Tags

Type your tag names separated by a space and hit enter

Differentiation of bacterial strains by thermal gradient gel electrophoresis using non-GC-clamped PCR primers for the 16S-23S rDNA intergenic spacer region.
FEMS Microbiol Lett. 2005 Feb 01; 243(1):235-42.FM

Abstract

The method for DNA fingerprinting of the 16S-23S rDNA intergenic spacer region was modified to increase resolution of bacterial strains by thermal gradient gel electrophoresis (TGGE) analysis. By utilizing the high melting temperature region of the tRNA gene located in the middle of the 16S-23S rDNA intergenic spacer region as an internal clamp for TGGE, multiple melting domain problems were solved. PCR primers lacking a stretch of GC-rich sequences (GC-clamp) amplified the intergenic spacer region more efficiently than GC-clamped primers. Therefore, PCR artifacts were avoided by using low, 17-cycle, PCR. The method was successfully applied to diverse bacterial species for strain differentiation by TGGE without requiring a special PCR primer set.

Authors+Show Affiliations

Department of Biology, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA 02125, USA. michie.yasuda@umb.eduNo affiliation info available

Pub Type(s)

Evaluation Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

15668024

Citation

Yasuda, Michie, and Michael Peter Shiaris. "Differentiation of Bacterial Strains By Thermal Gradient Gel Electrophoresis Using non-GC-clamped PCR Primers for the 16S-23S rDNA Intergenic Spacer Region." FEMS Microbiology Letters, vol. 243, no. 1, 2005, pp. 235-42.
Yasuda M, Shiaris MP. Differentiation of bacterial strains by thermal gradient gel electrophoresis using non-GC-clamped PCR primers for the 16S-23S rDNA intergenic spacer region. FEMS Microbiol Lett. 2005;243(1):235-42.
Yasuda, M., & Shiaris, M. P. (2005). Differentiation of bacterial strains by thermal gradient gel electrophoresis using non-GC-clamped PCR primers for the 16S-23S rDNA intergenic spacer region. FEMS Microbiology Letters, 243(1), 235-42.
Yasuda M, Shiaris MP. Differentiation of Bacterial Strains By Thermal Gradient Gel Electrophoresis Using non-GC-clamped PCR Primers for the 16S-23S rDNA Intergenic Spacer Region. FEMS Microbiol Lett. 2005 Feb 1;243(1):235-42. PubMed PMID: 15668024.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Differentiation of bacterial strains by thermal gradient gel electrophoresis using non-GC-clamped PCR primers for the 16S-23S rDNA intergenic spacer region. AU - Yasuda,Michie, AU - Shiaris,Michael Peter, PY - 2004/08/11/received PY - 2004/12/06/revised PY - 2004/12/09/accepted PY - 2005/1/26/pubmed PY - 2005/5/10/medline PY - 2005/1/26/entrez SP - 235 EP - 42 JF - FEMS microbiology letters JO - FEMS Microbiol Lett VL - 243 IS - 1 N2 - The method for DNA fingerprinting of the 16S-23S rDNA intergenic spacer region was modified to increase resolution of bacterial strains by thermal gradient gel electrophoresis (TGGE) analysis. By utilizing the high melting temperature region of the tRNA gene located in the middle of the 16S-23S rDNA intergenic spacer region as an internal clamp for TGGE, multiple melting domain problems were solved. PCR primers lacking a stretch of GC-rich sequences (GC-clamp) amplified the intergenic spacer region more efficiently than GC-clamped primers. Therefore, PCR artifacts were avoided by using low, 17-cycle, PCR. The method was successfully applied to diverse bacterial species for strain differentiation by TGGE without requiring a special PCR primer set. SN - 0378-1097 UR - https://www.unboundmedicine.com/medline/citation/15668024/Differentiation_of_bacterial_strains_by_thermal_gradient_gel_electrophoresis_using_non_GC_clamped_PCR_primers_for_the_16S_23S_rDNA_intergenic_spacer_region_ L2 - https://academic.oup.com/femsle/article-lookup/doi/10.1016/j.femsle.2004.12.011 DB - PRIME DP - Unbound Medicine ER -