A Simple Solution for Oligonucleotide Design

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Oligo Sequence:

Tm:
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Oligo length:
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Common Data ID:

Taxonomy ID:

GI Number:

CommonData ID: MP0314Publication date: 12/99
PMID: 10598089GI: 6572136 Taxonomy ID: 12122
Virus Name: Foot-and-mouth disease virus SAT 1; Foot-and-mouth disease virus SAT 2; Foot-and-mouth disease virus SAT 3Product size (PCR):
bp
MgCl2: 1.5 mMdNTPs: mMType: RT-PCR
Temp (PCR cycle):95C 5min>(95C 15sec>60C 60sec)*25>60C 6min
Buffer: 20mM Tris-HCl (pH 8.4), 50mM KCl
Polymerase: 0.1U/microL Taq DNA poly (Gibco Life Technologies)Cycler: Touchdown Thermocycler (Hybaid, UK)
Note: Mulitplex PCR.
Primer set P1/P126/P151/P152/P153 amplifies SAT1 [Taxonomy:12122].
Primer set P1/P168/P169/P170 amplifies SAT2 [Taxonomy:35292].
Primer set P1/P130/P158/P159/P160/P161 amplifies SAT3 [Taxonomy:12123].

Total RT volume is 10microL containing 0.5microL RNA, 1microM random hexanuclotide mix (Promega), 50mM Tris-HCl (pH 8.3), 75mM KCl, 3mM MgCl2, 0.125mM each dNTP, 10mM dithiothreitol, and 10U/microL MMLV RTase (Gibco Life Technologies).
RT temperature: 37C 15min

Total PCR volume is 50microL containing 5microL cDNA and 0.2microM each primers P1, P126, P151, P152, P153, P168, P169, P170, P130, P158, P159, P160, and P161 in a multiplex PCR format.
For continued list of primers, [see MP0315].

For other PCRs in this article, [see MP0307], [see MP0308], [see MP0310], and [see MP0312].
Reverse(P1) primer
Oligo type: Degeneracy: 1
Target: 3551-3531Tm: 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.
Universal primer specific to [GI:6572136].
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].
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(P168) primer
Oligo type: Degeneracy: 2
Target: 3477-3496Tm: 73.6 C at salt 1000.0mMLength:
Sequence: GGCGTTGAAAAACAACT(G/C)TG
(4 other experimental conditions)
Note: Specific to [GI:6572136].
Forward(P169) primer
Oligo type: Degeneracy: 1
Target: 3477-3496Tm: 74.1 C at salt 1000.0mMLength:
Sequence: GGCGTCGCGAAACAGCTTTT
(7 other experimental conditions)
Note: Specific to [GI:6572136].
Forward(P169) primer
Oligo type: Degeneracy: 1
Target: 3477-3496Tm: 74.1 C at salt 1000.0mMLength:
Sequence: GGCGTCGCGAAACAGCTTTT
(7 other experimental conditions)
Note: Specific to [GI:6572136].
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