Function of non-coding sequences/ secondary structure

Michael Freitag freitag at MOREL.UOREGON.EDU
Wed Mar 6 19:50:43 EST 1996

Hi there,

I am interested in estimating the likelihood of particular short 
sequences of DNA folding into unusual secondary structures such as 
cruciforms, hairpins etc.
The sequences in question are 200 to 400 bp long and some of them code 
for 5S RNA (therefore they have inherently a propensity to form unimolecular 
secondary structures in solution).

I wonder whether anybody can point me in the direction of software that 
would allow input of dsDNA sequence and estimation of free energy of 

I looked in the literature, but most studies pertain to very short 
sequences in vitro.

Thanks so much,
Michael Freitag
Univ. of Oregon

On Mon, 4 Mar 1996, Shane McKee wrote:

> recombination hot-spots near repeats etc - all of these turn out
> to be importants genomic features, despite the simplicity of their
> coding DNA sequences. 
> You've hit upon one of my favourite notions here - that repeats
> (which are often highly polymorphic) may be able to influence
> gene expression, and thus act as a further source of evolutionary
> variability without affecting protein structure or expressor
> sequences (which are more dangerous things). 

> The twists and coils and higher structure of the DNA molecule and
> chromosome are often quite complex, but in a different sense from
> what we're talking about here. For instance, slight changes in
> sequence are unlikely to bring about much change in this structure
> (correct me if I'm wrong, folks). 

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