[MeltSim] Question about strand concentration

J.W. Bizzaro jeff at bioinformatics.org
Fri Mar 26 17:54:45 EDT 2010

Hi Guys,

Although you're all probably aware of this, it's an import distinction to make: the simulated melting of short oligos (< 50 bp) is more commonly performed using the "nearest neighbor model" described by Philip Borer and colleagues in:

Borer, P.N. et al. 1974. J. Mol. Biol. 86:843-853. (current parameters given in SantaLucia, J., Jr. et al. 1996. Biochemistry 35:3555-3562.)

MeltSim uses the "statistical-mechanical approach" described by Douglas Poland in:

Poland, D. 1974. Biopolymers 13:1859-1871. (current parameters given in Blake, R.D. and Delcourt, S.G. 1998. Nucleic Acids Research 26(14):3323-3332.)

The latter approach holds better for long (>50 bp) sequences.  These are two "schools," if you will, and the thermodynamic parameters are not directly interchangeable.


On 3/26/10 3:56 PM, richard blake wrote:
> Strand concentrations are important only for short DNAs, of for DNA
> strands interacting with oligonucleotides. The effects of concentration
> are nil for DNAs longer than about 20-mers. The literature on the
> effects of concentration is ancient, perhaps fifty years old, but it is
> what some of us cut our teeth on.
> On Mar 25, 2010, at 12:06 PM, Zachary L Dwight wrote:
>> Is strand concentration not included as a parameter because the range
>> of concentrations most likely being used would have no effect on the
>> TM? Thanks so much,
>> Zach Dwight
>> Univ of Utah
>> Dept of Pathology

J.W. Bizzaro
Bioinformatics Organization, Inc. (Bioinformatics.Org)
E-mail: jeff at bioinformatics.org
Phone:  +1 978 621 8258

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