Non-canonical base pairs

Figure 6.2 Structure of frans-activation response (TAR)-aptamer kissing complexes. The DNA D-04 (left) and the RNA aptamer R-06 (right) are shown in green. The crucial non-canonical base pairs are indicated in red (Collin et al 2000 Duconge and Toulme, 1999). (see Color Plate 5)...

Non-canonical base pairs The helices in RNA are generally short (lObp or less) and usually include unpaired nucleotides and non-canonical bps (bps other than G—C and A—U). Non-canonical bps present chemical groups in either the major or minor groove of the helix that can be used for unique tertiary interactions. 

GenBank of the NCBI, NIH Non-canonical base pair database Nucleic Acid Database (NDB) Oligonucleotide calculation PseudoBase ... 

Nagaswamy U, Voss N, Zhang ZD, Fox GE Database of non-canonical base pairs found in known RNA structures. NucleicAcids Research 2000, 28(1) 375— 376. 

It is demonstrated that the spatial proximity of H nuclei in hydrogen bonded base-pairs in RNAs can be conveniently mapped via solid-state MAS NMR experiments involving proton spin diffusion driven chemical shift correlation of low-frequency nuclei such as the imino and amino nitrogens of nucleic acid bases.As different canonical and non-canonical base-pairing schemes encountered in nucleic acids are characterised by topologically different networks of proton dipolar couplings, different base-pairing schemes lead to characteristic cross-peak intensity patterns in such correlation spectra. The method was employed in a study of a 100 kDa RNA composed of 97 CUG repeats that has been implicated in the neuromuscular disease myotonic dystrophy. N- N chemical shift correlation studies confirmed the presence of Watson-Crick GC base pairs in (CUG)g7. 

The field of aptamer and aptazyme research has seen an explosion of publications over the last few years, and there have been reviews published during this review period,together with some method development advances. As in previous years most aptamers and aptazymes are evolved using DNA rather than RNA, despite the fact that RNA can adopt more structures and many non-canonical base pairs, though of course this is probably a reflection of the fact that RNA is far more susceptible to degradation. During this review period there are also examples of aptamers constructed from non-native oligonucleotides. 

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