Tm prediction : more

Darren Natale camdna at ubvmsb.cc.buffalo.edu
Tue Feb 9 10:07:00 EST 1993

In article <C25JG9.837 at dartvax.dartmouth.edu>, Robert.H.Gross at dartmouth.edu (Bob Gross) writes...
>In article <1993Feb8.190445.1 at hkucc.hku.hk>
>vldnaseq at hkucc.hku.hk writes:
>> Naturally, Tm is DNA concentration dependent
>Shouldn't Tm be DNA concentration INdependent? It just represents the
>energy needed to pull the two strands of DNA apart - that is
>independent of how many molecules of DNA there are. Reassociation of
>the two strands obviously is concentration dependent.
Tm is defined as the temperature at which 50% of the DNA molecules are 
single-stranded. The strand separation/strand annealing steps are both
reversible processes. Therefore, the ability of a single stranded molecule
to become annealed to its complement will depend on the likelihood of
"finding" that complement--thus it is concentration dependant.

Contrary to your supposition, Tm does not represent the energy needed to
pull the strands apart. In fact, at the Tm, the energy released by the
annealing of strands equals the energy required to separate them (since
it is at equilibrium) and therefore no _extra_ energy input is required.

The Tm of a DNA molecule depends on such factors as the primary sequence
and the salt concentration. Tm is also defined as the temperature at which
delta H (heat of enthalpy) equals delta S (heat of entropy). The deltas
H and S values for all possible dinucleotide pairs (GA,AT,TT, etc.) are
known (Breslauer et. al. PNAS 83:3746-3750) as is the effect of salt on
the Tm. The programs that calculate Tm use these values (at least I know
some do--others may simply use base composition).


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