Canonical base pairings

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)...

The presence of ions not only affects canonical base pairs [22], but promotes the formation of triplexes and other non-canonical DNA structures [23]. The effects of these interactions span from modifications of the renaturation kinetics of thermally denaturated DNA [24] to the known anti-tumoral and mutagenic activity of cisplatin [25]. 

The theoretical. Sj nonradiative lifetimes by Markwick and Doltsinis [55] are in agreement with recent experimental observations [2, 79] which suggest that the canonical base pairs are extremely short-lived, the GC lifetime being of the order of 100 fs. This is also in accord with the scenario sketched by ab initio... 

The fact that U38, a conserved residue critical for catalytic activity in the L1L family, is docked into the ligation site and makes a canonical base pair with a constituent of the ligation site A51 in the docked conformation, whereas in the undocked conformation it is positioned 40 A away from the site, has led to the postulate that the former is more likely representative of a catalytically active state [64]. 

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. 

Fig. 24.1 Structure of the B-DNA double helix. Enlarged Lewis structures depict the single strand and the canonical base pairs (AT and GC) with their hydrogen bond donor/acceptor pattern inside the minor and major groove indicated by arrows...

There is a general pattern of the DNA base pair - water interaetions. One may see that the interaction with water molecules destabilize hydrogen-bonded rare tautomers. In other words, the interaction with water molecules makes more stable canonic base pairs. This is in complete correspondence with the above... 

Abstract This review summarizes computational studies devoted to interactions of metal cations with nucleobases, nucleotides, and short oligonucleotides considered as DNA/RNA models. Since this topic is complex, basically only the results obtained using ab initio and DFT methods are discussed. Part 1 focuses mainly on the interactions of the isolated bases with metal cations in bare, hydrated, and ligated forms. First, interactions of bare cations with nucleobases in gas phase approach are mentioned. Later, solvation effects using polarizable continuum models are analyzed and a comparison with explicitly hydrated ions is presented. In Part II, adducts of alkali metal, metal of alkaline earth, and zinc group metal cations with canonical base pairs are discussed. A separate section is devoted to platinum complexes related to anticancer treatment. Stacked bases and larger systems are discussed in last section. Here, semiempirical methods and molecular modeling are also discussed due to extensive size of studied complexes. 

Figure 1 GAGA tetraloop extracted form the sarcin-ricin loop, (a) Secondary structure of the tetraloop. The backbone connectivity is shown with thin lines, the canonical pairing with a thick line, and the non-canonical piairing with a thin dotted line. Only the last canonical base pair of the stem is shown, (b) Stereoview of one of the NMR spectroscopy three-dimensional structures. The Cu Gig Watson-Crick base pair is shown in blue. The non-canonical A G base pair is shown in green...

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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