Use of DNA toolbox for the characterization of mutation scanning methods. II: Evaluation of single-strand conformation polymorphism analysis

W Edward Jr. Highsmith, Arun J. Nataraj, Qian Jin, Jacquelyn M. O'Connor, Sohbi H. El-Nabi, Noriko Kusukawa, Mark M. Garner

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

Single-strand conformation polymorphism (SSCP) is one of the most commonly used methods for searching for unknown base changes (mutations). In order to characterize systematically the effects of important physical parameters on the sensitivity and specificity of SSCP, we used the DNA toolbox constructed as described in the companion paper [2]. Using this set of DNA molecules as polymerase chain reaction (PCR) templates, amplicons of various lengths with the same base, mutated to all other bases, were generated. The behavior of these constructs in manual and automated SSCP was analyzed as a function of the size, overall base content of the fragment, nature and location of the base change, and the temperature and pH of electrophoresis. Our results demonstrate that all of these variables interact to determine the rate of detection of single-base changes, with the GC content being the predominant determinant of detection sensitivity.

Original languageEnglish (US)
Pages (from-to)1195-1203
Number of pages9
JournalElectrophoresis
Volume20
Issue number6
DOIs
StatePublished - 1999
Externally publishedYes

Fingerprint

Polymorphism
Conformations
Scanning
Mutation
DNA
Base Composition
Electrophoresis
Polymerase chain reaction
Sensitivity and Specificity
Polymerase Chain Reaction
Temperature
Molecules

Keywords

  • Mutation scanning
  • Single-strand conformation polymorphism

ASJC Scopus subject areas

  • Clinical Biochemistry

Cite this

Use of DNA toolbox for the characterization of mutation scanning methods. II : Evaluation of single-strand conformation polymorphism analysis. / Highsmith, W Edward Jr.; Nataraj, Arun J.; Jin, Qian; O'Connor, Jacquelyn M.; El-Nabi, Sohbi H.; Kusukawa, Noriko; Garner, Mark M.

In: Electrophoresis, Vol. 20, No. 6, 1999, p. 1195-1203.

Research output: Contribution to journalArticle

Highsmith, W Edward Jr. ; Nataraj, Arun J. ; Jin, Qian ; O'Connor, Jacquelyn M. ; El-Nabi, Sohbi H. ; Kusukawa, Noriko ; Garner, Mark M. / Use of DNA toolbox for the characterization of mutation scanning methods. II : Evaluation of single-strand conformation polymorphism analysis. In: Electrophoresis. 1999 ; Vol. 20, No. 6. pp. 1195-1203.
@article{ae15b5ee80bf400a85dd9cc7c6e31ace,
title = "Use of DNA toolbox for the characterization of mutation scanning methods. II: Evaluation of single-strand conformation polymorphism analysis",
abstract = "Single-strand conformation polymorphism (SSCP) is one of the most commonly used methods for searching for unknown base changes (mutations). In order to characterize systematically the effects of important physical parameters on the sensitivity and specificity of SSCP, we used the DNA toolbox constructed as described in the companion paper [2]. Using this set of DNA molecules as polymerase chain reaction (PCR) templates, amplicons of various lengths with the same base, mutated to all other bases, were generated. The behavior of these constructs in manual and automated SSCP was analyzed as a function of the size, overall base content of the fragment, nature and location of the base change, and the temperature and pH of electrophoresis. Our results demonstrate that all of these variables interact to determine the rate of detection of single-base changes, with the GC content being the predominant determinant of detection sensitivity.",
keywords = "Mutation scanning, Single-strand conformation polymorphism",
author = "Highsmith, {W Edward Jr.} and Nataraj, {Arun J.} and Qian Jin and O'Connor, {Jacquelyn M.} and El-Nabi, {Sohbi H.} and Noriko Kusukawa and Garner, {Mark M.}",
year = "1999",
doi = "10.1002/(SICI)1522-2683(19990101)20:6<1195::AID-ELPS1195>3.0.CO;2-A",
language = "English (US)",
volume = "20",
pages = "1195--1203",
journal = "Electrophoresis",
issn = "0173-0835",
publisher = "Wiley-VCH Verlag",
number = "6",

}

TY - JOUR

T1 - Use of DNA toolbox for the characterization of mutation scanning methods. II

T2 - Evaluation of single-strand conformation polymorphism analysis

AU - Highsmith, W Edward Jr.

AU - Nataraj, Arun J.

AU - Jin, Qian

AU - O'Connor, Jacquelyn M.

AU - El-Nabi, Sohbi H.

AU - Kusukawa, Noriko

AU - Garner, Mark M.

PY - 1999

Y1 - 1999

N2 - Single-strand conformation polymorphism (SSCP) is one of the most commonly used methods for searching for unknown base changes (mutations). In order to characterize systematically the effects of important physical parameters on the sensitivity and specificity of SSCP, we used the DNA toolbox constructed as described in the companion paper [2]. Using this set of DNA molecules as polymerase chain reaction (PCR) templates, amplicons of various lengths with the same base, mutated to all other bases, were generated. The behavior of these constructs in manual and automated SSCP was analyzed as a function of the size, overall base content of the fragment, nature and location of the base change, and the temperature and pH of electrophoresis. Our results demonstrate that all of these variables interact to determine the rate of detection of single-base changes, with the GC content being the predominant determinant of detection sensitivity.

AB - Single-strand conformation polymorphism (SSCP) is one of the most commonly used methods for searching for unknown base changes (mutations). In order to characterize systematically the effects of important physical parameters on the sensitivity and specificity of SSCP, we used the DNA toolbox constructed as described in the companion paper [2]. Using this set of DNA molecules as polymerase chain reaction (PCR) templates, amplicons of various lengths with the same base, mutated to all other bases, were generated. The behavior of these constructs in manual and automated SSCP was analyzed as a function of the size, overall base content of the fragment, nature and location of the base change, and the temperature and pH of electrophoresis. Our results demonstrate that all of these variables interact to determine the rate of detection of single-base changes, with the GC content being the predominant determinant of detection sensitivity.

KW - Mutation scanning

KW - Single-strand conformation polymorphism

UR - http://www.scopus.com/inward/record.url?scp=0345279870&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0345279870&partnerID=8YFLogxK

U2 - 10.1002/(SICI)1522-2683(19990101)20:6<1195::AID-ELPS1195>3.0.CO;2-A

DO - 10.1002/(SICI)1522-2683(19990101)20:6<1195::AID-ELPS1195>3.0.CO;2-A

M3 - Article

C2 - 10380759

AN - SCOPUS:0345279870

VL - 20

SP - 1195

EP - 1203

JO - Electrophoresis

JF - Electrophoresis

SN - 0173-0835

IS - 6

ER -