Ultrafast cooling reveals microsecond-scale biomolecular dynamics

Abstract

The temperature-jump technique, in which the sample is rapidly heated by a powerful laser pulse, has been widely used to probe the fast dynamics of folding of proteins and nucleic acids. However, the existing temperature-jump setups tend to involve sophisticated and expensive instrumentation, while providing only modest temperature changes of B10-15°C, and the temperature changes are only rapid for heating, but not cooling. Here we present a setup comprising a thermally conductive sapphire substrate with light-absorptive nanocoating, a microfluidic device and a rapidly switched moderate-power infrared laser with the laser beam focused on the nano-coating, enabling heating and cooling of aqueous solutions by B50°C on a 1-ms time scale. The setup is used to probe folding and unfolding dynamics of DNA hairpins after direct and inverse temperature jumps, revealing low-pass filter behaviour during periodic temperature variations.

Relating sequence encoded information to form and function of intrinsically disordered proteins

“…Preliminary work has focused on the impact of sequence-specific contributions to internal friction [20,81–84]. Advances in nuclear magnetic resonance [85–89] and single molecule spectroscopies [90–92] combined with novel computational and theoretical methodologies [93–95] should pave the way for comprehensive characterization of IDP dynamics and assessing their impact on the dynamical regulation of cellular phenotypes [96,97]. Overall, it is clear that continued synergistic investigations must be brought to bear in order to build on the insights that have been forthcoming with regard to connecting information encoded in IDP sequences to their form and function.…”

Direct Measurement of Single‐Molecule DNA Hybridization Dynamics with Single‐Base Resolution

“…The hairpin loop is a secondary structural motif frequently observed in DNAs and RNAs that is involved in gene expression and regulation . A two‐state mechanism of DNA hairpin formation, where the hairpin DNA transits between a folded base‐paired state and an unfolded random‐coil state with the relaxation time ranging from several microseconds to hundreds of microseconds, has been well studied as an important system of DNA hybridization using fluorescence correlation spectroscopy (FCS), single‐molecule fluorescence resonance energy transfer (smFRET), single‐molecule force spectroscopy, and laser temperature jumping . These studies also suggested a complicated, multistate model of fast hairpin folding, which requires experimental techniques capable of probing both long‐ and short‐lived reaction intermediates in a wide range of detection times.…”

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

“…However, the ability to study DNA behaviour as a function of salt would allow quantitative comparison with a greatly expanded set of experiments, and, in particular, if we wish to apply oxDNA to biological systems, we would like to work at physiological salt ([Na + ] ≈ 0.15M). At the same time, the wealth of experimental data for the thermodynamic and mechanical properties of DNA as a function of salt concentration [47][48][49][50] makes fitting the saltdependent properties of an extended model possible.…”