This web application is aimed to calculate properties of natural, modified and therapeutic oligonucleotides.
It can calculate:
- NEW! 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.
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