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OligoAnalyzer 3.1

Sequence  Bases
5'- -3'

 
 
Parameter sets
Target type
Oligo Conc µM
Na+ Conc mM
Mg++ Conc mM
dNTPs Conc  mM
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RESULTS

 
SEQUENCE
COMPLEMENT
LENGTH
GC CONTENT
MELT TEMP
MELT TEMP RANGE
MIN MEAN MAX
MOLECULAR WEIGHT
EXTINCTION COEFFICIENT
nmole/OD260:
µg/OD260:
MODIFICATIONS
SEQUENCE VALUE MODIFICATION NAME

MELTING TEMPERATURE SETTINGS

TARGET TYPE
OLIGO CONC
Na+ CONC
Mg++ CONC
dNTPs CONC

MELTING TEMPERATURE ASSUMPTIONS AND LIMITATIONS

  • Predictions are accurate for oligos from 8 to 60 bases in length, in neutral buffered solutions (pH 7 - 8) with monovalent cation (Na+) concentrations from 1.2 M down to 1.5mM, divalent cation (Mg++) concentrations from 600 mM down to 0.01 mM, and triphosphates (dNTPs) concentrations up to 120% of the divalent cation concentration.
  • Oligo concentration is assumed to be significantly larger (at least 6x) than concentration of the complementary target, which is true in majority of molecular biology experiments. If this is not a case, concentration of the target cannot be ignored and you should enter in the box,

    • Oligo Conc = [strand1] – [strand2]/2 when [strand1] ≥ [strand2]
    • Oligo Conc = ([strand1] + [strand2])/4 when [strand1] = [strand2]

  • Melting temperature accuracy and models: (Oligo/Template)
    DNA/DNA +/- 1.4ºC (Allawi '97)
    LNA/DNA +/- 2.0ºC (McTigue '04, Owczarzy, 2011)
    RNA/DNA +/- 2.7ºC (Sugimoto '95)
    DNA/RNA +/- 2.7ºC (Sugimoto '95)
    RNA/RNA +/- 1.3ºC (Xia '98)
    Divalent cation correction +/- 0.5ºC (Owczarzy '08)
    Triphosphate correction +/- 0.0ºC (Owczarzy '08)
    Monovalent cation correction +/- 2.0ºC (Owczarzy '04)
  • Consecutive LNA bases hybridized to a DNA template use a model from Owczarzy '11. In the absence of empirical data, LNA bases on an RNA template assume RNA values, and predictions are therefore less accurate.

  • Non-consecutive LNA bases hybridized to a DNA template use a model from McTigue '04. Consecutive LNA bases on a DNA template and any LNA bases on an RNA template assume RNA energetic parameters and predictions are therefore less accurate.

  • Effects of chemical modifications are neglected except when the modification contains a base, e.g., 5-Methyl dC, Internal Fluorescein dT. Energetic effects of these modifications are only approximated.

General Information

 

oC
mM
mM
%

Warning: if there is very little or no secondary structure, using a temperature higher than the default may give odd results.

Structures

Structure Name Image ΔG(kcal.mole-1) Tm (oC) ΔH(kcal.mole-1) ΔS(cal.K-1mole-1) Output

*Note dNTP Concentration is not taken into account.

IDT's licensed UNAFold software is available to our customers for the design of oligonucleotide sequences and for use of the resulting oligos purchased from IDT in the purchaser's research applications only. To obtain access to a license to or a copy of the UNAFold software for any other application, including commercial applications, please visit http://mfold.rna.albany.edu/?q=DINAMelt/commercial-license. For the latest information on UNAFold development and additional resources, visit http://mfold.rna.albany.edu/?q=unafold-man-pages

Copyright © Rensselaer Polytechnic Institute 2006. All rights reserved.
Copyright © Washington University 2000. All rights reserved.

Homo-Dimer Analysis

The delta G is calculated by taking into account the longest stretch of complementary bases. These pairs of complementary bases are represented by a solid line. Dotted lines represent additional complementary bases for that dimer structure, but their presence does not impact calculated delta G values. Actual delta G values may vary based on presence of additional complementary bases. The Maximum Delta G value refers to the free energy of the oligo sequence binding to its perfect complement.
 
For questions regarding the Dimer Analysis contact our Technical Support Group
1-800-328-2661 or e-mail TechSupport@idtdna.com

Hetero-Dimer Analysis

Primary Sequence:

5'- -3'

Secondary Sequence:

5'- -3'
The delta G is calculated by taking into account the longest stretch of complementary bases. These pairs of complementary bases are represented by a solid line. Dotted lines represent additional complementary bases for that dimer structure, but their presence does not impact calculated delta G values. Actual delta G values may vary based on presence of additional complementary bases. The Maximum Delta G value refers to the free energy of the oligo sequence binding to its perfect complement.
 
 

    
For questions regarding the Dimer Analysis contact our Technical Support Group
1-800-328-2661 or e-mail TechSupport@idtdna.com

Exact and Single Base Mismatch DNA Thermodynamics


Primary Sequence: 5' to 3'; Target Sequence: 3' to 5'

Additional
Target Base
Additional
Target Base
5'- 

3'-
|
 -3'

-5'
 


Hybridization Temperature

oC

5'-
-3'
|
3'-  
  -5'

Melting Temperatures
EXACT MATCH TM:
MISMATCH TM:
DELTA TM:
Percent Bound At
EXACT MATCH:
MISMATCH:
Mismatch Settings
NUCLEOTIDE TYPE:
OLIGO CONC:
Na+ CONC:
Mg++ CONC:
dNTPs CONC:
TARGET CONC:
HYBRIDIZATION TEMP:
Sequence:
Position Problem Problem Description
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  Mod Code Name Category Purif Req Allow Page Min Scale Price/Availability
More Info
Scale Price

Scientific Details

MW
Extinction Coefficient
Emission Max
Absorbance Max
Extinction Coefficient
(At Absorbance Max)
Loading...
  Mod Code Name Category Purif Req Allow Page Min Scale Price/Availability
More Info
Scale Price

Scientific Details

MW
Extinction Coefficient
Emission Max
Absorbance Max
Extinction Coefficient
(At Absorbance Max)
Loading...
  Mod Code Name Category Purif Req Allow Page Min Scale Price/Availability
More Info
Scale Price

Scientific Details

MW
Extinction Coefficient
Emission Max
Absorbance Max
Extinction Coefficient
(At Absorbance Max)

Standard Mixed Base Instructions

To use a Standard Mixed Base, simply type in the IUB symbol (from the table below) which represents the desired mix.

Custom Mixed Base Instructions

To use Custom Mixed Bases
  • Enter the desired percentage of each base (Integers Only, Totaling 100%).
  • Press 'Use Mix Base' button to add your custom mixed base.

Please note: An additional charge is applied for hand mixing these custom bases.


Base Notations

  • DNA = A, C, G, T and U, I
  • Mixed Bases = Please enter bases in UPPERCASE
  • Phosphorothioated DNA = A*, G*, C*, T*
  • RNA = rA, rG, rC, rU
  • Phosphorothioated RNA = rA*, rG*, rC*, rU*
  • 2'O-Methyl RNA = mA, mG, mC, mU
  • Phosphorothioated 2'O-Methyl RNA = mA*, mG*, mC*, mU*
  • Locked Nucleic Acid (LNA) = +A, +G, +C, +T

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