Sam:LabNotes/Microbione/2009-2-3: Difference between revisions
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>Sam Chiang (New page: ='''Primer design for human 18S and Bacteria 16S'''= ==Objective== Besides the realtime monitoring, #Design 18S primers for positive control / validation purpose of a successful MDA rea...) |
>Sam Chiang No edit summary |
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=Human S18 primer= | ==Human S18 primer== | ||
#Collect the human S18 cDNA sequence | #Collect the human S18 cDNA sequence | ||
# | #Clean the sequcne and mask the inconsistat nucleotide | ||
#Paste the | #Paste the sequence on KZ's Primer3 calculator[http://www.example.com link title] | ||
#Criteria: | |||
Primer size: Min: 18bp, opt:20 bp, Max: 22bp | |||
Product size: ~200 bp; ~300 bp | |||
Annealing Temp: Min:57, Opt:58, Max:59 | |||
#Pick up two primers with differnt size of amplicon. | |||
>h18S_211_f | |||
TTGCTGCAGTTAAAAAGCTC | |||
>h18S_211_r | |||
CATTATTCCTAGCTGCGGTA | |||
OLIGO start len tm gc% any 3' seq | |||
LEFT PRIMER 758 20 57.86 40.00 6.00 2.00 TTGCTGCAGTTAAAAAGCTC | |||
RIGHT PRIMER 968 20 57.56 45.00 4.00 2.00 CATTATTCCTAGCTGCGGTA | |||
SEQUENCE SIZE: 1969 | |||
INCLUDED REGION SIZE: 1969 | |||
PRODUCT SIZE: 211, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 1.00 |
Revision as of 06:31, 9 February 2009
Primer design for human 18S and Bacteria 16S
Objective
Besides the realtime monitoring,
- Design 18S primers for positive control / validation purpose of a successful MDA reaction using human genome template.
- Design 16S primers for positive control / validation purpose of a successful MDA reaction using bacteria genome template.
- These primers could also be used to detect the contamination of exogenus gDNA.
Human S18 primer
- Collect the human S18 cDNA sequence
- Clean the sequcne and mask the inconsistat nucleotide
- Paste the sequence on KZ's Primer3 calculatorlink title
- Criteria:
Primer size: Min: 18bp, opt:20 bp, Max: 22bp Product size: ~200 bp; ~300 bp Annealing Temp: Min:57, Opt:58, Max:59
- Pick up two primers with differnt size of amplicon.
>h18S_211_f TTGCTGCAGTTAAAAAGCTC >h18S_211_r CATTATTCCTAGCTGCGGTA
OLIGO start len tm gc% any 3' seq LEFT PRIMER 758 20 57.86 40.00 6.00 2.00 TTGCTGCAGTTAAAAAGCTC RIGHT PRIMER 968 20 57.56 45.00 4.00 2.00 CATTATTCCTAGCTGCGGTA SEQUENCE SIZE: 1969 INCLUDED REGION SIZE: 1969 PRODUCT SIZE: 211, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 1.00