Biology Reference
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190
RIBOSE RING STRUCTURE
As illustrated in Fig. 7-1, the ribose ring structure is not planar. The C 2 '
atom or the C 3 ' atom can be displaced out of the plane towards the C 5 ' atom.
Thus, even though the C 3 '-C 4 ' bond is not free to rotate, it can assume
several different positions, commonly referred to as pucker (Sarma, 1980).
Thus, it provides additional complication to the backbone structure of
polynucleotides, similar to the idea that peptide bonds in polypeptides may
not be completely planar.
Therefore, to understand the complete nature of periodic or secondary
structures of DNA and RNA requires detailed calculations of all sterically
allowed configurations. Such calculations must be carried out in the five-
dimensional space defined by angles and together with the
glycosidic bond defined by and the puckering phase and amplitude of the
ribose ring structure (Marzec and Day, 1993; Murthy et al ., 1999). As
mentioned before, various authors use different designations for these
angles. Some of them are listed in Table 7-2.
Table 7-2. Notations used to designate rotations around single bonds of a nucleotide.
Bond
Wu, 1968
Metzler, 1977
Murthy et al ., 1999
Unified notations, as well as conventions of angles, can then provide a
careful study of polynucleotides conformations (Murthy et al ., 1999) similar
to the Ramachandran plot for polypeptides.
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