Screening for and analysis of methylation differences using methylation-sensitive single-strand conformation analysis

Alexander Dobrovic; Tina Bianco; Lor Wai Tan; Tanya Sanders; Damian Hussey

doi:10.1016/S1046-2023(02)00065-8

Screening for and analysis of methylation differences using methylation-sensitive single-strand conformation analysis

Alexander Dobrovic, Tina Bianco, Lor Wai Tan, Tanya Sanders, Damian Hussey

Research output: Contribution to journal › Article › peer-review

19 Citations (Scopus)

Abstract

Methylation-sensitive single-strand conformation analysis (MS-SSCA) is a method of screening for methylation changes at CpG sites in a region of DNA. After bisulfite modification, the region of interest is amplified using primers specific for bisulfite-modified sequences. The amplified products are denatured and run on a nondenaturing polyacrylamide gel. The sequence differences caused by methylation lead to the formation of different secondary structures (conformers) with different mobilities. MS-SSCA is a convenient and rapid method for screening large numbers of samples for methylation. Individual bands can readily be isolated and sequenced allowing more detailed analysis of methylation changes. In this article, we present a protocol for MS-SSCA and outline strategies for the design of primers for amplifying bisulfite-modified DNA sequences.

Original language	English
Pages (from-to)	134-138
Number of pages	5
Journal	Methods
Volume	27
Issue number	2
DOIs	https://doi.org/10.1016/S1046-2023(02)00065-8
Publication status	Published - Jun 2002
Externally published	Yes

Keywords

Bisulfite
Cancer
Genomic sequencing
Methylation
p16
Silencing
Single-strand conformation analysis
Single-strand conformation polymorphism
Tumor

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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title = "Screening for and analysis of methylation differences using methylation-sensitive single-strand conformation analysis",

abstract = "Methylation-sensitive single-strand conformation analysis (MS-SSCA) is a method of screening for methylation changes at CpG sites in a region of DNA. After bisulfite modification, the region of interest is amplified using primers specific for bisulfite-modified sequences. The amplified products are denatured and run on a nondenaturing polyacrylamide gel. The sequence differences caused by methylation lead to the formation of different secondary structures (conformers) with different mobilities. MS-SSCA is a convenient and rapid method for screening large numbers of samples for methylation. Individual bands can readily be isolated and sequenced allowing more detailed analysis of methylation changes. In this article, we present a protocol for MS-SSCA and outline strategies for the design of primers for amplifying bisulfite-modified DNA sequences.",

keywords = "Bisulfite, Cancer, Genomic sequencing, Methylation, p16, Silencing, Single-strand conformation analysis, Single-strand conformation polymorphism, Tumor",

author = "Alexander Dobrovic and Tina Bianco and Tan, {Lor Wai} and Tanya Sanders and Damian Hussey",

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journal = "Methods",

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T1 - Screening for and analysis of methylation differences using methylation-sensitive single-strand conformation analysis

AU - Dobrovic, Alexander

AU - Bianco, Tina

AU - Tan, Lor Wai

AU - Sanders, Tanya

AU - Hussey, Damian

PY - 2002/6

Y1 - 2002/6

N2 - Methylation-sensitive single-strand conformation analysis (MS-SSCA) is a method of screening for methylation changes at CpG sites in a region of DNA. After bisulfite modification, the region of interest is amplified using primers specific for bisulfite-modified sequences. The amplified products are denatured and run on a nondenaturing polyacrylamide gel. The sequence differences caused by methylation lead to the formation of different secondary structures (conformers) with different mobilities. MS-SSCA is a convenient and rapid method for screening large numbers of samples for methylation. Individual bands can readily be isolated and sequenced allowing more detailed analysis of methylation changes. In this article, we present a protocol for MS-SSCA and outline strategies for the design of primers for amplifying bisulfite-modified DNA sequences.

AB - Methylation-sensitive single-strand conformation analysis (MS-SSCA) is a method of screening for methylation changes at CpG sites in a region of DNA. After bisulfite modification, the region of interest is amplified using primers specific for bisulfite-modified sequences. The amplified products are denatured and run on a nondenaturing polyacrylamide gel. The sequence differences caused by methylation lead to the formation of different secondary structures (conformers) with different mobilities. MS-SSCA is a convenient and rapid method for screening large numbers of samples for methylation. Individual bands can readily be isolated and sequenced allowing more detailed analysis of methylation changes. In this article, we present a protocol for MS-SSCA and outline strategies for the design of primers for amplifying bisulfite-modified DNA sequences.

KW - Bisulfite

KW - Cancer

KW - Genomic sequencing

KW - Methylation

KW - p16

KW - Silencing

KW - Single-strand conformation analysis

KW - Single-strand conformation polymorphism

KW - Tumor

UR - http://www.scopus.com/inward/record.url?scp=0036315004&partnerID=8YFLogxK

U2 - 10.1016/S1046-2023(02)00065-8

DO - 10.1016/S1046-2023(02)00065-8

M3 - Article

C2 - 12095271

AN - SCOPUS:0036315004

SN - 1046-2023

VL - 27

SP - 134

EP - 138

JO - Methods

JF - Methods

IS - 2

ER -

Screening for and analysis of methylation differences using methylation-sensitive single-strand conformation analysis

Abstract

Keywords

UN SDGs

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