Primer Tm estimation methods: Difference between revisions
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! example primer | ! example primer | ||
! GC+AT=length | |||
! style="background:lightgrey"|Marmur rule | ! style="background:lightgrey"|Marmur rule | ||
! style="background:lightgrey"|Wallace rule | ! style="background:lightgrey"|Wallace rule | ||
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| 50/50 mixed: AGAGAGAGAGAGAGAGAGAG | | 50/50 mixed: AGAGAGAGAGAGAGAGAGAG | ||
| 10+10=20 | |||
| 60 | | 60 | ||
| 52 | | 52 | ||
| Line 15: | Line 17: | ||
|- | |- | ||
| 50/50 separated: AAAAAAAAAAGGGGGGGGGG | | 50/50 separated: AAAAAAAAAAGGGGGGGGGG | ||
| 10+10=20 | |||
| 60 | | 60 | ||
| 52 | | 52 | ||
| Line 21: | Line 24: | ||
|- | |- | ||
| ActB F: TTGCTGACAGGATGCAGAAG | | ActB F: TTGCTGACAGGATGCAGAAG | ||
| 10+10=20 | |||
| 60 | | 60 | ||
| 52 | | 52 | ||
| Line 27: | Line 31: | ||
|- | |- | ||
| ActB R: TGATCCACATCTGCTGGAAG | | ActB R: TGATCCACATCTGCTGGAAG | ||
| 10+10=20 | |||
| 60 | | 60 | ||
| 52 | | 52 | ||
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|- | |- | ||
| Tubb5 F: GATCGGTGCTAAGTTCTGGGA | | Tubb5 F: GATCGGTGCTAAGTTCTGGGA | ||
| 11+10=21 | |||
| 64 | | 64 | ||
| 54 | | 54 | ||
| Line 38: | Line 44: | ||
| 53.7 | | 53.7 | ||
|- | |- | ||
| 11+10=21 | |||
| Tubb5 R: AGGGACATACTTGCCACCTGT | | Tubb5 R: AGGGACATACTTGCCACCTGT | ||
| 64 | | 64 | ||
Revision as of 01:52, 28 September 2009
| example primer | GC+AT=length | Marmur rule | Wallace rule | Breslauer '86 | SantaLucia '98 |
|---|---|---|---|---|---|
| 50/50 mixed: AGAGAGAGAGAGAGAGAGAG | 10+10=20 | 60 | 52 | 46.3 | 47.7 |
| 50/50 separated: AAAAAAAAAAGGGGGGGGGG | 10+10=20 | 60 | 52 | 66.0 | 52.7 |
| ActB F: TTGCTGACAGGATGCAGAAG | 10+10=20 | 60 | 52 | 60.1 | 52.4 |
| ActB R: TGATCCACATCTGCTGGAAG | 10+10=20 | 60 | 52 | 59.8 | 51.5 |
| Tubb5 F: GATCGGTGCTAAGTTCTGGGA | 11+10=21 | 64 | 54 | 61.5 | 53.7 |
| 11+10=21 | 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
- online tool using Wallace formula for oligos >13
- Breslauer et al. 1986, PMID 3459152 combined with Schildkraut et al. 1965, PMID 5889540 salt correction formulae
- Primer3 and Primer3Plus default maintained for backwards compatibility
- SantaLucia 1998, PMID 9465037 thermodynamics & salt correction
- Primer3 recommended setting; also default settings of the NCBI's Primer BLAST
