By Li G., Datta S.
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Extra resources for A bootastrap approach to non-parametric regression for right censored data
Sample text
However, there is a practical difficulty in defining RNA structures precisely by NMR because NOE and J-coupling–based structure calculation relies on either short range distance (<6Å) or local torsion angle information. RNAs often are elongated structures, which are better approximated as cylindrical rather than globular shapes. There is a lack of NOE information between distant ends of the molecule; as a result, the relative orientations of helical segments at opposite ends of the molecule are poorly defined.
The observable upper stem G and U residues are shown in bold gray and lower stem G and U residues in bold black. 42 Scott and Hennig qualitatively with the combination of H1′-H2′ and H3′-H4′ coupling constants being the most useful for smaller RNAs. The 3J(H1′,H2′) vicinal coupling is >8 Hz for C2′-endo puckers and ~1 Hz for C3′-endo puckers (Fig. 8), typically found in A-form helices (48–50). The opposite behavior is expected for the 3J(H3′,H4′) coupling constant with C2′-endo puckers associated with small and C3′-endo puckers with relatively large coupling constant values (see Note 23).
6. 5 volumes cold 100% ethanol at −20°C. 7. The crude RNA precipitate is collected by centrifugation, and resuspended in equal volumes of 80% Formamide Stop/ Loading Buffer and 8M urea. 8. The sample is suitable for loading to a denaturing polyacrylamide gel. 2. RNA Purification by Denaturing Polyacrylamide Electrophoresis 1. These instructions are general and are easily adaptable to other formats, and reaction scales, including minigels. C. Johnson), and finally 95% ethanol. 2. Prepare a polyacrylamide gel of the appropriate percentage, size, and thickness by mixing acrylamide/bisacrylamide solution, 1 µL APS and 1 µL TEMED per mL acrylamide/ bisacrylamide solution (32).