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
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=Human S18 primer=
==Human S18 primer==
#Collect the human S18 cDNA sequence
#Collect the human S18 cDNA sequence
#Mask the inconsistat nucleotide
#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,

  1. Design 18S primers for positive control / validation purpose of a successful MDA reaction using human genome template.
  2. Design 16S primers for positive control / validation purpose of a successful MDA reaction using bacteria genome template.
  3. These primers could also be used to detect the contamination of exogenus gDNA.


Human S18 primer

  1. Collect the human S18 cDNA sequence
  2. Clean the sequcne and mask the inconsistat nucleotide
  3. Paste the sequence on KZ's Primer3 calculatorlink title
  4. Criteria:
    Primer size: Min: 18bp, opt:20 bp, Max: 22bp
    Product size: ~200 bp; ~300 bp
    Annealing Temp: Min:57, Opt:58, Max:59
  1. 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