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Direct Sequencing with Highly Degenerate and lnosine-Containing Primers

  • Zhiyuan Shen
  • Jingmei Liu
  • Robert L. Wells
  • Mortimer M. Elkind
Part of the Methods in Molecular Biology™ book series (MIMB, volume 65)

Abstract

Among the many techniques of cloning new genes, one approach involves degenerate primers (1, 2, 3, 4, 5, 6, 7). The approach usually requires three steps:
  1. 1.

    Using degenerate primers to amplify part of the gene of interest by PCR: The degenerate primers’ sequences may be designed from known protein sequences or conserved regions of a gene family (e.g., 2,4). Because deoxyinosine can base pair with all of the four deoxyribonucleotides it has been substituted for specific nucleic acids in degenerate primers to reduce the number of different primer sequences that would otherwise be needed in the reaction (2,7,8).

     
  2. 2.

    A determination of which amplified PCR product(s) is from the gene of interest: If the target gene and the primers are only partially homologous, a moderate annealing stringency in the PCR reaction is usually necessary to obtain amplitication. Moderate stringency may result in multiple PCR products. Although from the size of the PCR products it may be possible to predict which is from the gene of interest, sequencing analysis of the PCR products may be required.

     
  3. 3.

    The screening of a cDNA library using the correct PCR product as a probe and cloning the gene of interest.

     

Keywords

Degenerate Primer Prime Extension Primer Annealing Temperature Specific Nucleic Acid Specific Base Sequence 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

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Copyright information

© Human Press Inc., Totowa, NJ 1996

Authors and Affiliations

  • Zhiyuan Shen
    • 1
  • Jingmei Liu
    • 1
  • Robert L. Wells
    • 2
  • Mortimer M. Elkind
    • 2
  1. 1.Life Sciences DivisionLos Alamos National LaboratoryLos Alamos
  2. 2.Department of Radiological Health SciencesColorado State UniversityFort Collins

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