Cleavage efficiency

This effect is particularly well documented for y - and -amino acid residues [217, 218] which in several natural products (bleomycin A2 [219], calyculins [220]) have been shown to play a substantial role in the pre-organization of the whole molecule into its bioactive conformation. For example, changes in the substitution pattern of the y-amino acid linker in bleomycin A2 result in reduced DNA cleavage efficiency [219]. In the case of y-peptides, changing the relative configuration like or unlike of y " -amino acids has been used as a strategy to generate different local conformations (Fig. 2.34) suitable either for the construction of helices [201] or turns ]202-204]. 

The relative amount of strand cleavage at each site of AQ-DNA(l) is indicated by the length of the solid vertical arrow shown in Fig. 4. As is often observed, the 5 -G of the GG steps react more often than do the 3 -G. In the case of AQ-DNA(l), the relative reactivity is ca. 1 3, but this ratio depends upon the specific base pair sequence surrounding a GG step, which may be an indication of radical cation delocalization to bases adjacent to the GG sequence. It is worth pointing out again that these reactions are carried out under single-hit conditions where the relative strand cleavage efficiency seen at various locations of AQ-DNA(l) reflect the statistical probability that the radical cation will be trapped by H20 at that site. 

A semi-log plot of the distance dependence of strand cleavage efficiency, see Fig. 8, gives a linear relationship with a slope experimentally indistinguishable from zero. DNA has occasionally been characterized as a molecu-... 

C). In addition, cleavage efficiency was enhanced when the resins were dried under vacuum before exposure to the TFA cleavage solution. 

To determine if a solid-phase reaction is complete, on-resin analytical methods are preferable [6]. First, the quantitative or qualitative information obtained from on-resin analysis is more relevant to solid-phase reactions. Secondly, this kind of analysis is fast, direct, and without any alteration to the sample. On the other hand, analysis after cleavage would depend on the cleavage efficiency (to be discussed later) and the stability of analyte to cleavage conditions such as TFA. The... 

Table 1 Cleavage Efficiency of pNA Peptides by HRV14 2A and 3C Protease...

Figure 5.4 DNA cleavage sites produced by the CAP178-1,10-phenanthroline conjugate. Longer arrows indicate sites where greater cleavage efficiency occurred.

The efficiency of the intein cleavage varies with the type of intein used for fusion and with the cleavage conditions (pH, temperature). Since usage of different thiol compounds results not only in a diverse splicing activity but also in a diverse rate of thioester hydrolysis, both parameters have to be taken into account. Specific protein properties, like the structure or the sequence at the C-terminus of the target protein, may also affect the cleavage efficiency (28,29). 

Other variations of the nitrobenzyl linker are the nitroveratryl (4) and hydroxynitrobenzyl (5) linkers, which are characterized by one or two alkoxy substituents on the nitrobenzene ring. The increased electron density at the benzylic position in these linkers improves photochemical cleavage efficiency through stabilization of radical intermediates in photolysis and also retards diketopiperazine formation during the coupling of the third amino acid in peptide synthesis. 

Table 17.2 Cleavage efficiency of various amino acids from nitrobenzyl derivatives.

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