Re: What forces are responsible for the stability of single stranded Poly A?

Hardeep:

That is a good question.  Your background says you are a science grad, so 
I am unclear as to whether you have taken undergraduate/graduate 
Biochemistry/Biophysics classes so try and pitch this somewhere in the 
middle.

The short answer is that the sugar phosphate backbone of the ssDNA 
provides most of the stability to the structure.  I think you are mixing 
base pairing and double helical stability with stability of the ss form, 
which actually arises from two separate chemical events.  The backbone of 
DNA and RNA is predominantly held together by covalent bonds, the major 
one of which is the C-C bond in the sugar residue, and what is often 
called second tier covalent bonds in the Phosphodiester bond between the 
backbone pieces.

ssDNA is only unstable insofar as environmental factors such as ssDNAses 
and such have access to attack it, this is one reason dsDNA is protected.  
The forces that hold ds DNA together are much weaker, atomically speaking, 
as they are almost exclusively hydrogen bonds, 2 per AT (U) base pair and 
three in a G-C base pair.  One simple way to illustrate this is that most 
reactions involving DNA, such as sequencing or PCR use heat to denature 
the double strand, but this technique leaves the backbone unscathed.

       In biophysical terms, the phosphodiester linkage is quite 
energetically unfavorable in aqueous environments at about +25kJ/mol 
change in free energy, but on the converse, the rate of hydrolysis in 
solution is exceedingly slow without catalysis that these molecules are 
stable in ss (or ds form) for years in aqueous environments, but can be 
extremely rapidly broken down with enzymes and other catalysts.

     Overall, this is the desire of life, in general to generate compounds 
and interactions which are stable, but not too stable, or you would never 
be able to change them or turn them off once they were completed or 
generated.  Such is the case with nucleotides as well.  They need to 
convey information, but not so much so that the cell is incapable of 
modifying and eliminating them when needed. 

I hope this helps you

-Matt-