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ssDNA modification (or binding..?)

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ssDNA modification (or binding..?)

Postby Skyrre » Wed Mar 31, 2010 12:42 pm

Hi,

I'm looking for a ssDNA modification which can prevent a complementary strand to bind in. Another complementary oligo is not an option though. Also, this modification should be possible to remove enzymatically (prefer some comercially available!).

Or does anyone have another suggestion to a similar property - to "unlock" ssDNA and making it available for hybridization? Perhaps by some protein binding?

Any thoughts or ideas are much appreciated!

Thanks in advance,
/Martin
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Postby JackBean » Wed Mar 31, 2010 1:03 pm

what about some bulk moiety, which could you hydrolyse away, when needed?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Re: ssDNA modification (or binding..?)

Postby jonmoulton » Wed Mar 31, 2010 3:51 pm

I don't know the reason that you eliminated strategies calling for a complementary oligo; this might not work in your system. However, photocaging the oligo with a second strand containing a photocleavable link has been reasonably successful.
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Re: ssDNA modification (or binding..?)

Postby Skyrre » Thu Apr 01, 2010 8:46 am

jonmoulton wrote:I don't know the reason that you eliminated strategies calling for a complementary oligo; this might not work in your system. However, photocaging the oligo with a second strand containing a photocleavable link has been reasonably successful.


Thanks for your answer! The reason that I didn't want to use another oligo was that I've made some experiments with a "blocking oligo" without success. The second reason was that I only thought of having U-bases and digest it with UNG excision mix, and that is the option that is out of the question (it will also digest something that I don't want digested). The method you suggest is definitely interesting, but the reaction should be very robust (reproducible) and be possible to carry out in a regular PCR machine (no light!).

I know that it's a lot to ask for, and perhaps there is no fitting method out there at the moment
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