Detailed Information on Publication Record
2007
Experimental design in intraspecific organelle DNA sequence studies II: Haplotype detection by Chemical Cleavage of Mismatch (CCM) using SYBR Green II staining
STONEBERG HOLT, Sierra Dawn, Lucie HOROVÁ and Petr BUREŠBasic information
Original name
Experimental design in intraspecific organelle DNA sequence studies II: Haplotype detection by Chemical Cleavage of Mismatch (CCM) using SYBR Green II staining
Name in Czech
Experimental design in intraspecific organelle DNA sequence studies II: Haplotype detection by Chemical Cleavage of Mismatch (CCM) using SYBR Green II staining
Authors
STONEBERG HOLT, Sierra Dawn (840 United States of America), Lucie HOROVÁ (203 Czech Republic) and Petr BUREŠ (203 Czech Republic, guarantor)
Edition
Taxon, Vienna, International Assoc. for Plant Taxonomy, 2007, 0040-0262
Other information
Language
English
Type of outcome
Článek v odborném periodiku
Field of Study
10600 1.6 Biological sciences
Country of publisher
Austria
Confidentiality degree
není předmětem státního či obchodního tajemství
Impact factor
Impact factor: 2.524
RIV identification code
RIV/00216224:14310/07:00022322
Organization unit
Faculty of Science
UT WoS
000244825300015
Keywords in English
chemical cleavage of mismatch (CCM); cpDNA; heteroduplex analysis (HA); intraspecific sequence studies; phylogeography; SYBR Green II staining
Tags
Tags
International impact, Reviewed
Změněno: 25/6/2009 11:09, prof. RNDr. Petr Bureš, Ph.D.
V originále
Studies of organelle DNA sequence at low taxonomic levels present a researcher with specific experimental design challenges. Such studies require sampling numerous individuals, many of which share identical haplotypes. The process is often limited by the time and money required for DNA sequencing. A number of screening techniques have been devised to combat this limitation, but many have not found wide-spread use in botany. An ideal screening technique would be fast, easy, safe, inexpensive, detect 100% of mutations, be suitable for DNA fragments of about 1 kb, and not require complex equipment. This paper compares the heteroduplex analysis (HA) and chemical cleavage of mismatch (CCM) methods for detecting known point mutations and a deletion in a 1 kb region of non-coding cpDNA from the Poa pratensis agg. A new CCM visualization method, staining with SYBR Green II, was tested. CCM is a powerful tool for discovering different haplotypes in DNA sequence studies at low taxonomic levels. It is quicker and less expensive than sequencing each sample. Compared to HA, CCM is much more sensitive and delivers results in a shorter time, although it is more expensive and considerably more labor intensive. Staining with SYBR Green II allows CCM to be effectively implemented in laboratories with limited access to automated sequencing equipment.
In Czech
Studies of organelle DNA sequence at low taxonomic levels present a researcher with specific experimental design challenges. Such studies require sampling numerous individuals, many of which share identical haplotypes. The process is often limited by the time and money required for DNA sequencing. A number of screening techniques have been devised to combat this limitation, but many have not found wide-spread use in botany. An ideal screening technique would be fast, easy, safe, inexpensive, detect 100% of mutations, be suitable for DNA fragments of about 1 kb, and not require complex equipment. This paper compares the heteroduplex analysis (HA) and chemical cleavage of mismatch (CCM) methods for detecting known point mutations and a deletion in a 1 kb region of non-coding cpDNA from the Poa pratensis agg. A new CCM visualization method, staining with SYBR Green II, was tested. CCM is a powerful tool for discovering different haplotypes in DNA sequence studies at low taxonomic levels. It is quicker and less expensive than sequencing each sample. Compared to HA, CCM is much more sensitive and delivers results in a shorter time, although it is more expensive and considerably more labor intensive. Staining with SYBR Green II allows CCM to be effectively implemented in laboratories with limited access to automated sequencing equipment.
Links
| LC06073, research and development project |
| ||
| MSM0021622416, plan (intention) |
|