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Low-Resolution Reconstruction of a Synthetic DNA Holliday Junction

Marcelo Nöllmann ^* , W. Marshall Stark  and Olwyn Byron ^*

^* Division of Infection & Immunity, Institute of Biomedical and Life Sciences, and Division of Molecular Genetics, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom

Correspondence: Address reprint requests to Marcelo Nöllmann, Division of Infection & Immunity, IBLS, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK. Tel.: 44-141-330-5113; Fax: 44-141-330-4878; E-mail: marcnol{at}chem.gla.ac.uk.

We have studied the low-resolution solution conformation of a Holliday (or four-way) DNA junction by using small-angle x-ray scattering, sedimentation velocity, and computational modeling techniques. The scattering data were analyzed in two independent ways: firstly, by rigid-body modeling of the scattering data using previously suggested models for the Holliday junction (HJ), and secondly, by ab initio reconstruction methods. The models found by both methods agree with experimentally determined sedimentation coefficients and are compatible with the results of previous studies using different techniques, but provide a more direct and accurate determination of the solution conformation of the HJ. Our results show that addition of Mg²⁺ alters the conformation of the HJ from an extended to a stacked arrangement.