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Topics - Hari Seldon

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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) 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.

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.