Result

s
POL
AND
for
ACE_
inserc
ja

Temperature of 50 % probability vs. sequence

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 Base pair probability vs. sequence vs. temperature

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Relative gel mobility with given stiffness vs. temperature

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UV hypochromicity at 260 and 282 nm vs. temperature

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Differentiated hypochromicity at 260 and 282 nm (dA/dT) vs. temperature

 Get as PostScript file (21 kByte)

You will get the basic output from here: Bunch of numbers (x,y values) (497 kByte)
The lowest temperature for calculation may be too low.
In case a floating point error occurs during calculation,
change the temperature(s) in the appropriate direction.

POLAND-BATCH
************

Using results produced by this service, please cite:

Steger G.
Thermal denaturation of double-stranded nucleic acids:
prediction of temperatures critical for gradient gel
electrophoresis and polymerase chain reaction.
Nucleic Acids Res. 1994 Jul 25; 22(14): 2760-2768.

Seq.label = ACE_insercja
calc. from = 1 nt
to = 479 nt
Seq.length = 479 nt
Mismatches = None
Temp. from = 40.0 °C
to = 110.0 °C
step = 2.00 °C
Points = 36
Sigma = 0.10E-02
Beta * c0 = 0.10E-08

Hypochromicity values according to

Blake, R.D. and Haydock, P.V. (1979) Biopolymers 18, 3089-3109.
Effect of sodium ion on the high-resolution melting of lambda DNA.

Internal loops according to:

Fixman, M. and Freire, J.J. (1977) Biopolymers 16, 2693-2704.
Theory of DNA melting curves.

Stiffness: 40., 90., 200.

 Thermodynamical values according to:
H.H. Klump (1990) in 'Landolt-Börnstein, New Series, VII Biophysics,
Vol. 1 Nucleic Acids, Subvol. c Spectroscopic and Kinetic Data,
'Physical Data I', W. Saenger (ed.), Springer-Verlag Berlin, p. 241-256.
Calorimetric studies on DNAs and RNAs. pp. 244-245.

DH [kJ/mol], DS [J/molK], T[°C]

3' A T G C
5' -DH -DS T -DH -DS T -DH -DS T -DH -DS T
A 32.3 95.6 64.7 31.2 95.3 54.2 36.0 102.4 78.4 35.8 100.4 83.4
T 31.2 95.3 54.2 32.3 95.6 64.7 35.8 100.4 83.4 36.0 102.4 78.4
G 36.0 102.4 78.4 35.8 100.4 83.4 35.1 93.9 100.7 39.8 102.4 115.5
C 35.8 100.4 83.4 36.0 102.4 78.4 39.8 102.4 115.5 35.1 93.9 100.7

Thermodynamic values are corrected with:

DS-Factor = 1.0000
DS-Factor (A:T) = 1.0000
DS-Factor (G:C) = 1.0000

Sequence:
479 ACE_insercja
CTGGAGACCACTCCCATCCTTTCTCCCATTTCTCTAGACCTGCTGCCTATACAGTCACTTTTTTTTTTTT
TTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCTCGGCTCACTGCAACGTC
CGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACCACAGCGCCCGCCACTA
CGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGTCTCGATCT
CCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGATACAGTCACTTTT
ATGTGGTTTCGCCAATTTTATTCCAGCTCTGAAATTCTCTGAGCTCCCCTTACAAGCAGAGGTGAGCTAA
GGGCTGGAGCTCAAGGCATTCAAACCCCTACCAGATCTGACGAATGTGATGGCCACATC
 Procedure
Elapsed time / ms

Calculation
115

Tm(p=50%) plot
41

3D plot
1065

Mobility plot
16

UV melting plot
34

Diff. UV melting plot

14

Total plotting
1291

PS2GIF conversion
812
Calculation No 99155. Thank You for using Poland Service!
Institut für Physikalische Biologie
(Department of Biophysics)
Heinrich Heine-Universität Düsseldorf, Germany
G. Steger, A. Wilm, S. Gräf, M. Labensky & A. Jäger
May. 03, 2009