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Letter

DNA Double Helices Recognize Mutual Sequence Homology in a Protein Free Environment

Supporting Info

Geoff S. Baldwin,*^† Nicholas J. Brooks,^‡ Rebecca E. Robson,^†^‡ Aaron Wynveen,^‡ Arach Goldar,^‡^§ Sergey Leikin,* John M. Seddon,*^‡ and Alexei A. Kornyshev*^‡

Division of Molecular Biosciences, Imperial College London, SW7 2AZ London, U.K., Department of Chemistry, Imperial College London, SW7 2AZ London, U.K., and Section on Physical Biochemistry, National Institute of Child Health and Human Development, National Institutes of Health, DHHS, Bethesda, Maryland 20892

J. Phys. Chem. B, 2008, 112 (4), pp 1060–1064

DOI: 10.1021/jp7112297

Publication Date (Web): January 9, 2008

To whom correspondence should be addressed. E-mail: g.baldwin@ imperial.ac.uk (G.S.B); leikins@mail.nih.gov (S.L.); j.seddon@imperial.ac.uk (J.M.S.); a.kornyshev@imperial.ac.uk (A.A.K).

†

Division of Molecular Biosciences, Imperial College London.

‡

Department of Chemistry, Imperial College London.

Current address: Service de Biologie Integrative et de Genetique Moleculaire, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France.

Section on Physical Biochemistry, NICHD/NIH.

Abstract

The structure and biological function of the DNA double helix are based on interactions recognizing sequence complementarity between two single strands of DNA. A single DNA strand can also recognize the double helix sequence by binding in its groove and forming a triplex. We now find that sequence recognition occurs between intact DNA duplexes without any single-stranded elements as well. We have imaged a mixture of two fluorescently tagged, double helical DNA molecules that have identical nucleotide composition and length (50% GC; 294 base pairs) but different sequences. In electrolytic solution at minor osmotic stress, these DNAs form discrete liquid-crystalline aggregates (spherulites). We have observed spontaneous segregation of the two kinds of DNA within each spherulite, which reveals that nucleotide sequence recognition occurs between double helices separated by water in the absence of proteins, consistent with our earlier theoretical hypothesis. We thus report experimental evidence and discuss possible mechanisms for the recognition of homologous DNAs from a distance.

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