This web application is aimed to calculate properties of natural, modified and therapeutic oligonucleotides.
It can calculate:
- NEW! Melting temperature of MGB-modified oligonucleotide probes
- Melting temperature of DNA oligonucleotide with DNA target
- Extinction coefficient (nearest neighbours model)
- Monoisotopic and average molecular weight and charge states
- Molecular formula of oligonucleotide
- Theoretical masses of fragments in MS/MS experiments
It can also quantify oligonucleotide based on user input of measured absorbanse at 260 nm and volume of oligonucleotide solution.
New Tool - TaqMan Find
This tool is made to help you find matching primers and probes for TaqMan assays within your specified target sequence. By providing the exact (single isotope) masses of both primers and the probe, the chemical modifications of the probe, the length of the amplicon, and the reference sequence (RefSeq), you can easily identify compatible components of your assay.
How to input a sequence:
Sequences are 5'→3' left to right. You may choose one of two input styles: 'DNA' and 'Therapeutic. On default it is assumed that two nucleotides have phosphodiester linkage. Use ' * ' as a separator to designate phosphorothioate linkage.
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DNA input style
Four deoxynucleotides (A, C, G, T) as well as eleven degenerate deoxynucleotides (W, S, M, K, R, Y, B, D, H, V, N) can be used with a single letter code. All other nucleotides with different sugar moieties as well as modifications have several letter codes and should be surrounded by square brackets, e.g. [FAM] or [BHQ1].
Examples:
ACGTACGTGGCAGGCA
[VIC]CCGGCGCGNTTSCGTC[MGB-ECLIPSE]
[+Cm]*[+G]*[+T]*A*A*C*C*T*G*A*C*C*G*[+A]*[+G]*[+A]
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Therapeutic input style
Every nucleotide, degenerate nucleotide or modification has a specific designation and should be separated with 'space' from the next nucleotide or phosphate entity.
Examples:
dA dC dG dT dA dC dG dT dG dG dC dA dG dG dC dA
VIC dC dC dG dG dC dG dC dG dN dT dT dS dC dG dT dC MGB-ECLIPSE
+Cm * +G * +T * dA * dA * dC * dC * dT * dG * dA * dC * dC * dG * +A * +G * +A
Available alphabet:
- Deoxynucleotides: dA, dC, dG, dT, dU, dCm
- Degenerate deoxinucleotides: dW, dS, dM, dK, dR, dY, dB, dD, dH, dV, dN
- Ribonucleotides: rA, rC, rG, rU
- 2'-OMe nucleotides: mA, mC, mG, mU
- 2'-F nucleotides: fA, fC, fG, fU
- 2'-MOE nucleotides: moeA, moeCm, moeG, moeT
- LNA nucleotides: +A, +Cm, +G, +T * Cm stands for 5-methylcytosine and T for 5-methyluracil
Available modifications:
- 5': po (phosphate), ALKYNE, FAM, TET, HEX, JOE, VIC, TMR-ACH, R6G, R6G-ACH, ROX-CLK, TR-CLK, AF594-CLK, CY3-ACH, CY5-CLK, CHOL-PRO, GALNAC-PRO
- 3': po (phosphate), BHQ1, BHQ2, MGB, MGB-ECLIPSE, ECLIPSE, CHOL-PRO, GALNAC-PRO, GALNAC3-ALN
- Internal: BHQ1, BHQ2, ECLIPSE, GALNAC-PRO
OligoShell Calculator is available online at www.oligoshell.com