All the data and source code for m6A excited states paper
This is all the source data and code files for the m6A Excited states paper
Ref: Liu et al, (2020) "m6A delays base-pairing through syn-anti isomerization of the methylamino group" BioRxiv
1. MD force field parameters (MD_forcefield)
m6a_new_rna.lib - force field parameters for m6A.
Load using ‘loadOff m6a_new_rna.lib’ in tleap module of AMBER suite
DMA_rna_parmbsc0.off and DMA_rna_parmbsc0.frcmod - force field parameter files for m62A.
Load using ‘loadOff DMA_rna_parmbsc0.off’ and ‘loadamberparams DMA_rna_parmbsc0.frcmod’ in tleap module of AMBER suite
2. Input RNA duplex (dsGGACU) structures for DFT calculation (dsRNA_structure)
In the folder, there are five ensembles, each of ensemble contains 100 conformers. DFT is computing the average of them.
dsGGACU.pdb: unmodified duplex
dsGGACUm6Aanti.pdb: m6A modified dsGGACU at residue 6, the m6A N6-methylamino group is in anti conformation
dsGGACUm6Asyn.pdb: m6A modified dsGGACU at residue 6, the m6A N6-methylamino group is in syn conformation
dsGGACUm6Aantistar.pdb: m6A modified dsGGACU at residue 6, the m6A N6-methylamino group is in anti* conformation
dsGGACUm62A.pdb: m62A modified dsGGACU at residue 6
3. Input mononucleoside structures for DFT calculation (mono_structure)
In the folder, there are three subfolders representing three different mononucleoside structures.
"rA" is the unmodified adenosine
"m62rA" is the m62A modified adenosine
"m6rA" is the m6A modifition, where the N6-methylamino group is rotated from 0 to 360 degree
HO2' means the hydroxl proton connect to O2'
HO3' means the hydroxl proton connect to O3'
HO5' means the hydroxl proton connect to O5'
C10 means the N6-methylamino group carbon in m6A
H20 H21 H22 means the N6-methyl group proton in m6A
C11 means the second N6-methylamino group carbon in m62A
H23 H24 H25 means the second N6-methyl group proton in m62A
OP3 means the fourth oxygen in phosphate acid group in monophosphate structure
monophosphate has two negative charge