HI Sahil

Can You elaborate your query a little bit more and what you have seen in literature...I am not sure, and do not promise...but may be able to work something (theoretically)....feasibility can be discussed later

bye

I didnt get the pattern of bands as seen in g quadruplex paper when I use control g quadruplex whose dms footprinting and  polymerase stop assay has already done.May be i am loading too much dna

I did use DMS probing to identify reactive N7 G for RNA (the protocol should be same as DNA). Check http://pubs.rsc.org/en/Content/ArticleLanding/2013/SC/C2SC21588H#!divAbstract, or the original citation in this paper (This paper is available on my research gate if you dont have acess to it).

But if you have some specific question you can ask and then we can reply you better.

cheers,

sandeep

Your assay is based on two step: a) DMS reaction b) RT stop. RT stop can be sometime misleading as RT can some time readover your modification and then give you different pattern than you expect.

Can you digest your qudraplex with nucleases and run on a sequencing gel to see the pattern?

cheers,

sandeep

Hi..thanks for your answer. i can run the sample on 15 cm long polyacylamide gel.