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OligoAnalyzer

Sequence 5' MOD INTERNAL 3' MOD MIXED BASES

CGG TCT GTG AGG AGC ATT GT

Bases 20 CLEAR SEQUENCE

Try the new batch mode here (/calc/analyzer/home/batch)

Parameter sets

SpecSheet (Default)

Target type DNA

Oligo Conc 0.25 µM

Na+ Conc 50 mM

Mg++ Conc 0 mM

dNTPs Conc 0 mM

ANALYZE

HAIRPIN

Results SELF-DIMER

RESUSPENSION HETERO-DIMER DILUTION

SEQUENCE NCBI BLAST 5'- CGG TCT GTG AGG AGC ATT GT -3'
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COMPLEMENT TM MISMATCH 5'- ACA ATG CTC CTC ACA GAC CG -3'

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LENGTH 20

GC CONTENT 55 %

MELT TEMP 57.3 ºC

MOLECULAR WEIGHT 6204.1 g/mole

EXTINCTION COEFFICIENT 191900 L/(mole·cm)

nmole/OD260: 5.21

µg/OD260: 32.33

MELTING TEMPERATURE SETTINGS

TARGET TYPE DNA

OLIGO CONC 0.25 µM

Na+ CONC 50 mM monovalent salt

Mg++ CONC 0 mM divalent salt

dNTPs CONC 0 mM nucleotide triphosphate

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.
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OligoAnalyzer

Sequence 5' MOD INTERNAL 3' MOD MIXED BASES

CGG TCT GTG AGG AGC ATT GT

Bases 20 CLEAR SEQUENCE

Try the new batch mode here (/calc/analyzer/home/batch)

Parameter sets

SpecSheet (Default)

Target type DNA

Oligo Conc 0.25 µM

Na+ Conc 50 mM

Mg++ Conc 0 mM

dNTPs Conc 0 mM

ANALYZE

HAIRPIN

General Information
SELF-DIMER

HETERO-DIMER

Image Batch date:

NCBI 2/20/2024
BLAST 4:02 AM
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TM MISMATCH

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 CGGTCTGTGAGGAGCATTGT

Nucleotide type Na Concentration

DNA 50 mM

Mg Concentration Suboptimality

0 mM 50 %

Sequence type Temperature

Linear 25
o
C

Max Foldings Start Position

20 0

Stop Position

UPDATE ADD TO ORDER

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

1 0.45 12.1 -9.9 -34.7

2 0.69 11 -13.9 -48.92

3 0.81 9 -14.2 -50.34

4 0.82 9.8 -15.2 -53.73

5 1.01 6 -14.8 -53.02

6 1.01 -3.1 -9.7 -35.92

7 1.02 4.6 -13.9 -50.05

8 1.27 -2.8 -12.4 -45.86

9 1.34 -1.8 -13.5 -49.76

*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 (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 (http://mfold.rna.albany.edu/?q=unafold-man-pages)

Copyright © Rensselaer Polytechnic Institute 2006. All rights reserved.

Copyright © Washington University 2000. All rights reserved.
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OligoAnalyzer

Sequence 5' MOD INTERNAL 3' MOD MIXED BASES

CGG TCT GTG AGG AGC ATT GT

Bases 20 CLEAR SEQUENCE

Try the new batch mode here (/calc/analyzer/home/batch)

Parameter sets

SpecSheet (Default)

Target type DNA

Oligo Conc 0.25 µM

Na+ Conc 50 mM

Mg++ Conc 0 mM

dNTPs Conc 0 mM

ANALYZE

HAIRPIN

Homo-Dimer Analysis
SELF-DIMER

HETERO-DIMER
The delta G is calculated by taking into account the longest stretch of complementary bases. These pairs of
NCBI BLAST
complementary bases are represented by a solid line. Dotted lines represent additional
Live complementary
Chat bases
for that dimer structure, but their presence does not impact calculated delta G values. Actual delta G values
TM MISMATCH

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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:
5'- CGGTCTGTGAGGAGCATTGT -3'
Maximum Delta G: -37.67 kcal/mol

Delta G: -3.61 kcal/mol Base Pairs: 2

5' CGGTCTGTGAGGAGCATTGT
||
3' TGTTACGAGGAGTGTCTGGC

Delta G: -3.14 kcal/mol Base Pairs: 2

5' CGGTCTGTGAGGAGCATTGT
||
3' TGTTACGAGGAGTGTCTGGC

Delta G: -1.95 kcal/mol Base Pairs: 2

5' CGGTCTGTGAGGAGCATTGT
|| ::
3' TGTTACGAGGAGTGTCTGGC

Delta G: -1.95 kcal/mol Base Pairs: 2

5' CGGTCTGTGAGGAGCATTGT
: || :: :
3' TGTTACGAGGAGTGTCTGGC

Delta G: -1.95 kcal/mol Base Pairs: 2

5' CGGTCTGTGAGGAGCATTGT
|| ::
3' TGTTACGAGGAGTGTCTGGC

Delta G: -1.6 kcal/mol Base Pairs: 2

5' CGGTCTGTGAGGAGCATTGT
|| ::
3' TGTTACGAGGAGTGTCTGGC

Delta G: -1.6 kcal/mol Base Pairs: 2

5' CGGTCTGTGAGGAGCATTGT
|| ::
3' TGTTACGAGGAGTGTCTGGC

Delta G: -1.57 kcal/mol Base Pairs: 2

5' CGGTCTGTGAGGAGCATTGT
|| ::
3' TGTTACGAGGAGTGTCTGGC

Delta G: -1.57 kcal/mol Base Pairs: 2

5' CGGTCTGTGAGGAGCATTGT
: || :: :
3' TGTTACGAGGAGTGTCTGGC

Delta G: -1.47 kcal/mol Base Pairs: 2

5' CGGTCTGTGAGGAGCATTGT
: || :
3' TGTTACGAGGAGTGTCTGGC

For questions regarding the Dimer Analysis contact our Application Support Group
1-800-328-2661 or e-mail Contact Us (/pages/about/contact-us)