Dear Sandie:
Check by MS your Fmoc-Arg(Pbf)-OH for Fmoc-Arg(Pbf)-Arg(Pbf)-OH content.
Fmoc-dipeptides are known to be the main (>10%) by-products in case
Fmoc-Cl is used to acylate amino acids under aqueous conditions.
Alternatively (and most likely), "Arg(Pbf) doubling" should take place
directly in the course of coupling reactions and may be attributed to
specific instability and premature cleavage of Fmoc group under coupling
conditions (-->false positive ninhydrine tests) or something like that.
I agree with you that it is reasonable to expect this kind of
complication during incorporation of each Arg, so that mole fractions of
normal peptide and 'RR' by-product are "1-x" and "x", respectively. But
this does not contradict with your data.
What you observe is cumulative effect which corresponds to average
doubling ca. 30% per Arg since major by-products have the same Mw:
Target peptide: GARRGKGR-NH2 - (1-x)3=0.3
Major by-products (mono-RR):
GARRGKGRR-NH2 - (1-x)2*x
GARRRGKGR-NH2 - [x*(1-x)*(1-x) + (1-x)*x*(1-x)]
Minor by-products:
GARRRGKGRR-NH2
GARRRRGKGR-NH2
GARRRRGKGRR-NH2
Perhaps Fmoc chemistry is great, but you'll have no such problems (and
many others as well) in Boc chemistry...(:-))
Regards,
Igor Rodionov
------------------------------------------------
Laboratory of Peptide Chemistry
Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
6 Science Avenue, Pushchino, Moscow Region
142290, Russian Federation
rodionov@fibkh.serpukhov.su
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