High-yield, ligation-free assembly of DNA constructs with nucleosome positioning sequence repeats for single molecule manipulation assays

Abstract

ABSTRACTForce and torque spectroscopy have provided unprecedented insights into the mechanical properties, conformational transitions, and dynamics of DNA and DNA-protein complexes, notably nucleosomes. Reliable single-molecule manipulation measurements require, however, specific and stable attachment chemistries to tether the molecules of interest. Here, we present a functionalization strategy for DNA that enables high-yield production of constructs for torsionally constrained and very stable attachment. The method is based on two subsequent PCR reactions: first ∼380 bp long DNA strands are generated that contain multiple labels, which are used as “megaprimers” in a second PCR reaction to generate ∼kbp long double-stranded DNA constructs with multiple labels at the respective ends. We use DBCO-based click chemistry for covalent attachment to the surface and biotin-streptavidin coupling to the bead. The resulting tethers are torsionally constrained and extremely stable under force, with an average lifetime of 60 ± 3 hours at 45 pN. The high yield of the approach enables nucleosome reconstitution by salt dialysis on the functionalized DNA and we demonstrate proof-of-concept measurements on nucleosome assembly statistics and inner turn unwrapping under force. We anticipate that our approach will facilitate a range of studies of DNA interactions and nucleoprotein complexes under forces and torques.