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General discussions (Q&As) / Creating Intercalation Site in the canonical DNA
« on: July 24, 2011, 02:00:41 pm »
Hi,
I am Pooja and would like to thank for creating such a great forum.
I have been working on the study of Intercalators. Currently I am working on the docking of ligands at the intercalation site ( using the DNA structures from PDB after removing the ligand). But most of the complexes deposited in PDB are limited to hexanucleotide sequence and mostly the ligand intercalated in the terminal dinucleotide step.
For my study, I want to dock the ligand molecule at the centre and of different sequences for which I thought of constructing canonical DNA and then creating the intercalation site. Since the rebuild in 3DNA reads the base pair step parameters, I increased the rise value to 6.8A without changing other parameters (of regular BDNA). But for attaching the sugar phosphate backbone I cannot use the bases with sugar-phosphate that are in ATOMIC folder.
I tried to superimpose the sugar phosphate backbone of the dinucleotide steps (intercalation site) of DNA extracted from the crystal structures but only few of them were superimposing well others were not. Can you please suggest me how can I get the parameters for sugar phosphate backbone? And I also the twist and buckle values differ depending on the ligand, so how should I take care of that thing while passing the parameters in rebuild?
Thanks in anticipation,
Pooja
I am Pooja and would like to thank for creating such a great forum.
I have been working on the study of Intercalators. Currently I am working on the docking of ligands at the intercalation site ( using the DNA structures from PDB after removing the ligand). But most of the complexes deposited in PDB are limited to hexanucleotide sequence and mostly the ligand intercalated in the terminal dinucleotide step.
For my study, I want to dock the ligand molecule at the centre and of different sequences for which I thought of constructing canonical DNA and then creating the intercalation site. Since the rebuild in 3DNA reads the base pair step parameters, I increased the rise value to 6.8A without changing other parameters (of regular BDNA). But for attaching the sugar phosphate backbone I cannot use the bases with sugar-phosphate that are in ATOMIC folder.
I tried to superimpose the sugar phosphate backbone of the dinucleotide steps (intercalation site) of DNA extracted from the crystal structures but only few of them were superimposing well others were not. Can you please suggest me how can I get the parameters for sugar phosphate backbone? And I also the twist and buckle values differ depending on the ligand, so how should I take care of that thing while passing the parameters in rebuild?
Thanks in anticipation,
Pooja