A Simple Solution for Oligonucleotide Design

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2. Search by PMID, VirOligoID, or taxonomy ID;

Virus name:

Oligo Sequence:

Tm:
°C± °C
Oligo length:
bp± bp



PMID:

Common Data ID:

Taxonomy ID:

GI Number:

CommonData ID: MP0392Publication date: 08/97
PMID: 9274816GI: 3367676 Taxonomy ID: 12122
Virus Name: Foot-and-mouth disease virus SAT 1Product size (PCR): 246 bp
MgCl2: 1.5 mMdNTPs: mMType: RT-Multiplex PCR
Temp (PCR cycle):95C 1min>(95C 15sec>60C 60sec)*35>60C 6min
Buffer: 10mM Tris-HCl (pH 8.8), 50mM KCl, 0.1% Triton X-100
Polymerase: 0.025U/microL Golstar DNA poly (Eurogentec)Cycler: Gene Amp PCR System 9600 (Perkin-Elmer)
Note: Primer P1, [GI:61076], is used with following primers in a multiplex PCR format:
P153/P126/P151/P152 all derived from [GI:3367676].
For more primers used in this PCR, [see MP0393] and [see MP0394].

Total RT volume is 10microL containing 6microL RNA, 0.6U/microL RNase inhibitor (TakaRa biochemicals), 50mM Tris-HCl (pH 8.3), 75mM KCl, 3mM MgCl2, 10mM dithiothreitol, 0.125mM each dNTP, 5microM primer P33 (described by Vangrysperre et al, (1996) [PMID:8634024]), and 10U/microL MMLV RTase (Life Technologies).
RT temperature: 42C 5min.

Total PCR volume is 10microL containing 0.2% cDNA, 0.6microM P1, 0.6microM P153, 0.3microM P126, 1.8microM P151, and 0.6microM P152.
Reverse(P33) primer
Oligo type: PCRDegeneracy: 1
Target: 3760-3741Tm: 74.1 C at salt 1000.0mMLength:
Sequence: AGCTTGTACCAGGGTTTGGC
(11 other experimental conditions)
Note:
Reverse(P1) primer
Oligo type: Degeneracy: 1
Target: 3578-3558Tm: 80.3 C at salt 1000.0mMLength:
Sequence: GAAGGGCCCAGGGTTGGACTC
(16 other experimental conditions)
Note: Target found in article (3649-3670) is different from target found in BLAST
Forward(P153) primer
Oligo type: Degeneracy: 1
Target: 2047-2069Tm: 76.8 C at salt 1000.0mMLength:
Sequence: AGGATTGCAAGCGAGACCCACAT
(4 other experimental conditions)
Note: Mismatch at position 2047.
Specific to [GI:3367676].
Forward(P126) primer
Oligo type: Degeneracy: 1
Target: 2047-2069Tm: 76.8 C at salt 1000.0mMLength:
Sequence: AGGATTGCCAGTGAGACCCACAT
(4 other experimental conditions)
Note: Mismatches at positions 2047 and 2055.
Target found in article (3424-3446) is different from target found in BLAST.
Specific to [GI:3367676].
Forward(P151) primer
Oligo type: Degeneracy: 16
Target: 2047-2069Tm: Max Tm 80.4 C Min Tm 73.2 C at salt 1000.0mMLength:
Sequence: AGGAT(T/C)GC(A/C)AG(T/C)GAGAC(A/G)CACAT
(4 other experimental conditions)
Note: Mismatch at position 2047.
Specific to [GI:3367676].
Forward(P152) primer
Oligo type: Degeneracy: 2
Target: 2047-2069Tm: Max Tm 75 C Min Tm 73.2 C at salt 1000.0mMLength:
Sequence: AGGATTGCTAGTGAGAC(A/C)CACAT
(4 other experimental conditions)
Note: Mismatch at position 2047.
Specific to [GI:3367676].
Reverse(P33) primer
Oligo type: Degeneracy: 1
Target: 3851-3832Tm: 74.1 C at salt 1000.0mMLength:
Sequence: AGCTTGTACCAGGGTTTGGC
(11 other experimental conditions)
Note:
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