I am currently interested in the kinetics of the melting DNA, we have some new theory of the double helix melting model, and we want to conduct the experiment to verify it.
We want to design a proper DNA which will not form too many loops and other secondary (even higher dimension)structures itself first.
how can we design a sequences like that? or does there any DNA around 200bp that has been proved to have the neat structure?
In therory, it would be very hard to choose 200 bp DNA sequences without any sencondary structures. but it is possible for 100 bp DNA. I suggest that you could firstly choose two 100 bp DNA without any sencondary structures and then join them. The DNAMAN soft will be a suitable tool for you to choose many random sequences less than 1000 bp.
You can choose various bioinformatic tools to select it. But also try performing a CD after wards with different salt conc., different salts (LiCl) and pH conditions and check if it changes.
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