Add C or T to 5' end of an RNA bound to QKI PDB file

[Hari Seldon]

Does 3DNA have a function to add a nucleotide to the 5' end of an RNA in a pdb file?

My project is to search the transcriptome for more sites that the RNA-binding proteins QKI and SF1 might compete.  We already know that they compete just upstream of Exon 12 of NUMB and if QKI wins it prevents SF1 from binding and prevents SF1 from recruiting the spliceosome there, so exon skipping of exon 12 happens.


I know the motif for the QKI dimer is NACUAAY-N(1-20)-UAAY and the motif for the SF1 monomer (it does not dimerize) is YNCURAY.  After I run molecular dynamics of QKI against the SF1 RNA motif I will compare the binding energies to see how well QKI binds against the SF1 motif to see how well QKI competes against SF1.

I have used 3DNA's mutate_bases in the past in this project, but now I need to add a C or T to the 5' end of the RNA bound to QKI, because 4JVH.pdb (QKI) http://www.rcsb.org/structure/4JVH has the RNA ACUAACAA and I need to trim that to _ACUAAC because that lines up the best with YNCURAY.  The underscore needs to be the C or T and to do that I need 3DNA to add the C or T to the 5' end of the ACUAAC.

[xiangjun]

Thanks for such a well-phrased question! Yes, 3DNA/DSSR has some utilities that may help in achieving your goal.

4JVH.pdb (QKI) http://www.rcsb.org/structure/4JVH has the RNA ACUAACAA and I need to trim that to _ACUAAC because that lines up the best with YNCURAY.  The underscore needs to be the C or T and to do that I need 3DNA to add the C or T to the 5' end of the ACUAAC.

I assume the conformation of the 5' C or T to be added is not defined, i.e. it can be any (reasonable) starting geometry. You could use frame_mol to set the ACUAAC fragment from 4JVH to be in the base reference of the first A. You can choose any (or your favorite) CA (or TA) dinucleotide from the PDB, and use the same frame_mol utility to reset it to the base reference frame of the ending A. Since both the ACUAAC fragment and the CA fragment share the same A base reference frame, you can overlay them together. With some manual editing, you should be able to get an approximate starting PDB structure with required RNA base sequence for your MD simulations.

Have a try and let me know if it works.

Xiang-Jun