@article{12950a8c7f494bde9aaef9930a790910,
title = "The flexibility of DNA double crossover molecules",
abstract = "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.",
author = "Phiset Sa-Ardyen and Vologodskii, {Alexander V.} and Seeman, {Nadrian C.}",
note = "Funding Information: A byproduct of these experiments with sealed central strands is a collection of relatively long DNA catenanes. The molecules we have generated are complex catenanes, wherein the cyclic strands are linked to both of the continuous strands. In our heat-induced breakdown used for analysis, we have generated simple cyclic catenanes of DNA. These catenanes could be generated reliably if we included a restriction site on the hairpins of the DX molecule. Likewise, similar restriction of the linear molecules at ambient temperatures would lead to a precursor for a rotaxane, a linear species on which cyclic molecules have been threaded (e.g., Sauvage and Dietrich-Buchecker, 1999 ); removal of the restricted strands by the techniques of Yurke et al. (2000) would produce a long multiple rotaxane. We thank Dr Lisa Wenzler Savin for guidance and discussions in the early stages of this project. This work has been supported by grants GM-29554 from the National Institute of General Medical Sciences, N00014-98-1-0093 from the Office of Naval Research, DMI-0210844, EIA-0086015, DMR-01138790, and CTS-0103002 from the National Science Foundation, and F30602-01-2-0561 from the Defense Advanced Research Projects Agency/Air Force Office of Scientific Research to N.C.S.; and by grant GM54215 from the National Institute of General Medical Sciences to A.V.V. ",
year = "2003",
month = jun,
day = "1",
doi = "10.1016/S0006-3495(03)75110-8",
language = "English (US)",
volume = "84",
pages = "3829--3837",
journal = "Biophysical journal",
issn = "0006-3495",
publisher = "Biophysical Society",
number = "6",
}