A Simple Solution for Oligonucleotide Design


Click here for a list of viruses in the database


Two search options:
1. Search by virus name and/or primer data
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:



Oligonucleotide information
Forward(UTR1) primer
Oligo ID:MP00440
Oligo type: PCR Denegeracy: 1
Target: 51-68 Tm: 58 CLength: 18
Sequence: GGCTAGCCATGCCCTTAG
(4 other experimental conditions)
Note: Used with 326, most effective at detecting virus

Experimental condition used for the oligonucleotide

Common Data ID: MP0044 Publication date: 03/00
PMID: 10730955 GI: 14113964 Taxonomy ID:144353
Virus Name: bovine viral diarrhea virus, BVDV Product size (PCR):
bp
MgCl2: 1.5 mM dNTPs: 0.23 mM Type: RT-PCR
Temp (PCR cycle):95C 4min>(95C 1min>56C 1.5min>74C 1min)*40
Buffer: 1x PCR buffer (Promega), 0.03U/microL Taq Extender (Stratagene)
Polymerase: 0.03U/microL Taq poly (Promega)Cycler: N/A
Note: Used with 326, most effective at detecting virus



Oligonucleotide information
Forward(5'UTR 1) primer
Oligo ID:PN00035
Oligo type: Denegeracy: 1
Target: 100-117 Tm: 58 CLength: 18
Sequence: GGCTAGCCATGCCCTTAG
(4 other experimental conditions)
Note: Used with 5'UTR 2.

Experimental condition used for the oligonucleotide

Common Data ID: SK0002 Publication date: 04/95
PMID: 7667908 GI: 9626649 Taxonomy ID:31656
Virus Name: Bovine viral diarrhea virus (strain SD-1), BVDV strain SD-1 Product size (PCR):
bp
MgCl2: 2.2 mM dNTPs: 0.2 mM Type: RT-PCR
Temp (PCR cycle):94C 4min>(94C 1min>55C 1.5min>72C 3min)*30>72C 7min
Buffer: 18mM Tris-HCl (pH 8.3), 55mM KCl, 2mM dithiothreitol
Polymerase: 0.025U/microL AmpliTaq poly (Perkin-Elmer Cetus Corp.)Cycler: DNA thermal cycler (Coy Laboratory Products Inc.; Ann Arbor, MI)
Note: Used with 5'UTR 2.



Oligonucleotide information
Forward(BVD100) primer
Oligo ID:PN00274
Oligo type: Denegeracy: 1
Target: 100-117 Tm: 58 CLength: 18
Sequence: GGCTAGCCATGCCCTTAG
(4 other experimental conditions)
Note:

Experimental condition used for the oligonucleotide

Common Data ID: SK0060 Publication date: 10/00
PMID: 11131328 GI: 9626649 Taxonomy ID:144353
Virus Name: Bovine viral diarrhea virus, BVDV Product size (PCR):
bp
MgCl2: 4.0 mM dNTPs: 0.6 mM Type: 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:



Oligonucleotide information
Forward(BVD 100) primer
Oligo ID:PB00489
Oligo type: Denegeracy: 1
Target: 100-117 Tm: 58 CLength: 18
Sequence: GGCTAGCCATGCCCTTAG
(4 other experimental conditions)
Note: Used with HCV 368 to amplify a 290bp product.

Experimental condition used for the oligonucleotide

Common Data ID: MP0257 Publication date: 10/00
PMID: 11131328 GI: 9629506 Taxonomy ID:31656
Virus Name: bovine viral diarrhea virus (strain SD-1), BVDV Product size (PCR): 290 bp
MgCl2: 4 mM dNTPs: 0.4 mM Type: RT-Nested PCR 1
Temp (PCR cycle):37C 45min>95C 5min>(94C 1min>55C 1min>72C 1min)*20>72C 10min
Buffer: 1x PCR buffer, 0.2% stock Triton X-100, 0.5mM dithiothreitol
Polymerase: 0.05 U/microL Taq poly (Promega, Madison, WI)Cycler: N/A
Note: Used with HCV 368 to amplify a 290bp product.



Oligonucleotide information
Forward(BVD 100) primer
Oligo ID:pc00105
Oligo type: Denegeracy: 1
Target: 100-117 Tm: 58 CLength: 18
Sequence: GGCTAGCCATGCCCTTAG
(4 other experimental conditions)
Note: Used with HCV 368 in RT and primary PCR.

Experimental condition used for the oligonucleotide

Common Data ID: BM0898 Publication date: 09/01
PMID: 11665882 GI: 323205 Taxonomy ID:31656
Virus Name: bovine viral diarrhea virus (strain SD-1) Product size (PCR):
bp
MgCl2: 4.0 mM dNTPs: 0.4 mM Type: RT-Nested PCR
Temp (PCR cycle):37C 45min>35C 5min>(94C 1min>55C 1min>72C 1min)*20>72C 10min
Buffer: 1x buffer, 0.2% Triton X-100, 0.5mM DTT, 0.2U/microL RNAsin, 2U/microL MMLV RTase (all Promega)
Polymerase: 0.05U/microL Taq poly (Promega)Cycler:
Note: Used with HCV 368 in RT and primary PCR.



Oligonucleotide information
Forward(BVD100) primer
Oligo ID:PN00274
Oligo type: Denegeracy: 1
Target: 100-117 Tm: 58 CLength: 18
Sequence: GGCTAGCCATGCCCTTAG
(4 other experimental conditions)
Note:

Experimental condition used for the oligonucleotide

Common Data ID: SK0060 Publication date: 10/00
PMID: 11131328 GI: 9626649 Taxonomy ID:144353
Virus Name: Bovine viral diarrhea virus, BVDV Product size (PCR):
bp
MgCl2: 4.0 mM dNTPs: 0.6 mM Type: 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:

Total 6 Oligos
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