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if you cap then you “block” all of the peptides that you are synthesizing.(?)

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Setting up glassware for manual peptide synthesis

My Question; I don't really understand why, because: if you cap then you "block" all of the peptides that you are synthesizing (?). Therefore, how can you add further onto the chain if you cap after each amino acid? This seems counterintuitive, or I might be a bit confused. If you are able to de-protect the cap to further couple on more amino acids, then what is the point of capping?

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Two major chemistries for solid phase peptide synthesis are Fmoc (base labile protecting group) and t-Boc (acid labile a-amino protecting group). Each method involves fundamentally different amino acid side-chain protection and consequent cleavage/deprotection methods, and resins; t-Boc method requires use of stronger HF containing anisole alone or anisole plus other scavengers, where peptide-resins assembled by Fmoc chemistry usually cleaved by less harsh Reagents K or R. Fmoc chemistry is known for peptide synthesis of higher quality and in greater yield than t-Boc chemistry. Impurities in t-Boc-synthesized peptides mostly attributed to cleavage problems, dehydration and t-butylation. For peptide assembly HBTU/HOBt, carbodiimide-mediated coupling and PyBOP/HOBt are the most popular routines. Peptides usually purified by reversed-phase HPLC (high performance liquid chromatography) using columns such as C-18, C-8, and C-4.

Biotage - Peptide Synthesis Instruments

This is a versatile resin, which is quite useful in multi-well, automated peptide synthesis, due to its minimal swelling in DCM.

Stepwise elongation, in which the amino acids are connected step-by-step in turn, is ideal for small peptides containing between 2 and 100 amino acid residues. Another method is fragment condensation, in which peptide fragments are coupled. Although the former can elongate the peptide chain without racemization, the yield drops if only it is used in the creation of long or highly polar peptides. Fragment condensation is better than stepwise elongation for synthesizing sophisticated long peptides, but its use must be restricted in order to protect against racemization. Fragment condensation is also undesirable since the coupled fragment must be in gross excess, which may be a limitation depending on the length of the fragment.

The allyloxycarbonyl (alloc) protecting group is often used to protect a carboxylic acid, hydroxyl, or amino group when an orthagonal deprotection scheme is required. It is sometimes used when conducting on-resin cyclic peptide formation, where the peptide is linked to the resin by a side-chain functional group. The alloc group can be removed using tetrakis(triphenylphosphine)palladium(0) along with a 37:2:1 mixture of chloroform, acetic acid, and N-methylmorpholine (NMM) for 2 hours. The resin must then be carefully washed 0.5 % DIPEA in DMF, 3x10 ml of 0.5 % sodium diethylthiocarbamate in DMF, and then 5x10 ml of 1:1 DCM:DMF.

After synthesis, the peptide is cleaved from the resin, ..

Before the Fmoc group became popular, the Boc group was commonly used for protecting the terminal amine of the peptide, requiring the use of more acid stable groups for side chain protection in orthogonal strategies. It retains usefulness in reducing aggregation of peptides during synthesis. Boc groups can be added to amino acids with boc anhydride and a suitable base.

The Fmoc (9-fluorenylmethyl carbamate) is currently a widely used protective group that is generally removed from the N terminus of a peptide in the iterative synthesis of a peptide from amino acid units. The advantage of Fmoc is that it is cleaved under very mild basic conditions (e.g. piperidine), but stable under acidic conditions. This allows mild acid labile protecting groups that are stable under basic conditions, such as Boc and benzyl groups, to be used on the side-chains of amino acid residues of the target peptide. This orthogonal protecting group strategy is common in the art of organic synthesis.

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For large scale synthesis of well known peptides solution or liquid phase peptide synthesis can be applied. These "classical" methods for synthesis in solution are labour, time, and skill intensive largely due to the unpredictable solubility characteristics of intermediates.

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Currently, two protective groups (Fmoc, Boc) are commonly used in solid-phase peptide synthesis. Their lability is caused by the carbamate group which readily releases CO2 for an irreversible decoupling step.

Peptide Sequencing and Synthesis

This method was introduced by R.C. Sheppard in 1971. Fmoc stands for 9-Fluorenylmethoxycarbonyl which describes the Fmoc protecting group. To remove an Fmoc from a growing peptide chain, basic conditions (usually 20% piperidine in DMF) are used. Removal of side-chain protecting groups and peptide from the resin is achieved by incubating in trifluoroacetic acid (TFA). Fmoc deprotection is usually slow because the anionic nitrogen produced at the end is not a particularly favorable product, although the whole process is thermodynamically driven by the evolution of carbon dioxide. The main advantage of Fmoc chemistry is that no hydrofluoric acid is needed. It is therefore used for most routine synthesis.

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Solid-phase peptide synthesis consists of three distinct sets of operations: 1) chain assembly on a resin; 2) simultaneous or sequential cleavage and deprotection of the resin-bound, fully protected chain; and 3) purification and characterisation of the target peptide. Various chemical strategies exist for the chain assembly and cleavage/deprotection operations, but purification and characterisation methods are more or less invariant to the methods used to generate the crude peptide product.

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When R. B. Merrifield invented SPPS in 1963, it was according to the tBoc method. t-Boc (or Boc) stands for tert-Butyloxycarbonyl. To remove Boc from a growing peptide chain, acidic conditions are used (usually neat TFA). Removal of side-chain protecting groups and the peptide from the resin at the end of the synthesis is achieved by incubating in hydrofluoric acid (which can be dangerous); for this reason Boc chemistry is generally disfavored. However for complex syntheses Boc is favourable. When synthesizing nonnatural peptide analogs which are base-sensitive (such as depsi-peptides), Boc is necessary.

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