oligo melting temperature

Brian Osborne bosborne at NATURE.BERKELEY.EDU
Wed May 15 12:32:12 EST 1996


>Dear netters,
>
>has someone compared the different equations out there to calculate
>the melting temperature of oligos? The Maniatis equation for short
>oligos did not work well in our hands. Is there a good program (for
>Macs) available which calculates reliabale Tm's?
>
>Thanks for your time, Bernd
>
>___________________________________________________________________________
>Bernd Weisshaar
>MPI fuer Zuechtungsforschung
>Abteilung Biochemie
>Carl-von-Linne-Weg 10
>50829 Koeln
>Germany
>
>Fax: +49-221-5062 313
>e-mail: weisshaa at mpiz-koeln.mpg.de

There is an algorithm based on 'nearest neighbor' thermodynamic values :

Breslauer, K. J., Frank, R., Blocker, H., and Marky, L. A. (1986).
Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad.
Sci. USA 83, 3746-3750.


This algorithm is applied to the Tm's of oligonucleotides in :

Rychlik, W., and Rhoads, R. E. (1989). A computer program for choosing
optimal oligonucleotides for filter hybridization, sequencing and in vitro
amplification of DNA. Nucl. Acid Res. 17, 8543-8551.


This is a table containing the values you'll need. It's from a program,
that's why it doesn't look like
a table! For example, the enthalpy for the AT dinucleotide is 8.6
(expressed  without the proper
units) :

function dH x,y
  -- returns enthalpies of adjacent pairs
  if x is "a" then
    if y is "a" then return "9.1"
    if y is "t" then return "8.6"
    if y is "g" then return "7.8"
    if y is "c" then return "6.5"
  end if
  if x is "t" then
    if y is "a" then return "6"
    if y is "t" then return "9.1"
    if y is "g" then return "5.8"
    if y is "c" then return "5.6"
  end if
  if x is "g" then
    if y is "a" then return "5.6"
    if y is "t" then return "6.5"
    if y is "g" then return "11"
    if y is "c" then return "11.1"
  end if
  if x is "c" then
    if y is "a" then return "5.8"
    if y is "t" then return "7.8"
    if y is "g" then return "11.9"
    if y is "c" then return "11"
  end if
end dH

function dS x,y
  -- returns entropies of adjacent pairs
  if x is "a" then
    if y is "a" then return "24"
    if y is "t" then return "23.9"
    if y is "g" then return "20.8"
    if y is "c" then return "17.3"
  end if
  if x is "t" then
    if y is "a" then return "16.9"
    if y is "t" then return "24"
    if y is "g" then return "12.9"
    if y is "c" then return "13.5"
  end if
  if x is "g" then
    if y is "a" then return "13.5"
    if y is "t" then return "17.3"
    if y is "g" then return "26.6"
    if y is "c" then return "26.7"
  end if
  if x is "c" then
    if y is "a" then return "12.9"
    if y is "t" then return "20.8"
    if y is "g" then return "27.8"
    if y is "c" then return "26.6"
  end if
end dS

I am afraid I don't have this alone as a program. Perhaps you can devise a
macro in a
spreadsheet program? or in Hypercard?

Brian I. Osborne                 bosborne at nature.berkeley.edu
Plant Gene Expression Center             FAX 510 559 5678
800 Buchanan St.                TEL 510 559 5919
Albany CA 94710 USA
http://pgebaker4.pw.usda.gov/bio/science.html





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