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A range of cleavage reagents for peptides synthesized on 2-chlorotrityl resin has been described. TFE/AcOH/DCM (1:1:3) has been developed by Barbs . Cleavage is also rapidly attained with 0.5% TFA/DCM as well as with HFIP/DCM (1:4 or 3:7) .
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The other approach is to introduce backbone protecting groups which will prevent the formation of hydrogen bonds. Such protection is made by the introduction of the Hmb group on the αnitrogen . It has been shown that the presence of a Hmb unit every 6-7 residues is sufficient to disrupt the peptide aggregation . The Hmb protected amino acid is introduced under the form of N,O-bis-Fmoc-N-(2hydroxy-4-methoxybenzyl) derivative, the O-Fmoc protection being cleaved during the following piperidine treatment. At the end of the synthesis the Hmb group is cleaved in the final TFA cleavage.
Repeated incomplete deprotection of the αamino function as well as difficulties in obtaining a complete coupling reaction are some of the problems caused by the on resin aggregation of the peptide chain.
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A special paragraph will be dedicated to the problems caused by peptide aggregation in the course of the synthesis. This phenomenon is a major cause of trouble as it is difficult to predict, is sequence dependent and no universal solution has been found up to now.
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Better results will be obtained by repeating a coupling with fresh reagents (and changing coupling parameters if a low conversion was obtained) rather than by prolonging the reaction. Generally, coupling protocols may be changed in the course of a synthesis, especially when optimizing an SPPS.
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- the choice of the solvent. It will in part determine the swelling of the peptide-resin and influence the accessibility to the reactive sites; it will also have a direct effect on the kinetics of the coupling reaction.
- the steric hindrance. It is determined by the nature of the side chains R1 and R2 and of their protecting groups.
- the reactivity of the activated carboxylic acid.
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Automated custom synthesis of peptides on a scale of 1-500 mg, purification (standard-purities: 80% or 95%) and analysis of all products by HPLC and mass spectrometry.
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As mentioned above, the generation and disappearance of Fmoc based chromophors allows the monitoring of the synthesis. Furthermore, samples may be taken to determine the load of Fmoc peptide. The completion of the deprotection reaction may be checked by cleaving samples and analyzing the obtained peptide.
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But, whichever cleavage reagent is preferred, it has to be washed out very carefully after Fmoc removal, the last washing must be neutral. When synthesizing large peptides the duration of Fmoc cleavage should be gradually increased. For safe removal of the deblocking reagent the resin may have to be washed more often.