OLIGOWIZARD
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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
With an Oligowizard account, you can even add your own nucleic acid building blocks and customise the calculations!
To start enter the sequence below and select the modifications You would like to include.
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
Nucleotide Code Conversion Tool
Backbone on 3' Linkage:
Capital Letters: Phosphodiester (
PO
)
Lower Case: Phosphothioate (
PS
)
Absorbance and Volume
Measured absorbance and volume to calculate the concentration and amount of your oligo
Measured absorbance
A260
Volume
µL
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
Cyanine 3
Cyanine 5
BHQ-1
BHQ-2
Amines
3'-Amino-Modifier C7
3'-PT-Amino-Modifier C3
3'-PT-Amino-Modifier C6
Thiols
3'-Thiol-Modifier C3 S-S
3'-Thiol-Modifier 6 S-S
5'-Modification:
Default
OH
Phosphates
Monophosphate
Triphosphate
Dyes / Quenchers
Fluorescein
Cyanine 3
Cyanine 5
BHQ-1
BHQ-2
Misc. Linkers
Maleimide
Hexynyl
5'-Aminooxy-Modifier-11
Amines
5'-Amino-Modifier 5
5'-Amino-Modifier C6
5'-Amino-Modifier C12
5'-Amino-Modifier TEG
5'-Amino-Modifier TEG PDA
5'-Amino-Modifier C12-PDA
Carboxylic acids
5'-Carboxy-Modifier C5
5'-Carboxy-Modifier C10
Thiols
5'-Thiol-Modifier C6
Thiol-Modifier C6 S-S
5' Modification was attached via PS linkage
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