Dear Jisha,
I would like to suggest 3D-NuS (
http://iith.ac.in/3dnus/RNA-DNA%20Hybrid.html),
https://doi.org/10.1016/j.jmb.2017.06.013, for building DNA-RNA hybrid
structures. The structural parameters used for modeling hybrid structures
are derived from DNA-RNA hybrid structures deposited in the PDB.
On Sun, 26 Apr, 2020, 11:54 AM Jisha B, <jisha.b.k0511.gmail.com> wrote:
> Respected all,
> Since I am a beginner in AMBER, I wonder if we could use the following
> procedure to create DNA/RNA hybrid duplex?
> Use the following script(as in the tutorial) to create a duplex and then
> edit the dT in the complementary strand to rU in the text file and load it
> to xleap and visualize. Would that work? Would such a a system be
> considered as a DNA/RNA hybrid? I have the doubt because literature
> suggests that the hybrid may not be strictly A type or B type. Also what
> would be the force field considerations in such a hybrid?So how to proceed
> in this. Thank you for any help you can provide.
> molecule m;
> m = fd_helix( "abdna", "aaaaaaaaaa", "dna" );
> putpdb( "nuc.pdb", m, "-wwpdb");
>
> --
> Jisha B.
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>
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Received on Mon Apr 27 2020 - 21:00:03 PDT
