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: SW0085Publication date: 11/00
PMID: 11044116GI: 450251 Taxonomy ID: 11246
Virus Name: Bovine respiratory syncytial virus, BRSVProduct size (PCR):
bp
MgCl2: 1.0 mMdNTPs: mMType: RT-Nested PCR 1
Temp (PCR cycle):94C 12min>(94C 60sec>58C 60sec>72C 90sec)*35>72C 10min
Buffer: 10mM Tris-HCl (pH 8.3), 50mM KCl
Polymerase: 0.025U/microL AmpliTaq Gold poly (Perkin-Elmer)Cycler: GeneAmp PCR system 480 (Perkin-Elmer)
Note: Each primer set is used in a separate PCR:
N2.1/N2/2 [GI:450251]
F2.1/F2.2 [GI:3451385]

10microL containing RNA and 0.2microM primer N2.1 or F2.1 are incubated 68C 10min>58C 10min and then chilled on ice.
Total RT volume is 25microL containing 400M each dNTP, 1.6U/microL RNasin (Promega), 8.0mM DTT (Gibco BRL), 4microL SuperScript TM II buffer (Gibco BRL), and 8.0U/microL SuperScript TM II (Gibco BRL).
RT temperature: 42C 50min>70C 15min.
Article cites 10mmol dNTPs being used in 25microL.

Total PCR volume is 100microL containing 10microL diluted cDNA (1:10) and 0.5microM each primer in a set.
Article cites 200mM each dNTP being used in PCR.

For secondary PCRs, [see SW0086] and [see SW0087].
For other PCRs in this article, [see SW0088] and [see SW0089].
Forward(N2.1) primer
Oligo type: PCRDegeneracy: 1
Target: 1-19Tm: 71.5 C at salt 1000.0mMLength:
Sequence: ATGGCTCTCAGCAAGGTCA
(1 other experimental conditions)
Note: RT and PCR. Specific to N gene [GI:450251].
Reverse(N2.2) primer
Oligo type: PCRDegeneracy: 1
Target: 1034-1013Tm: 72.9 C at salt 1000.0mMLength:
Sequence: TCTTGGTTTCTTGGTGTACCTC
(1 other experimental conditions)
Note: Specific to N gene [GI:450251].
Forward(F2.1) primer
Oligo type: PCRDegeneracy: 1
Target: 136-157Tm: 71 C at salt 1000.0mMLength:
Sequence: AGTGCATTAAGAACTGGATGGT
(0 other experimental conditions)
Note: Used for RT and PCR. Specific to gene F, [GI:3451385].
Reverse(F2.2) primer
Oligo type: PCRDegeneracy: 1
Target: 1470-1450Tm: 70.5 C at salt 1000.0mMLength:
Sequence: TGCATCAAACTCATCAGAAGG
(0 other experimental conditions)
Note: Specific to gene F [GI:3451385].
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