OLIGO MELTING Release 2011_03
Calculate Thermodynamic Parameters of DNA Hybridization
(Melting Temperature, Entropy, Enthalpy)
by Ivano Zara & Renato.Schiavon
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Oligo
*        [ Conc. * µM] (5'→3'') For
(5'→3') Rev
(3'←5') Rev (as strand '+')
Template (strand +)
(optional; is required only if the template is not complementary)
1)  * Manual aligment
Automatic aligment
[Conc.* fM ]
(if you put more bases on the rigth or/and on the left, the thermodynamic parameters can be calculate with dangling-end parameters)
[Na+]
* mM
[Mg++]
* mM            dNTPs(total) mM
[% DMSO] * % (V/V)     OR       [% Formamide] * % (V/V)  
 
* required        * optional
Automatic or manual alignment:
- With the Automatic alignment, the program, with its own algorithm, aligns the oligo with the template sequence, inserting each gap. Any other symbol of gap ('-'), entered by the user, will not be considered.
- Instead, with manual alignment, it will be the user to insert any gap ('-'). In this case the two sequences (in the form of string of characters) must have the same length. Any dangling-end must be reported by inserting the gap symbol ('-') on the right AND/OR on the left

Example of manual alignment
ACCTGCA--CCAGGAAACCGGAATCG
ACATGCACCCCAGGTAACC-GAATCG
          
Example of manual alignment with dangling-end DX and SX:
-ACCTGCA--CCAGGAAACCGGAATCG-
TACATGCACCCCAGGTAACC-GAATCGC

Usualy Buffer in PCR:
- TAQ DNA polymerase: Na+=50mM    Mg2+=1.5mM

The main program calculates the thermodynamics parameter (melting temperature, Entropy and Enthalpy variation, with the Nearest-Neighbor method.
It uses data from SantaLucia et al.(1998) and for salt correction from von Ahsen et al. (2001).
In case of multi-mismatch or terminal mismatches it use Mfold parameter by Zuker M. (2003) and made approssimation parameter.

The program shows template fractions at some temperature near melting temperature.
It shows the quantity of primer that forms duplex at a certain temperature and estimates the quantity of primer that could be elonged after a polymerase or ligase reaction.
Moreover, the program calculates melting temperature with other methods
(Wallac (1979), Howley et al. (1979)) and salt correction with Wetmur (1991),
SantaLucia et al.(1996), Nakano et al. (1999) for Mg++ and to compare the methods.

Warning:
Thermodynamic parameters depend from salt and DMSO concentration, so insert exact salt concentration and DMSO,
because a little variation of these components could strongly affect thermodynamic parameters.