OligoShell Calculator is a comprehensive web application designed for calculating various properties of natural (DNA, RNA), modified, therapeutic oligonucleotides, as well as phosphorodiamidate morpholino oligos (PMO), thiomorpholino oligos (TMO), morpholino oligos (MO), and different chimeras with available nucleic acids. Our tool offers advanced features that meet the needs of researchers and professionals in the fields of nucleic acid chemistry and molecular biology.
Key Features:
- NEW! Calculate properties of phosphorodiamidate morpholino oligos (PMO), thiomorpholino oligos (TMO), morpholino oligos (MO), and various chimeric oligonucleotides.
- Compose oligonucleotides with different backbones including phosphodiester, phosphorothioate, phosphorodithioate, mesyl phosphoramidate, and dimethylamino phosphoramidate.
- Calculate melting temperatures of MGB-modified oligonucleotide probes, similar to Primer Express 3.0 software.
- Determine melting temperatures of DNA oligonucleotides with DNA targets.
- Compute extinction coefficients using nearest neighbors model.
- Obtain monoisotopic and average molecular weights and charge states.
- Generate molecular formulas for oligonucleotides.
- Predict theoretical masses of fragments in MS/MS experiments.
- Quantify oligonucleotides based on user input of measured absorbance at 260 nm and volume of the oligonucleotide solution.
New Tool: TaqMan Finder
This tool simplifies the process of finding 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, chemical modifications of the probe, length of the amplicon, and the reference sequence (RefSeq), you can easily identify compatible components of your assay.
Sequence Input Guidelines:
Sequences must be entered from 5' to 3'. You can choose whether your oligonucleotide is primarily DNA, RNA, or Therapeutic. For sequences containing phosphorothioate linkages, use an asterisk (*) as a separator.
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DNA / RNA Input
Use single-letter codes for standard nucleotides (A, C, G, T/U) and degenerate nucleotides (W, S, M, K, R, Y, B, D, H, V, N). These single-letter codes represent deoxy-nucleotides for DNA and ribo-nucleotides for RNA. For other nucleotides or modifications, use their designated multi-letter codes enclosed in square brackets, e.g., [+Cm], [FAM], or [GALNAC-PRO].
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Therapeutic Input
Enter each nucleotide, degenerate nucleotide, or modification using its specific designation. Separate each entity (nucleotide, modification, or phosphate backbone) with a space.
- To facilitate input, use dropdown menus with modifications of nucleotides from the 'keyboard'.
Examples:
- DNA: ACGTACGTGGCAGGCA
- DNA: [VIC]CCGGCGCGNTTSCGTC[MGB-ECLIPSE]
- RNA: [po]ACGUGGCUSGACUGVUUGAUNG
- RNA: GUGCGAAGGGACGGUGCGGAGAGGAGAGCAC[GALNAC3-ALN]
- Therapeutic: +A +Cm +G dT dA dC dG dT dG dG dC dA dG +G +Cm +A
- Therapeutic: +Cm * +G * +T * dA * dA * dC * dC * dT * dG * dA * dC * dC * dG * +A * +G * +A
- Therapeutic (PMO): morC # morC # morT # morC # morC # morG # morG # morT # morT # morC # morT
Available Nucleotides:
- Deoxynucleotides: dA, dC, dG, dT, dU, dCm
- Degenerate deoxynucleotides: dW, dS, dM, dK, dR, dY, dB, dD, dH, dV, dN
- Ribonucleotides: rA, rC, rG, rU
- Degenerate ribonucleotides: rW, rS, rM, rK, rR, rY, rB, rD, rH, rV, rN
- 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
- Constrained ethyl (cEt) nucleotides: cetA, cetC, cetG, cetU
- Morpholino nucleosides: morA, morC, morG, morT * Cm stands for 5-methylcytosine and T for 5-methyluracil
Experience full functionality of the OligoShell Calculator online at www.oligoshell.com