Topics

1

General discussions (Q&As) / constructing a modified sugar

« on: September 08, 2011, 01:40:02 pm »

Friends,
i want to incorporate a modified sugar into a canonical DNA duplex. Basically i am interested in incorporating a locked nucleic acid sugar, where the 2' oxygen and 4' carbon of the sugar has a methylene linkage. Such a structure is available in pdb:2X2Q. i would like to know the possibility of using 3DNA for replacing the normal sugar with such modified sugar in a DNA duplex.

Thanks,
Subbu

2

General discussions (Q&As) / building a parallel stranded DNA

« on: September 05, 2011, 11:59:36 am »

Friends,
I have to construct a duplex structure of 10mer oligo. I want to construct the model as parallel stranded (ps) DNA. I would like to know
i) if it is possible to construct such a model using 3DNA and
ii) there is an experimental structure of such ps duplex with completely different base composition, is there any way that i can use as am a template in 3DNA to model my structure. I am also planning to do a short simulation to optimize the model further.

Thanks,
Subramanian