Hello, I was wondering if anyone knows of a method that can be used to search the PDB for DNA/RNA structures (essentially a Dali search for DNA/RNA)?
I have recently obtained a 2.3 A protein structure bound in complex with DNA. X3DNA has shown the DNA to be B-form generally but the 3DNA output and the structure both show a significant bend in the DNA chain. Other than apparently non-specific nuclease activity, we do not know the function of the protein in vivo. It would be very useful to be able to look at other proteins that bind DNA/RNA that target/produce similar bends in DNA/RNA structure, independent of base sequence. However, with thousands of structures in the PDB containing DNA it would be impossible to do this by eye! Thanks for reading, I look forward to hearing your suggestions. Sophie, Sheffield University
