A Simple Solution for Oligonucleotide Design

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Virus name:

Oligo Sequence:

Tm:
°C± °C
Oligo length:
bp± bp



PMID:

Common Data ID:

Taxonomy ID:

GI Number:

CommonData ID: SK0060Publication date: 10/00
PMID: 11131328GI: 9626649 Taxonomy ID: 144353
Virus Name: Bovine viral diarrhea virus, BVDVProduct size (PCR):
bp
MgCl2: 4.0 mMdNTPs: mMType: RT-Nested PCR
Temp (PCR cycle):(94C 60sec>55C 60sec>72C 45sec)*30>72C 10min
Buffer: 1x Buffer (Promega)
Polymerase: 0.075U/microL Taq poly (Promega)Cycler:
Note: RT and primary PCR are performed in a single step with a final volume of 50microL containing 1x buffer (Promega), 4mM MgCl2, 0.4mM dNTPs, 0.1microM each primers BVD100 and HCV368, 0.2% Triton X-100, 0.5mM dithiothreitol, 0.05U/microL RNAsin, 0.025U/microL Taq polymerase, and 1U/microL MMLV RTase.
RT and primary PCR cycle: 37C 45min>95C 5min>(94C 1min>55C 1min>72C 1min)*20>72C 10min.

0.4microM each primers BVD180 and HCV368, 0.2mM dNTPs and 0.00625U/microL Taq polymerase (dried in 5microL of 22% Trehalose on the lid) is added to the initial PCR mixture for performing nested PCR.

The primer set BVD100/HCV368 amplifies a 290bp product.
Primer set BVD180/HCV368 amplifies a 213bp product of size 213bp.
Forward(BVD100) primer
Oligo type: Degeneracy: 1
Target: 100-117Tm: 58 CLength:
Sequence: GGCTAGCCATGCCCTTAG
(4 other experimental conditions)
Note:
Reverse(HCV368) primer
Oligo type: Degeneracy: 1
Target: 389-373Tm: 52 CLength:
Sequence: CCATGTGCCATGTACAG
(4 other experimental conditions)
Note:
Forward(BVD180) primer
Oligo type: Degeneracy: 3
Target: 176-197Tm: Max Tm 78.5 C Min Tm 76.6 C at salt 1000.0mMLength:
Sequence: CCTGAGTACAGGG(G/A/T)AGTCGTCA
(0 other experimental conditions)
Note:
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