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The Flexibility of DNA Double Crossover Molecules

Department of Chemistry, New York University, New York, New York 10003 USA

Correspondence: Address reprint requests to Nadrian C. Seeman, 24 Waverly Pl., Suite 1066, New York, NY 10003. Tel.: 212-998-8395; Fax: 212-260-7905; E-mail: ned.seeman{at}nyu.edu.

Double crossover molecules are DNA structures containing two Holliday junctions connected by two double helical arms. There are several types of double crossover molecules, differentiated by the relative orientations of their helix axes, parallel or antiparallel, and by the number of double helical half-turns (even or odd) between the two crossovers. They are found as intermediates in meiosis and they have been used extensively in structural DNA nanotechnology for the construction of one-dimensional and two-dimensional arrays and in a DNA nanomechanical device. Whereas the parallel double helical molecules are usually not well behaved, we have focused on the antiparallel molecules; antiparallel molecules with an even number of half-turns between crossovers (termed DAE molecules) produce a reporter strand when ligated, facilitating their characterization in a ligation cyclization assay. Hence, we have estimated the flexibility of antiparallel DNA double crossover molecules by means of ligation-closure experiments. We are able to show that these molecules are approximately twice as rigid as linear duplex DNA.

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