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Oligonucleotide Properties Calculator
Enter Oligonucleotide Sequence
Oligonucleotide is
DNA
RNA
Therapeutic
5'-Labels
FAM
Carboxyfluorescein
TET
Tetrachlorofluorescein
JOE
Dichlorodimethoxycarboxyfluorescein
VIC
2'-Chloro-7'-phenyl-1,4-dichloro-6-carboxyfluorescein
HEX
Hexachlorofluorescein
R6G
Carboxyrhodamine 6G
R6G-ACH
Carboxyrhodamine 6G, aminocyclohexanol linker
CY3-ACH
Indocarbocyanine 3, aminocyclohexanol linker
TMR-ACH
Tetramethylcarboxyrhodamine, aminocyclohexanol linker
ROX-CLK
Carboxyrhodamine X, via click with ALKYNE
TR-CLK
Texas Red, via click with ALKYNE
AF594-CLK
Alexa Fluor 594, via click with ALKYNE
CY5-CLK
Indodicarbocyanine 5, via click with ALKYNE
ATTO647N-CLK
ATTO-647N, via click with ALKYNE
po
Phosphate
ALKYNE
5'-terminal alkyne, aminocyclohexanol linker
CHOL-PRO
Cholesterol, hydroxyprolinol linker
GALNAC-PRO
Monomer GalNAc, hydroxyprolinol linker
MOR-TEG
Triethylene Glycol for Morpholino
Internal
ECLIPSE
Eclipse Quencher
BHQ1
Black Hole Quencher 1
BHQ2
Black Hole Quencher 2
GALNAC-PRO
Monomer GalNAc, hydroxyprolinol linker
3'-Labels
ECLIPSE
Eclipse Quencher
MGB-ECLIPSE
MGB-Eclipse Quencher
BHQ1
Black Hole Quencher 1
BHQ2
Black Hole Quencher 2
po
Phosphate
MGB
CDPI3 Minor groove binder
CHOL-PRO
Cholesterol, hydroxyprolinol linker
GALNAC-PRO
Monomer GalNAc, hydroxyprolinol linker
GALNAC3-ALN
Trimer GalNAc, Alnylam design
Show all available nucleotides and modifications
Parameters for Tm estimation
Parameter sets
Default
qPCR
Target type
DNA
Oligo Conc
μM
Na
+
Conc
mM
Mg
2+
Conc
mM
dNTPs Conc
mM
Quantification
OD
260
(10 mm)
AU
Volume
mL
dA
dC
dG
dT
dCm
dU
rA
rC
rG
rU
mA
mC
mG
mU
fA
fC
fG
fU
moeA
moeCm
moeG
moeT
+A
+Cm
+G
+T
cetA
cetC
cetG
cetU
morA
morC
morG
morT
* / ps
ps2
ms
# / dma
W
S
M
K
R
Y
B
D
H
V
N
* / ps
ps2
ms
# / dma
Nucleotides
Degenerate NTs
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