Helix, coaxial

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]...

Using the pitch, symmetry, monomer geometries and other stereochemical constraints, a number of types of molecular model can be constructed. Typical dilemmas are whether the molecular helix is left- or right-handed, whether the molecule is a single helix or coaxial double-helix (and in the later case whether the two chains in the duplex are parallel or antiparallel), or whether, if there are two or more molecules in the unit cell, the molecules are parallel or antiparallel. Solution of a structure therefore involves refinement and adjudication All candidate models are refined until the fit with the measured x-ray amplitudes or steric factors allows one model to be declared significantly superior to the others by some standard statistical test. 

A left-handed 4(—0.85) helix was proposed for hyaluronate. From attempts to refine the model structures, and calculation of Fourier synthesis, it was shown that two hyaluronate chains pass through the tetragonal unit-cell, with a = 0.99 nm and c = 3.39 nm. The chains are antiparallel, but not coaxial. The double-helix model was excluded. 

Using special strategies such as those involving, e.g., a coaxial jet mixer [79], a packed bed connector [80] or a metal helix insertion [66]. 

Fig. 6.4.6. Developable domains in the columnar phase, (a) The developable surface is degenerated into a straight line d common to the planes P. The columnar axes C form coaxial circles about 5. b) The developable surface Z) is a cylinder. The columns (or the layers in the case of smectic A) are a set of parallel and equispaced involutes of a circle, (c) A Reimann surface generated by half-tangents to a helix. The columns are normal to the half-tangents. (Bouligand. )...

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... 

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.

The cylinder representations were particularly useful for comparing 3D models from the various SRP RNAs. First we superimposed cylinders from the M. jannaschii structure and the atom coordinates of the human SRP RNA to improve the human model. We then used the cylinder representations of the human S RNA to adjust the atom coordinates of M. jannaschii SRP RNA. These two sequences illustrate well how comparative modeling is mutually beneficial. For example, a coaxial orientation of helices 5b, 5c, and 5d in the human SRP RNA model is supported by the extended helix (5bcd) of the M. jannaschii SRP RNA. On the other hand, the M. jannaschii sequence inserts extra nucleotides in the loop of helix 4 and between helix 2 and helix 5 a however, the high degree of potential flexibility that would normally result from these insertions, is contained by comparison with the human model. 

To overcome some problems associated with using a solid central conductor, the inner part of the coaxial cavity was constructed from a finely wound shallow pitched helix, which stands freely against the inner wall of a quartz test tube (internal... 

Fig. 15 The EPR-visible part of the Allendoerfer coaxial cell is that between the wire helix and the quartz sample tube (shaded region). The inner part of the helix is free to house the reference and counter electrodes without interference with the EPR.

The double-Helix Coil transition of synthetic oligonucleotides has been studied [15, 16] with conventional and also with a fast temperature-jump apparatus [17]. In this instrument a short coaxial cable is used as discharge capacitor, resulting in heating times as short as 50 n. Its only disadvantage is common to all Joule-heating type temperature-jump apparatuses the need for supporting electrolytes. 

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