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Related Experiment Videos

Single-strand conformation polymorphism (SSCP) analysis as a tool for viroid characterisation.

A Palacio1, N Duran-Vila

  • 1Departamento de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain.

Journal of Virological Methods
|February 24, 1999
PubMed
Summary

Single-strand conformation polymorphism (SSCP) analysis effectively characterizes viroid variants by detecting sequence differences in citrus exocortis viroid (CEVd). This method aids in screening viroid populations before sequencing.

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Area of Science:

  • Molecular Biology
  • Plant Pathology
  • Virology

Background:

  • Viroid characterization is crucial for understanding plant diseases.
  • Citrus exocortis viroid (CEVd) is a significant plant pathogen.
  • Accurate methods for identifying viroid variants are needed.

Purpose of the Study:

  • To evaluate the potential of single-strand conformation polymorphism (SSCP) analysis for routine viroid characterization.
  • To assess SSCP's ability to detect sequence variations in CEVd.

Main Methods:

  • Electrophoresis of 311 cloned full-length CEVd DNA inserts using non-denaturing 14% polyacrylamide gels.
  • Analysis of cDNA and hDNA strands to identify migration shifts.
  • Sequence analysis to confirm the relationship between SSCP profiles and nucleotide variations.

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  • SSCP analysis of partial viroid DNA to map affected regions.

    • Main Results:

    • Seven distinct groups of CEVd variants were identified using SSCP under a single set of electrophoresis conditions.
    • SSCP detected variations ranging from one to six nucleotide changes.
    • Adjusting gel dimensions improved resolution, revealing additional single nucleotide variations.
    • Sequence analysis confirmed that SSCP profiles accurately reflected nucleotide sequence differences.

    Conclusions:

    • SSCP analysis is a viable tool for characterizing viroid populations.
    • The method can identify and differentiate viroid variants efficiently.
    • SSCP can serve as a preliminary screening tool for viroid populations before sequencing, saving time and resources.