Science  04 Mar 2005:
Vol. 307, Issue 5714, pp. 1409b
DOI: 10.1126/science.307.5714.1409b

We wish to retract our Research Article “The bacterial condensin MukBEF compacts DNA into a repetitive, stable structure” (1). The conclusions of our paper, which used a single-molecule assay with an optical-trap microscope, were based on the interpretation of a flat sawtooth pattern in the force-extension curves as a progressive unraveling of compact MukBEF/DNA filaments. However, subsequent experiments done after the paper appeared suggested that the sawtooth pattern corresponds to the unzipping of the two strands of DNA (2). We now believe that nicks that arose indiscriminately along the DNA molecules from normal pipetting allowed interior biotin and Digoxigenin derivitization of the DNA tether. The combination of interior and terminal labels most likely generated a pulling geometry between the beads that led to the denaturation of the DNA. To test these ideas, we have now performed an extensive set of experiments.

First, the double-strand DNA was cross-linked with one psoralen cross-link per 100 base pairs to prevent the opposite strands from separating. The cross-linked DNA alone produced the expected force-extension curves for naked DNA (102 out of 103 cases). When the cross-linked DNA was incubated with purified MukBEF protein under our published conditions, in no case (n = 180) did we observe the previously observed sawtooth pattern.

Second, we designed a DNA tether that had both a nick and an adjacent biotin label 2-kb interior from its Digoxigenin-labeled end. The labels and nick were placed so that if the streptavidin bead attaches to both the interior and end-labeled biotin and the anti-Digoxigenin bead attaches to the Digoxigenin labeled DNA end, then pulling the beads apart would unzip the DNA between the interior- and the end-biotin label. With this DNA alone, the flat sawtooth pattern in the force-extension curves was readily observed, displaying little or no hysteresis between the pulling and relaxation paths. When these tethers were incubated with MukBEF protein, hysteresis then appeared between the pulling and relaxing pathways and the pattern was indistinguishable from the published sawtooth pattern.

Thus, we now believe that two DNA attachments were made to one of the beads in our published experiments. MukBEF interacted with the unzipped tether to slow reannealing, giving rise to the observed hysteresis. We deeply regret the misinterpretation and the confusion the original publication has caused.


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