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© Research
Publication : Electrophoresis

Anomalous electrophoretic migration of short oligodeoxynucleotides labelled with 5′-terminal Cy5 dyes

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Electrophoresis - 05 Jun 2014

Killelea T, Saint-Pierre C, Ralec C, Gasparutto D, Henneke G

Link to Pubmed [PMID] – 24659099

Electrophoresis 2014 Jul;35(14):1938-46

By using a fluorescent exonuclease assay, we reported unusual electrophoretic mobility of 5′-indocarbo-cyanine 5 (5′-Cy5) labelled DNA fragments in denaturing polyacrylamide gels. Incubation time and enzyme concentration were two parameters involved in the formation of 5′-Cy5-labelled degradation products, while the structure of the substrate was slightly interfering. Replacement of positively charged 5′-Cy5-labelled DNA oligonucleotides (DNA oligos) by electrically neutral 5′-carboxyfluorescein (5′-FAM) labelled DNA oligos abolished the anomalous migration pattern of degradation products. MS analysis demonstrated that anomalously migrating products were in fact 5′-labelled DNA fragments ranging from 1 to 8 nucleotides. Longer 5′-Cy5-labelled DNA fragments migrated at the expected position. Altogether, these data highlighted, for the first time, the influence of the mass/charge ratio of 5′-Cy5-labelled DNA oligos on their electrophoretic mobility. Although obtained by performing 3′ to 5′ exonuclease assays with the family B DNA polymerase from Pyrococcus abyssi, these observations represent a major concern in DNA technology involving most DNA degrading enzymes.

http://www.ncbi.nlm.nih.gov/pubmed/24659099