CODEHOP PCR and CODEHOP PCR Primer Design

Methods in Molecular Biology

Volumn 687, Issue , 2011, Pages 57-73

  Staheli, Jeannette P ^a   Boyce, Richard ^c   Kovarik, Dina ^d   Rose, Timothy M ^a,b  

^a Seattle Children's Research Institute   (United States)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^d Northwest Association for Biomedical Research   (United States)

Author keywords

Acyl coA binding protein; CODEHOP; Consensus; Degenerate; PCR

Indexed keywords

PRIMER DNA;

AMINO ACID SEQUENCE; ARTICLE; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; BASE SEQUENCE; DNA PRIMERS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 79952279466     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-60761-944-4_5     Document Type: Chapter

References (19)

1. Rose, T.M., Schultz, E.R., Henikoff, J.G., Pietrokovski, S., McCallum, C.M., and Henikoff, S. (1998) Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences. Nucleic Acids Res 26, 1628–35.
2. Rose, T.M., Henikoff, J.G., and Henikoff, S. (2003) CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design. Nucleic Acids Res 31, 3763–6.
3. Boyce, R., Chilana, P., and Rose, T.M. (2009) iCODEHOP: a new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide primers from multiply aligned protein sequences. Nucleic Acids Res 37, W222–8.
4. Rose, T.M., Schultz, E.R., and Todaro, G.J. (1992) Molecular cloning of the gene for the yeast homolog (ACB) of diazepam binding inhibitor/endozepine/acyl-CoA-binding protein. Proc Natl Acad Sci U S A 89, 11287–91.
5. Gersuk, V.H., Rose, T.M., and Todaro, G.J. (1995) Molecular cloning and chromosomal localization of a pseudogene related to the human acyl-CoA binding protein/diazepam binding inhibitor. Genomics 25, 469–76.
6. VanDevanter, D.R., Warrener, P., Bennett, L., Schultz, E.R., Coulter, S., Garber, R.L., and Rose, T.M. (1996) Detection and analysis of diverse herpes viral species by consensus primer PCR. J Clin Microbiol 34, 1666–71.
7. Rose, T.M., Strand, K.B., Schultz, E.R., Schaefer, G., Rankin, G.W., Jr., Thailess, M.E., Tsai, C.C., and Bosch, M.L. (1997) Identification of two homologs of the Kaposi’s sarcoma-associated herpesvirus (human herpesvirus 8) in retroperitoneal fibromatosis of different macaque species. J Virol 71, 4138–44.
8. CODEHOP: consensus-degenerate hybrid oligonucleotide primers. (1998) (Accessed at http://blocks.fhcrc.org/blocks/codehop. html).
9. Wilson, C.A., Wong, S., Muller, J., Davidson, C.E., Rose, T.M., and Burd, P. (1998) Type C retrovirus released from porcine primary peripheral blood mononuclear cells infects human cells. J Virol 72, 3082–7.
10. Osterhaus, A.D., Pedersen, N., van Amerongen, G., Frankenhuis, M.T., Marthas, M., Reay, E., Rose, T.M., Pamungkas, J., and Bosch, M.L. (1999) Isolation and partial characterization of a lentivirus from talapoin monkeys (Myopithecus talapoin). Virology 260, 116–24.
11. Schultz, E.R., Rankin, G.W., Jr., Blanc, M.P., Raden, B.W., Tsai, C.C., and Rose, T.M. (2000) Characterization of two divergent lineages of macaque rhadinoviruses related to Kaposi’s sarcoma-associated herpesvirus. J Virol 74, 4919–28.
12. Rose, T.M., Ryan, J.T., Schultz, E.R., Raden, B.W., and Tsai, C.C. (2003) Analysis of 4.3 kilobases of divergent locus B of macaque retroperitoneal fibromatosis-associated herpesvirus reveals a close similarity in gene sequence and genome organization to Kaposi’s sarcoma-associated herpesvirus. J Virol 77, 5084–97.
13. Rose, T.M. (2005) CODEHOP-mediated PCR – a powerful technique for the identification and characterization of viral genomes. Virol J 2, 20.
14. Staheli, J.P., Ryan, J.T., Bruce, A.G., Boyce, R., and Rose, T.M. (2009) Consensus-degenerate hybrid oligonucleotide primers (CODEHOPs) for the detection of novel viruses in non-human primates. Methods 49, 32–41.
15. Bruce, A.G., Bakke, A.M., Gravett, C.A., DeMaster, L.K., Bielefeldt-Ohmann, H., Burnside, K.L., and Rose, T.M. (2009) The ORF59 DNA polymerase processivity factor homologs of Old World primate RV2 rhadinoviruses are highly conserved nuclear antigens expressed in differentiated epithelium in infected macaques. Virol J 6, 205.
16. Burton, M., Rose, T.M., Faergeman, N.J., and Knudsen, J. (2005) Evolution of the acyl-CoA binding protein (ACBP). Biochem J 392, 299–307.
17. Bio-itest. Northwest Association for Biomedical Research. (Accessed at http://www.nwabr.org/education/itest.html).
18. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J., and Higgins, D.G. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–8.
19. iCODEHOP: Interactive Program for Creating Consensus-Degenerate Hybrid Oligonucleotide Primers. (2008) (Accessed at https://i codehop. cphi. washi ngton. edu/i-codehop-context/Welcome).