RNA fragmentation

Figure 16.19 Schematic drawing illustrating the structure and sequence of the RNA fragment that is recognized and bound by the coat protein of bacteriophage MS2. The RNA fragment forms a base-paired stem with a bulge at base -10 and a loop of four bases. Bases that form sequence-specific Interactions with the coat protein are red. (Adapted from a diagram provided by L. Llljas.)...

TABLE 4.10 Recommended TSK-GEL SW and TSK-GEL PW Columns for Separating Double-Stranded DNA and RNA Fragments... 

BLOTTING is a method to detect specific DNA (or RNA) fragments that contain sequences that are complementary to sequences in the labeled probe molecule. Only a few of the many DNA fragments on a gel will contain the sequence of interest, and only these will be seen (light up) on the blot. Specific proteins can also be visualized by blotting techniques using a specific antibody to detect a specific protein. 

Since NMR data may reflect the conformational averaging resulting from a substantial flexibility of DNA/RNA fragments, the parameters of the ensemble of structures obtained by MD refinement and experimental NMR restraints can display internal inconsistency. James and coworkers developed a method to determine the family of structural conform-ers and their populations based on NMR data [83]. This approach applies multiple-copy refinement with floating weights, which better reflects the conformational dynamics of nucleic acids. 

Quantitative PCR has been widely used to determine the amount (number of molecules) of DNA molecules in a test sample. The best quantitative PCR method involves the addition of known amounts of a similar DNA or RNA fragment, such as one containing a short deletion or specific mutation, to the test sample before amplification. Such internal standards must be precisely calibrated to ensure that they are amplified and detected in a form and manner that are similar to the test sample. The ratio of the internal standard and the targeted template will depend on the amount of internal standard added and allows for the determination of the amount of the targeted molecule in the test sample. Therefore, the ideal standard for quantitative amplification based assays should have a structure that is comparable to the template of interest and which allows for the simultaneous amplification of both template and standard using a single primer pair. 

Agilent Technologies Agilent 2100 DNA, RNA fragments 12 runs/chip sodium dodecyl sulfate (SDS), proteins... 

Recently, Tor and co-workers have analysed the interaction between the cyclic analog 2 and the corresponding paromomycin derivative with the A-site sequence and also with the HIV TAR RNA fragment [47]. At pH 7.5, the decrease in affinity for the locked derivatives with respect to the parent aminoglycosides is 22-14 fold for the A-site and 11-2 fold for the HIV TAR sequence. The differences with respect to the natural ligands are significantly reduced at acid pH. 

Figure 14.8 Four self-complementary RNA fragments containing a tandem array of two E. coli 16S ribosomal A site modules.

Cp6 together with the Intercalator acridine orange solved at atoaiic resolution (36). It can be seen tha the 3 end of the double helical RNA fragment has adopted the C2 endo conformation while the S end maintains the normal C3 endo conformation. A large number of intercalator structures of this type have been solved and they have been summaried elsewhere. Sobell and his colleages pointed out that the Intercalation is associated with a modification of the pucker of the ribonucleotide chain on the 3 end of the intercalator (37-38). Although intercalation is generally associated with the conformations similar to those seen in Fig. 10. a number of alternative conformations have been found with more complex Intercalators. 

Dotted lines or "crossed-out" base pairs denote modified base-pairing in P. polycephalum. The letters "a" and "b" indicate the termini of RNA fragments isolated as a base-paired complex. From Brimacombe.38... 

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