Measuring the geometry of DNA grooves
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Updated: Nov 9, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
1Laboratoire de Biochimie Théorique (CNRS URA 77), Institut de Biologie Physico-Chimique, Paris, France.
Abstract:
We present a new method for measuring the widths and depths of the grooves formed within DNA helices. This method overcomes the limitations of simply measuring interstrand phosphate-phosphate distances and has the advantage of yielding continuous values for groove geometry along a DNA fragment. In the case of oligonucleotides, it also clearly indicates the zones in which grooves exist, bounded by two phosphodiester backbones. The methodology has been developed within the Curves algorithm for studying irregular DNA geometries and is based on the optimal, and generally curved, helical axis obtained by this analysis.
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