3DNA Forum

Questions and answers => RNA structures (DSSR) => Topic started by: lvelve0901 on November 16, 2017, 11:22:19 pm

Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · Reproduce DSSR · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Title: Can DSSR detect stacking interaction between ligand and nucleic acid
Post by: lvelve0901 on November 16, 2017, 11:22:19 pm
Hi Xiangjun,

My new target structure is 1F1T from RCSB. It is a malachite green aptamer with a ligand called N,N'-TETRAMETHYL-ROSAMINE (ROS).
If you go to the PDB website and search for this PDB, you can see there is a stacking interaction between ROS and one of the adenine base in the 2D Diagram & Interactions.

http://www.rcsb.org/pdb/explore/explore.do?structureId=1f1t

My question is whether DSSR can detect such ligand and RNA interaction?

Here, I also attach the PDB file and json file that I generated for your convenience.

Best,
Honglue



Title: Re: Can DSSR detect stacking interaction between ligand and nucleic acid
Post by: lvelve0901 on November 16, 2017, 11:25:12 pm
Hi Xiangjun,

Also, generally speaking, can DSSR detect protein/peptide and nucleic acid stacking interaction? For example, the stacking between aromatic ring of Phenylalanine and nucleic acid base?

Best,
Honglue
Title: Re: Can DSSR detect stacking interaction between ligand and nucleic acid
Post by: xiangjun on November 17, 2017, 09:15:08 am
Quote
there is a stacking interaction between ROS and one of the adenine base in the 2D Diagram & Interactions.

http://www.rcsb.org/pdb/explore/explore.do?structureId=1f1t

My question is whether DSSR can detect such ligand and RNA interaction?

No, in general. This feature is beyong DSSR’s design scope, at least for now. Why not using the result from reported from the RCSB PDB website? It is an ‘authoritative’ resource, isn't it?

Quote
Also, generally speaking, can DSSR detect protein/peptide and nucleic acid stacking interaction? For example, the stacking between aromatic ring of Phenylalanine and nucleic acid base?

You may find SNAP helpful. Again, do not forget the many other resources/tools in the field.

Xiang-Jun

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.