Helices coaxial stacking

Fig. 7 The two-stage folding scheme for the hammerhead ribozyme, as proposed by Tilley s group [77-80]. The arrow indicates the cleavage site. The scheme consists of two steps to generate the Y- or y-shaped ribozyme/substrate complex. The higher affinity of Mg is related to formation of domain II (structural scaffold non-Watson-Crick pairings between G12-A9, Ais-Gg and A14-U7 forming a coaxial stack between hehces II and III that runs through G12A13A14) and the lower affinity of Mg to formation of domain I (catalytic domain formation by the sequence C3U4G5A6 and the C17 with the rotation of helix I around into the same quadrant as helix II) [78]...

This preliminary report presents recent progress in secondary structure prediction based on free energy minimization. The following changes have been implemented The method for forcing base pairs has been improved. A filter that removes isolated Watson-Crick or G-U base pairs (those that cannot stack on any other Watson-Crick or G-U pair) has been incorporated. Recently measured free energies for 2 by 2 internal loops (Xia, T. McDowell, J. A. Turner, D. H. In preparation.), 2 by 1 internal loops (75), and hairpin loops 18) have also been incorporated. Finally, a new model for coaxial stacking of helixes has been developed. 

Figure 1. Coaxial Stacking of two helixes with an intervening mismatch. Stack 1 is the stack of the mismatch with a continuous backbone. Stack 2 is the stack of the mismatch with an open backbone.

An essential characteristic of DNA is x-stacking. The base pairs are separated by 3.4 A, which is the rise of the double helix per base pair. The stacking is not offset and the different base pairs are essentially coaxial with the local stacking axis. The stacking stabilizations per single base in DNA were measured via the effects of additional nucleoside bases at the end of a DNA sequence. These experiments, on realistic condensed phases (1 M aqueous NaCl, 10 mM sodium phosphate buffer, pH 7, 37°C), yield stacking free energies of 1-2 kcal There... 

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