Preferential cleavage sites

Properties such as thermodynamic values, sequence asymmetry, and polymorphisms that contribute to RNA duplex stability are taken into account by these databases (Pei and Tuschl 2006). In addition, artificial neural networks have been utilized to train algorithms based on the analysis of randomly selected siRNAs (Huesken et al. 2005). These programs siphon significant trends from large sets of RNA sequences whose efficacies are known and validated. Certain base pair (bp) positions have a tendency to possess distinct nucleotides (Figure 9.2). In effective nucleotides, position 1 is preferentially an adenosine (A) or uracil (U), and many strands are enriched with these nucleotides along the first 6 to 7 bps of sequence (Pei and Tuschl 2006). The conserved RISC cleavage site at nucleotide position 10 favors an adenosine, which may be important, while other nucleotides are... 

Table II summarizes those amino acids that contain more than an un-reactive aliphatic chain, namely a reactive site which may be a functional group in the traditional sense such as sulfhydryl, thiomethyl, hydroxyl, carboxyl, carbamide, amino, or guanido, or may be an activated aromatic ring or heterocycle such as the phenolic part of tyrosine, the pyrrole unit in troptophan, and the imidazole part in histidine. Phenylalanine would only be considered in this connection as the reactive di- or tetrahydro derivative ring. iV-Peptides derived from proline and hydroxyproline are in a separate class because they are tertiary amides carrying no proton at the nitrogen atom. It may be possible to utilize this special feature for a preferential cleavage under proper conditions.

Figure 4 Major glycosidic cleavage pathways. The sodiated B and Y ions are the major fragment ions afforded by the sodiated molecular Ions (a) although C and Z ions can also be formed at certain sites. The specification of a HexNAc at the cleavage site In the schematic drawings is meant to emphasize that such glycosidic cleavages are preferentially directed to HexNAc for the permethyl derivatives. The N- and O-glycan cartoons illustrate the resulting key ions that are informative of core and terminal structures. For protonated molecular ions (b), the oxonium ions formed at the HexNAcs are the most prominent key ions, which are often accompanied by elimination at position 3.

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