Improving the sensitivity of single-strand conformation polymorphism (SSCP) to study the variability of PLMVd.
Single-strand conformation polymorphism (SSCP) was used to characterize viroids. Eight cDNA clones, which showed identical profiles in preliminary existing SSCP analysis but had different sequences, were chosen to develop a sensitive SSCP technique for identifying the variability of Peach latent mosaic viroid (PLMVd). Polyacrylamide Gel Electrophoresis (PAGE) conditions were optimized to improve the sensitivity of the existing SSCP, and a modified SSCP protocol was developed. The results indicated that the modified SSCP protocol provided an overall sensitivity in identifying the variability of these clones, and showed higher resolution than the existing one and its improved versions. As shown by sequence analyses of cDNA clones of PLMVd and the modified SSCP profiles, there is no close correlation between the number of base changes and variation of the modified SSCP band patterns. The potential use of the modified SSCP analysis is discussed as a tool for viroids characterization.
Xu
Wen Xing
WX
College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
Hong
Ni
N
Zhang
Jian Kun
JK
Wang
Guo Ping
GP
D001483:Base Sequence; D008969:Molecular Sequence Data; D009029:Mosaic Viruses / Q000235:genetics*; D018807:Polymorphism, Single-Stranded Conformational; D027861:Prunus / Q000821:virology*; D012680:Sensitivity and Specificity; D014772:Viroids / Q000235:genetics*