Structural studies of CNG repeats.
Bottom Line: Each homobasic pair is accommodated in the helical context in a unique manner, with consequences for the local helical parameters, solvent structure, electrostatic potential and potential to interact with ligands.The detailed three-dimensional profiles of RNA CNG repeats can be used in screening of compound libraries for potential therapeutics and in structure-based drug design.Here is a brief survey of the CNG structures published to date.
Affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.Show MeSH
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Mentions: What keeps the uridines apart and prevents them from realising their full base-pairing potential? It is likely that this non-canonical pairing is stabilized by the strong flanking C-G and G-C pairs, which maintain the duplex in a clearly recognisable A-form (Figure 3A). The stability of the U-U pairing is reinforced by ordered water molecules in the major and minor grooves. These waters contribute to the H-bonding network and can be considered a part of the structure. Duplexes comprising CUG repeats have a characteristic pattern of surface electrostatic potential in their minor groove (Figure 4) that comprises alternating bands of positive and negative potential along the direction of the helix axis. The major groove shows no regularity and is predominantly electronegative with positive patches. The hydrogen-bonding potential of the duplexes is demonstrated by their interactions with ordered water molecules and small ligands present in the crystallisation medium (glycerol and sulphate ions). These interactions could be used as a guide in structure-based drug design. The paper also includes a new analysis of the data obtained by Mooers et al. (62). After detwinning the diffraction intensities, the structure of the [(CUG)6]2 duplex (PDB code 3gm7) corresponds closely with the structure of the shorter duplexes.
Affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.