Primer Tm estimation methods: Difference between revisions
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(SantaLucia Tms corrected (previous values old Schildkraut salt correction)) |
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| Line 12: | Line 12: | ||
| 52 | | 52 | ||
| 60.1 | | 60.1 | ||
| | | 52.4 | ||
|- | |- | ||
| ActB R: TGATCCACATCTGCTGGAAG | | ActB R: TGATCCACATCTGCTGGAAG | ||
| Line 18: | Line 18: | ||
| 52 | | 52 | ||
| 59.8 | | 59.8 | ||
| | | 51.5 | ||
|- | |- | ||
| Tubb5 F: GATCGGTGCTAAGTTCTGGGA | | Tubb5 F: GATCGGTGCTAAGTTCTGGGA | ||
| Line 24: | Line 24: | ||
| 54 | | 54 | ||
| 61.5 | | 61.5 | ||
| | | 53.7 | ||
|- | |- | ||
| Tubb5 R: AGGGACATACTTGCCACCTGT | | Tubb5 R: AGGGACATACTTGCCACCTGT | ||
| Line 30: | Line 30: | ||
| 54 | | 54 | ||
| 60.8 | | 60.8 | ||
| | | 55.1 | ||
|} | |} | ||
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* SantaLucia 1998, DOI:10.1073/pnas.95.4.1460 | * SantaLucia 1998, DOI:10.1073/pnas.95.4.1460 | ||
: Primer3 recommended setting | : Primer3 recommended setting; also default settings of the NCBI's [http://www.ncbi.nlm.nih.gov/tools/primer-blast/primertool.cgi Primer BLAST] | ||
Revision as of 06:57, 24 September 2009
| example primer | Marmur rule | Wallace rule | Breslauer '86 | SantaLucia '98 |
|---|---|---|---|---|
| ActB F: TTGCTGACAGGATGCAGAAG | 60 | 52 | 60.1 | 52.4 |
| ActB R: TGATCCACATCTGCTGGAAG | 60 | 52 | 59.8 | 51.5 |
| Tubb5 F: GATCGGTGCTAAGTTCTGGGA | 64 | 54 | 61.5 | 53.7 |
| Tubb5 R: AGGGACATACTTGCCACCTGT | 64 | 54 | 60.8 | 55.1 |
- Marmur formula: Tm = 4 x GC + 2 x AT
- not recommended for more than 13nt; assumes 50mM monovalent cations
- Marmur J and Doty P (1962) J Mol Biol 5:109-118; PMID 14470099
- Wallace formula: Tm = 64.9 +41*(yG+zC-16.4)/(wA+xT+yG+zC)
- Wallace RB et al. (1979) Nucleic Acids Res 6:3543-3557, PMID 158748
- Breslauer et al. 1986, DOI:10.1073/ pnas.83.11.3746
- Primer3 and Primer3Plus default maintained for backwards compatibility
- SantaLucia 1998, DOI:10.1073/pnas.95.4.1460
- Primer3 recommended setting; also default settings of the NCBI's Primer BLAST
