Attaching a double stranded DNA to a surface - (Oct/23/2009 )

I would like to have a plasmid attached to either some beads or another surface. It is important, that the plasmid is only attached at one or a few places in its sequence. A non-circular DNA strand attached at each end (forming a semicircle) will also do.

Any great ideas?

uaaa on Oct 23 2009, 12:41 AM said:

I ain't sure how are nucleotides bound to microarray chips so you should take a look at it.

If you know part of the sequence you may try to bind the complementary sequence to the chip.

Of course the sequence should be complementary to each strand on that sequence and use dna double strand forming dinamics like in PCR.

It would be similar to having a PCR primer fixed on a rigid surface. After that you could just expose the dna and let it bound like in a PCR.

In mammals, telomeres sequences may be used. I haven't worked with plasmids but you probably know part of it sequence or can insert some kind of exclusive high affinity nucleotide sequence.

Probably the longer the plasmid the longer the primer to hold it into place.

I know you haven't ask for this, but lest image you want to hold it by both extremes.

If you wanted to hold it straigh by it extremes you should keep in mind nucleotides lengh.

If a nucleotide is 0,33nm long then 1Kbp would be 0,33um. And 1Mbp 0,33mm

A human chromosome may be around 200Mbp (6,6cm).

A plasmid is 1Kbp-1Mbp so it is 0,33-330um

I know that the separation between 2 glass plates is 1-10 um.
If your plasmic folds in this range you would be ready to go. If it is smaller you could try with plastic plates under weight pressure.
This would probably allow you to attach the plasmid at two extremes.

Regards.