Dear Amber Users,
I am currently interested in simulating some internal oligoribonucleotide pyrophosphates - e.g., of the form 3'-N...A-p-p-A...N-3', generated by the formal 5'-5' condensation of two 5'-phosphate-terminated oligos (5'-pA...N-3') - but have come unstuck in preparing the appropriate topology files for such systems. I was hoping someone could kindly nudge me in the correct direction.
>From online tutorials etc., I largely understand the manner in which nucleotide fragments are configured/connected with Leap (i.e, as central, 5'- terminal or 3'-terminal residues), but it seems internal pyrophosphates of the form described above may not be (?) easily compatible with the standard approach: the systems I am interested in comprise only one strand, but both termini are 3', with polarity reversal occurring at the internal pyrophosphate linkage.
I was trying to approach the problem by creating a separate pyrophosphate residue (i.e., as Me-p-p-Me, in methyl capped form)., but so far I have failed to work the connectivity out; I also note there are some parameters available for some terminal pyrophosphates on the Bryce group website (Manchester), but again I remain unsure as to how I might - or whether I should - incorporate these (partially) for internal pyrophosphates.
Any help/advice would be most appreciated.
Best wishes,
Harvey
________________________________________________
Dr Harvey J. A. Dale
Research Fellow
Royal Commission for the Exhibition of 1851
John Henry Coates Research Fellow
Emmanuel College | Cambridge | CB2 3AP | hd487.cam.ac.uk<mailto:hd487.cam.ac.uk>
Postdoctoral Researcher
MRC Lab of Molecular Biology | Cambridge | CB2 0QH
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Received on Tue Apr 04 2023 - 16:00:02 PDT
