Optical measurement of mechanical forces inside short DNA loops.

Knowledge of the mechanical properties of double-stranded DNA (dsDNA) is essential to understand the role of dsDNA looping in gene regulation and the mechanochemistry of molecular machines that operate on dsDNA. Here, we use a newly developed tool, force sensors with optical readout, to measure the forces inside short, strained loops composed of both dsDNA and single-stranded DNA. By varying the length of the loops and their proportion of dsDNA, it was possible to vary their internal forces from 1 pN to >20 pN. Surprisingly, internal loop forces changed erratically as the amount of dsDNA was increased for a given loop length, with the effect most notable in the smallest loop (57 nucleotides). Monte Carlo simulations based on the helical wormlike chain model accurately predict internal forces when more than half of the loop is dsDNA but fail otherwise. Mismatches engineered into the double-stranded regions increased flexibility, suggesting that Watson-Crick basepaired dsDNA can withstand high compressive forces without recourse to multibase melts. Fluorescence correlation spectroscopy further excluded transient melting (microsecond to millisecond duration) as a mechanism for relief of compressive forces in the tested dsDNAs. DNA loops with integrated force sensors may allow the comprehensive mapping of the elasticity of short dsDNAs as a function of both sequence and salt.

Scanning-induced growth on single crystal calcite with an atomic force microscope.

We report observations of localized growth on the (1014) surface of single-crystal CaCO3 in supersaturated solutions while scanning with the tip of an atomic force microscope (AFM). At low contact forces, AFM scanning strongly enhances deposition along preexisting steps. This enhancement increases rapidly with increasing solution supersaturation, and is capable of filling in multilayer etch pits to produce defect-free surfaces at the resolution of the AFM. Attempts to achieve similar deposition rates in the absence of scanning require high supersaturations that produce three-dimensional crystal nuclei, which are important defects. Localized deposition produced by drawing the AFM tip back and forth across step edges can produce monolayer deposits extending well over a micron from the scanned area. These tip-induced deposits provide convincing evidence for the importance of ledge diffusion in calcite crystal growth.