BIOPHYSICAL THEORY AND MODELING |
Nucleotide specificity versus complex heterogeneity in exonuclease activity measurements
Joerg Enderlein 1*
1 Forschungszentrum Juelich
* To whom correspondence should be addressed. E-mail: j.enderlein{at}fz-juelich.de.
Submitted on August 23, 2006
Revised on September 20, 2006
Accepted on 13 November 2006
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Abstract |
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In a recent publication, Werner et al. (Biophys. J. 88, 2006, p.1402) reported on meas-urements of Exonuclease I activity using a real-time fluorescence method which measures the time required by molecules of Exonuclease I to hydrolyze single-stranded DNA that was syn-thesized to have two fluorescently labelled nucleotides. The observed fluorescence intensity curves were interpreted as a sign of strong heterogeneity of the activity of Exonuclease I. Here, we propose a different model which assumes that Exonuclease I activity is nucleotide dependent, and that a fluorescent label bound to a nucleotide significantly slows its cleavage rate. The presented model fits the observed data equally well, but can be used to make specific predictions upon observable sequence dependence of measured fluorescence intensity curves.
Key Words:
Exonuclease I, enzyme activity, fluorescence assay
