We report the development of technology that allows interstrand coupling between various positions across minor or major grooves within one turn of DNA duplex. 2ʼ-Modified nucleotides were synthesized as protected phosphoramidites and incorporated into DNA structures (1-2). The modified nucleotides contained five-atom linkers, with either amine or carboxylic acid functional groups at their termini. Chemical coupling of amine and carboxylic acid groups in designed strands resulted in the formation of an amide bond linking two complementary strands. Interstrand crosslinks were formed specifically between nucleotides placed at preselected positions rather than selective formation between various positions as observed in previous studies. The trajectory lengths of linkers determined if the termini could reach each other to enable reactions to occur. Modeling (3) and calculated crosslink trajectory distances were in agreement our conclusions from experimental data. This technology enables approaches that can control regiospecific and distance dependent linkage formation, offering tools to use site-specific cross-links to probe biological phenomena (4). In addition, this approach can also be applied to DNA nanotechnology to help build nanoscale structures along DNA templates.



Acknowledgements This research has been supported by the following grants to JWC and NCS: National Science Foundation (CTS-0608889) and the Office of Naval Research (N000140911118). This work has also been supported by grants to NCS from the National Institute of General Medical Sciences (GM-29544) the National Science Foundation (CCF-0726378), the Army Research Office (48681-EL and W911NF-07-1-0439), and a grant from the W.M. Keck Foundation. This work was supported partially by the MRSEC Program of the National Science Foundation under Award Number DMR-0820341.

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