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These A-B intermediate forms adopt the sugar pucker properties and/or the base conformation of both DNA forms. In one study, the characteristic C3'-endo pucker is found on the first three sugars of the DNA strand, while the last three sugars have a C2'-endo pucker, like B-DNA. [2]
Parameters taken from the spectrum, mainly NOESY cross-peaks and coupling constants, can be used to determine local structural features such as glycosidic bond angles, dihedral angles (using the Karplus equation), and sugar pucker conformations. For large-scale structure, these local parameters must be supplemented with other structural ...
L-Ribose Fischer Projection. Ribose is a simple sugar and carbohydrate with molecular formula C 5 H 10 O 5 and the linear-form composition H−(C=O)−(CHOH) 4 −H. The naturally occurring form, d-ribose, is a component of the ribonucleotides from which RNA is built, and so this compound is necessary for coding, decoding, regulation and expression of genes.
Deoxyribose, or more precisely 2-deoxyribose, is a monosaccharide with idealized formula H−(C=O)−(CH 2)−(CHOH) 3 −H. Its name indicates that it is a deoxy sugar, meaning that it is derived from the sugar ribose by loss of a hydroxy group.
The relationship between Z-DNA and the more familiar B-DNA was indicated by the work of Pohl and Jovin, [2] who showed that the ultraviolet circular dichroism of poly(dG-dC) was nearly inverted in 4 M sodium chloride solution and that the structure of poly d(I–C)·poly d(I–C) was in fact a right-handed D-DNA conformation.
The altered conformation makes yDNA more similar to B-DNA in its orientation by changing the interstrand hydrogen bonds. Stability is highly dependent on the bases' rotation about the link between the base and the sugar of the backbone. yDNA's altered preference for this orientation makes it more stable overall than xDNA.
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Macrocycles can access a number of stable conformations, with preference to reside in conformations that minimize transannular nonbonded interactions within the ring (e.g., with the chair and chair-boat being more stable than the boat-boat conformation for cyclooctane, because of the interactions depicted by the arcs shown).