OligoAnalyzer

Please note that we recently updated our default parameter set to “qPCR” to align with the most commonly used OligoAnalyzer Tool setting.
If you would like to switch the parameters to the previous default of “SpecSheet”, this can be selected from the “Parameter sets” dropdown menu.

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Sequence

Bases

Try the new batch mode here

Target type

Oligo Conc

µM

Na⁺ Conc

Mg⁺⁺ Conc

dNTPs Conc

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	DETAILS
		Details

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

Image

Nucleotide type

Na Concentration

Mg Concentration

Suboptimality

Sequence type

Temperature

^oC

Max Foldings

Start Position

Stop Position

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

Structures

structure	Image	ΔG (kcal.mole^-1)	T_m (^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

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.

Dimer Sequence:

Maximum Delta G:

Delta G: Base Pairs:

For questions regarding the Dimer Analysis contact our Application Support Group
1-800-328-2661 or e-mail Contact Us

Hetero-Dimer Analysis

Primary Sequence:

5'- -3'

Secondary Sequence:

5'- -3'

Primary Sequence:

Secondary Sequence:

Maximum Delta G:

Delta G: Base Pairs:

For questions regarding the Dimer Analysis contact our Application Support Group
1-800-328-2661 or Contact Us

Exact and Single Base Mismatch DNA Thermodynamics

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

Additional
Target Base

5'-

3'-

-3'

-5'

Hybridization Temperature

Use Exact Complement T_m
User Defined ^oC
Target Concentration

5'-

-3'

3'-

-5'

Melting Temperatures

EXACT MATCH T_M
MISMATCH T_M
DELTA T_M

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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OligoAnalyzer

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Results

MELTING TEMPERATURE SETTINGS

MELTING TEMPERATURE ASSUMPTIONS AND LIMITATIONS

General Information

Structures

Homo-Dimer Analysis

Hetero-Dimer Analysis

Primary Sequence:

Secondary Sequence:

Exact and Single Base Mismatch DNA Thermodynamics

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