Analyzing RNA and DNA folding using temperature gradient gel electrophoresis (TGGE) with application to in vitro selections.

Durga M. Chadalavada, Philip C. Bevilacqua

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Gel electrophoresis is a ubiquitous separation technique in nucleic acid biochemistry. Denaturing gel electrophoresis separates nucleic acids on the basis of length, while native gel electrophoresis separates nucleic acids on the basis of both shape and length. Temperature gradient gel electrophoresis (TGGE), in which a temperature gradient is present across the gel, combines the advantages of denaturing and native gel electrophoresis by having native gel-like properties at low temperatures and denaturing gel-like properties at high temperatures. We describe here the techniques of perpendicular and parallel TGGE and some of their applications. Isolation of stable and unstable RNA and DNA sequences from combinatorial libraries is accomplished with TGGE-SELEX, while thermodynamic characterization of an RNA tertiary motif is performed by perpendicular TGGE-melts. Specific examples are chosen from the literature to illustrate the methods. TGGE provides a powerful biophysical approach for analyzing RNA and DNA that complements more traditional methodologies.

Original languageEnglish (US)
Pages (from-to)389-408
Number of pages20
JournalMethods in enzymology
Volume468
StatePublished - Jan 1 2009

Fingerprint

RNA Folding
Denaturing Gradient Gel Electrophoresis
Electrophoresis
Thermal gradients
Gels
RNA
DNA
Nucleic Acids
Unstable DNA Sequences
Temperature
Nucleotide Motifs
In Vitro Techniques
Thermodynamics
Biochemistry
DNA sequences

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology

Cite this

@article{f5f40a0dbcb74701a26c538885cc0b81,
title = "Analyzing RNA and DNA folding using temperature gradient gel electrophoresis (TGGE) with application to in vitro selections.",
abstract = "Gel electrophoresis is a ubiquitous separation technique in nucleic acid biochemistry. Denaturing gel electrophoresis separates nucleic acids on the basis of length, while native gel electrophoresis separates nucleic acids on the basis of both shape and length. Temperature gradient gel electrophoresis (TGGE), in which a temperature gradient is present across the gel, combines the advantages of denaturing and native gel electrophoresis by having native gel-like properties at low temperatures and denaturing gel-like properties at high temperatures. We describe here the techniques of perpendicular and parallel TGGE and some of their applications. Isolation of stable and unstable RNA and DNA sequences from combinatorial libraries is accomplished with TGGE-SELEX, while thermodynamic characterization of an RNA tertiary motif is performed by perpendicular TGGE-melts. Specific examples are chosen from the literature to illustrate the methods. TGGE provides a powerful biophysical approach for analyzing RNA and DNA that complements more traditional methodologies.",
author = "Chadalavada, {Durga M.} and Bevilacqua, {Philip C.}",
year = "2009",
month = "1",
day = "1",
language = "English (US)",
volume = "468",
pages = "389--408",
journal = "Methods in Enzymology",
issn = "0076-6879",
publisher = "Academic Press Inc.",

}

Analyzing RNA and DNA folding using temperature gradient gel electrophoresis (TGGE) with application to in vitro selections. / Chadalavada, Durga M.; Bevilacqua, Philip C.

In: Methods in enzymology, Vol. 468, 01.01.2009, p. 389-408.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Analyzing RNA and DNA folding using temperature gradient gel electrophoresis (TGGE) with application to in vitro selections.

AU - Chadalavada, Durga M.

AU - Bevilacqua, Philip C.

PY - 2009/1/1

Y1 - 2009/1/1

N2 - Gel electrophoresis is a ubiquitous separation technique in nucleic acid biochemistry. Denaturing gel electrophoresis separates nucleic acids on the basis of length, while native gel electrophoresis separates nucleic acids on the basis of both shape and length. Temperature gradient gel electrophoresis (TGGE), in which a temperature gradient is present across the gel, combines the advantages of denaturing and native gel electrophoresis by having native gel-like properties at low temperatures and denaturing gel-like properties at high temperatures. We describe here the techniques of perpendicular and parallel TGGE and some of their applications. Isolation of stable and unstable RNA and DNA sequences from combinatorial libraries is accomplished with TGGE-SELEX, while thermodynamic characterization of an RNA tertiary motif is performed by perpendicular TGGE-melts. Specific examples are chosen from the literature to illustrate the methods. TGGE provides a powerful biophysical approach for analyzing RNA and DNA that complements more traditional methodologies.

AB - Gel electrophoresis is a ubiquitous separation technique in nucleic acid biochemistry. Denaturing gel electrophoresis separates nucleic acids on the basis of length, while native gel electrophoresis separates nucleic acids on the basis of both shape and length. Temperature gradient gel electrophoresis (TGGE), in which a temperature gradient is present across the gel, combines the advantages of denaturing and native gel electrophoresis by having native gel-like properties at low temperatures and denaturing gel-like properties at high temperatures. We describe here the techniques of perpendicular and parallel TGGE and some of their applications. Isolation of stable and unstable RNA and DNA sequences from combinatorial libraries is accomplished with TGGE-SELEX, while thermodynamic characterization of an RNA tertiary motif is performed by perpendicular TGGE-melts. Specific examples are chosen from the literature to illustrate the methods. TGGE provides a powerful biophysical approach for analyzing RNA and DNA that complements more traditional methodologies.

UR - http://www.scopus.com/inward/record.url?scp=79952196862&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79952196862&partnerID=8YFLogxK

M3 - Article

VL - 468

SP - 389

EP - 408

JO - Methods in Enzymology

JF - Methods in Enzymology

SN - 0076-6879

ER -