Locked Nucleic Acid Biomolecular Handles Functionalize Double-Stranded DNA for Single Molecule Manipulation

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This work shows that short mixmers composed of Locked Nucleic Acid (LNA) and DNA can be used to add functional groups to specific sequences within a double stranded DNA molecule for single molecule manipulation (SMM) experiments. Traditional immobilization protocols often preclude experiments on native biomolecular complexes; the use of these biomolecular LNA handles could broaden the experimental possibilities by providing a simple, non-pertubative labeling strategy. We show triplex-forming LNA probes with functional moities can immobilize DNA stably and specifically with one simple hybridization step. Further investigations of stability show that, although the LNA handles are stable under shear forces up to 10 pN for long times, they are up to two orders of magnitude less stable when force is applied in a geometry which sequentially destabilizes the triplexes (i.e. an unzipping configuration). We provide a set of rules for the esign and use of LNA handles in SMM applications and show results using biomolecular handles on DNA structures from E. coli.