Calculate Oligonucleotide Properties
This tool allows You to calculate the physical properties of modified and mixmer oligonucleotides including commonly used 3' and 5' modifications.
You can calculate: Molecular Weight (DMT-ON/OFF), Molar Extinction Coefficient, Concentration, Theoretical Melting Temperature, GC Content, Inverse Complement
To start enter the sequence below and select the modifications You would like to include.
If You have an Oligowizard account, You can map custom nucleotides to the numbers 0-9 and our tool will insert them automatically
Enter Your Sequence Here:
Nucleotide Letter Code for 2' Modifications:
DNA: A / C / G / T
RNA: D / E / F / U
LNA: H / I* / J / K
MOE: L / M* / N / O
OMe: P / Q / R / S
2'- F: V / W / X / Y
* 5-Me
Click here for our
Nucleotide Code Conversion Tool
(opens in new window)
Backbone on 3' Linkage:
Capital Letters: Phosphodiester (
PO
)
Lower Case: Phosphothioate (
PS
)
Measured absorbance at 260 nm:
You may specify a measured absorbance value to calculate the concentration of Your oligonucleotide
A260=
Salt Concentrations:
You may specify Ion Concentrations to adjust melting temperature Calculations
mM Na
+
mM K
+
mM Mg
2+
3'-Modification:
Default
OH
Phosphates
Monophosphate
Triphosphate
Dyes / Quenchers
Fluorescein (
#20-2963
)
Cyanine 3 (
#20-5913
)
Cyanine 5 (
#20-5915
)
BHQ-1 (
#20-5931
)
BHQ-2 (
#20-5932
)
Amines
3'-Amino-Modifier C7 (
#20-2958
)
3'-PT-Amino-Modifier C3 (
#20-2954
)
3'-PT-Amino-Modifier C6 (
#20-2956
)
Thiols
3'-Thiol-Modifier C3 S-S (
#20-2933
)
3'-Thiol-Modifier 6 S-S (
#20-2938
)
5'-Modification:
Default
OH
Phosphates
Monophosphate
Triphosphate
Dyes / Quenchers
Fluorescein (
#10-1963
)
Cyanine 3 (
#10-5913
)
Cyanine 5 (
#10-5915
)
BHQ-1 (
#10-1961
)
BHQ-2 (
#10-1962
)
Misc. Linkers
Maleimide (
#10-1938
)
Hexynyl (
#10-1908
)
5'-Aminooxy-Modifier-11 (
#10-1919
)
Amines
5'-Amino-Modifier 5 (
#10-1905
)
5'-Amino-Modifier C6 (
#10-1906
)
5'-Amino-Modifier C12 (
#10-1912
)
5'-Amino-Modifier TEG (
#10-1917
)
5'-Amino-Modifier TEG PDA (
#10-1949
)
5'-Amino-Modifier C12-PDA (
#10-1948
)
Carboxylic acids
5'-Carboxy-Modifier C5 (
#10-1945
)
5'-Carboxy-Modifier C10 (
#10-1935
)
Thiols
5'-Thiol-Modifier C6 (
#10-1926
)
Thiol-Modifier C6 S-S (
#10-1936
)
5' Modification was attached via PS linkage
For
technical questions
or feature requests please contact:
support@oligowizard.com
When You're ready to submit the query press enter or click the button below:
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