The effect of ethidium bromide on mobility of DNA fragments in agarose gel electrophoresis

Electrophoresis
J Sigmon, L L Larcom

Abstract

Ethidium Bromide (EtBr) is sometimes added to running buffer during the separation of DNA fragments by agarose gel electrophoresis. It is used because upon binding of the molecule to the DNA and illumination with a UV light source, the DNA banding pattern can be visualized. The mode of binding of EtBr is intercalation between the base pairs. This binding changes the charge, weight, conformation, and flexibility of the DNA molecule. Since DNA molecules are sized by their relative movement through a gel compared to a molecular weight standard, mobility measurements can be critical to size determinations. After running two identical gels, one without EtBr and one with 0.25, 0.5, 0.75 or 1.0 microgram/mL EtBr in the running buffer, the mobilities of lambda HindIII DNA fragments were compared. The mobility of DNA was always less in the gels with EtBr. Using the reptation theory equation, which describes the mobility of DNA molecules through gel, changes in frictional coefficients were calculated. It was determined that the change in frictional coefficients brought about by the addition of EtBr is directly proportional to the fraction of base pairs of a fragment bound to EtBr. This change in friction is greatest in the largest fragme...Continue Reading

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Citations

Feb 10, 1998·Electrophoresis·W M Sunada, H W Blanch
Jan 27, 2000·Journal of Biochemical and Biophysical Methods·K NathC J Di Como
Jan 1, 2007·Occupational Therapy in Health Care·Anne Marie Witchger HansenDebra Tupé
Jul 21, 2009·Journal of Pharmaceutical and Biomedical Analysis·Rie AkamineMasatoshi Kataoka
Oct 24, 2007·Nursing Outlook·Elizabeth A DownesShelly L Brownsberger
Feb 2, 2010·Electrophoresis·Katerina AfanasievaAndrei Sivolob
Oct 9, 2013·Biochimica Et Biophysica Acta·Katerina AfanasievaAndrei Sivolob
Jul 12, 2016·Electrophoresis·Tania FurstAnne-Catherine Servais
Aug 26, 2016·ACS Nano·Eric KruegerDaniel Fologea
Nov 2, 2019·Nucleosides, Nucleotides & Nucleic Acids·Asmaa AbdelrahmanJesper Wengel
Jan 4, 2019·Cold Spring Harbor Protocols·Michael R Green, Joseph Sambrook
Feb 12, 2020·Analytical Biochemistry·Colin A Fox, Robert O Ryan
Jul 14, 2020·ACS Applied Bio Materials·Raj Kumar ThapaMillicent O Sullivan
Jul 22, 2021·Nucleic Acids Research·Arivazhagan RajendranTakashi Morii
Mar 14, 2016·ACS Biomaterials Science & Engineering·Mohammadali SafaviehHadi Shafiee

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