It provides a comprehensive analysis of sequences containing standard and mixed bases, as well as DNA/RNA, methylated, locked and phosphorothioated bases. The tool calculates the physical properties of sequences, including length, GC content, melting temperature, molecular weight, extinction coefficient, optical density (OD) and sequence linguistic complexity. It can also detect self-dimers and G-quadruplexes.
| Parameters for calculation of oligonucleotide Tm: | Dilution of oligo: | |||
| Primer concentration (0.01-5 µM): | Target volume (µl): | |||
| Total salt (Na+, K+, NH4+, Tris+) concentration (1-1000 mM): | Target concentration (µM): | |||
| Mg2+ concentration (0-10 mM): | Volume of the stock (µl): | |||
| Value of the sensivity for primer dimer detection (1-10): | MQ water or TE buffer (µl): |
| Amount of oligo: | Preparing stock solution: | |||
| OD (A260): | Stock concentration (µM): | |||
| Mass (µg): | ||||
| nmol: |
Features
Dimers
- A name is not required for oligonucleotide (eg. agtcagtcagtcagtcagtc).
- Degenerate primer sequences are also accepted, each letter represents a combination of one or several nucleotides: B=(C,G,T), D=(A,G,T), H=(A,C,T), K=(G,T), M=(A,C), N=(A,C,G,T), R=(A,G), S=(G,C), V=(A,C,G), W=(A,T), Y=(C,T). U=Uracil, I=Inosine and LNA: dA=E, dC=F, dG=J, dT=L.
- Linguistic sequence complexity (LC%) is a measure of the 'vocabulary richness' of a genetic text. It is based on counting the number of possible nucleotide combinations ("entropy" of the set of possibilities) compared to the theoretical maximum. This sequence value is converted to a percentage, with 100% representing the highest level.
- Linguistic sequence complexity (YR%) is a measure of the 'harmony' of genetic text. It is based on counting the number of possible combinations of purines and pyrimidines relative to the theoretical maximum. This sequence value is converted into a percentage, with 100% representing the highest possible level.
- Melting temperature calculations are based on nearest neighbor thermodynamic parameters for standard and degenerate oligonucleotides, including LNA and other modifications. And provides a dilution and resuspension calculator for stocks.
The Analyzer provides the following results:
- Tm (°C)
- CG content (%)
- Sequence linguistic complexity (LC%)
- Length of the primers (nt)
- Number of individual bases (A, T, C and G)
- Extinction coefficient (l/(mol·cm))
- Molecular weight (g/mol)
- Amount/OD unit (nmol/OD260)
- Mass (µg/OD260)
- Primer-dimer estimation