Sorry for the noobie question, but is it possible to build a triplex DNA from scratch? If not, is it possible to take a .pdb file of a triplex DNA and mutate it to my own sequence? This would involve insertion of an extra residue in the loop region. I would later like to save the new coordinates in .pdb format for molecular dynamics studies.
This is good question: it clearly illustrates the need for a tool to manipulate/build/edit nucleic acid structures in 3-dimensional space. Ideally, it would be with an interactive GUI. Aren't there tools already available, commercial or free, that fit the bill?
As far as 3DNA goes, some of its 55 fiber models are triplexes. Starting from a PDB file of a triplex DNA and then mutating it to your specific sequence, or inserting an extra residue in the loop region, are doable with 3DNA, along the same line as shown the thread
"mutating DNA in DNA protein complex". Of course, the operations are not automated -- tedious and error-prone: you've got to know exactly what you want to do, and better have some programming skills to perform necessary geometric transformations.
Overall, 3DNA can do a lot, but there are many more things that can
not be done easily or at all. It is a long journey from
SCHNAaP/SCHNArP to 3DNA, and I have felt strongly for quite some time the need to move forward -- based on my 10+ years experience in creating and supporting SCHNAaP/SCHNArP/3DNA, I have been building a new set of tools that can better meet the challenge of structure explosions. Among its many possible functionalities, it would make some of the requests in the forum, including this one, possible or much easier.
HTH,
Xiang-Jun
Topic: Noobie question on building triplex DNA (Read 14940 times)