181 non-fused furanose rings in fragments of type 11 found in the CSD release July 1991 (no disorder, no error flag, i <0.08). The numbers show the position of some selected ring conformations 1(0°) envelope (e) with mirror plane through C(2 ) endo 2(144°) e C(3 ) endo 3(324°) e C(3 ) exo 4(180°) e C(2 ) exo 5(126°) twist with C2 axis through C(T) 6(72°) e O(l ) endo...

One characteristic difference between the A and B forms of DNA is the pucker of the furanose rings that changes from C-2 -endo-anti in the B form to C-3 -endo-anti in the A form. It is this change in ring pucker that gives rise to the A-form marker band at 811 3 cm mentioned above. 

Sugar pucker The furanose rings are twisted out of plane in order to minimize nonbonded interactions between their substituents. This puckering is described by identifying the major displacement of C2 and C3 of pentose from the median plane of CT—04 —C4. Thus if the endo-displacement of C2 is greater than the exodisplacement of C3, the conformation is called CT-endo and so on. The endo-face of the furanose is on the same side as C5 and the base the exo-face is on the opposite face to the base. 

For the furanose ring, which is adopted by some hexoses and pentoses, the five-member ring is only slightly puckered and exists in three forms, the more common envelope (E) and the less common twist (T). For the more stable envelope forms, and E3, the conformation is defined by the C3 atom that is above or below, the plane (described by C1,C2, C4 and 04). 

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