Label-free optical detection of single enzyme-reactant reactions and associated conformational changes

Monitoring the kinetics and conformational dynamics of single enzymes is crucial in order to better understand their biological functions as these motions and structural dynamics are usually unsynchronized among the molecules. Detecting the enzyme-reactant interactions and associated conformational changes of the enzyme on a single molecule basis, however, remain as a challenge with established optical techniques due to the commonly required labeling of the reactants or the enzyme itself. The labeling process is usually non-trivial and the labels themselves might skew the physical properties of the enzyme. Here we demonstrate an optical, label-free method capable of observing enzymatic interactions and the associated conformational changes on the single molecule level. We monitor polymerase/DNA interactions via the strong near-field enhancement provided by plasmonic nanorods resonantly coupled to whispering gallery modes in microcavities. Specifically, we employ two different recognition schemes: one in which the kinetics of polymerase/DNA interactions are probed in the vicinity of DNA-functionalized nanorods, and the other in which these interactions are probed via the magnitude of conformational changes in the polymerase molecules immobilized on nanorods. In both approaches we find that low and high polymerase activities can be clearly discerned via their characteristic signal amplitude and signal length distributions. Furthermore, the thermodynamic study of the monitored interactions suggests the occurrence of DNA polymerization. This work constitutes a proof-of-concept study of enzymatic activities via plasmonically enhanced microcavities and establishes an alternative and label-free method capable of investigating structural changes in single molecules

Simultaneous SAXS/SANS Method at D22 of ILL: Instrument Upgrade

A customized portable SAXS instrument has recently been constructed, installed, and tested at the D22 SANS instrument at ILL. Technical characteristics of this newly established plug-and-play SAXS system have recently been reported (J. Appl. Cryst. 2020, 53, 722). An optimized lead shielding arrangement on the SAXS system and a double energy threshold X-ray detector have been further implemented to substantially suppress the unavoidable high-energy gamma radiation background on the X-ray detector. The performance of the upgraded SAXS instrument has been examined systematically by determining background suppression factors (SFs) at various experimental conditions, including different neutron beam collimation lengths and X-ray sample-to-detector distances (SDDX-ray). Improved signal-to-noise ratio SAXS data enables combined SAXS and SANS measurements for all possible experimental conditions at the D22 instrument. Both SAXS and SANS data from the same sample volume can be fitted simultaneously using a common structural model, allowing unambiguous interpretation of the scattering data. Importantly, advanced in situ/real time investigations are possible, where both the SAXS and the SANS data can reveal time-resolved complementary nanoscale structural information

Internal Structure of Nanometer-Sized Droplets Prepared by Antisolvent Precipitation

Antisolvent precipitation (AP) is a low-cost and less-invasive preparation alternative for organic nanoparticles compared to top-down methods such as high-pressure homogenization or milling. Here we report on particularly small organic nanoparticles (NPs) prepared by AP. It has been found for various materials that these NPs in their liquid state exhibit a significant degree of molecular order at their interface toward the dispersion medium including ubiquinones (coenzyme Q10), triglycerides (trimyristin, tripalmitin), and alkanes (tetracosane). This finding is independent of the use of a stabilizer in the formulation. While this is obviously a quite general interfacial structuring effect, the respective structural details of specific NPs systems might differ. Here, a detailed structural characterization of very small liquid coenzyme Q10 (Q10) NPs is presented as a particular example for this phenomenon. The Q10 NPs have been prepared by AP in the presence of two different stabilizers, sodium dodecyl sulfate (SDS) and pentaethylene glycol monododecyl ether (C12E5), respectively, and without any stabilizer. The NPs’ size is initially analyzed by photon correlation spectroscopy (PCS). The SDS-stabilized Q10 NPs have been studied further by differential scanning calorimetry (DSC), small-angle X-ray and neutron scattering (SAXS, SANS), wide-angle X-ray scattering (WAXS), and cryogenic transmission electron microscopy (CryoTEM). A simultaneous analysis of SAXS and contrast variation SANS studies revealed the molecular arrangement within the interface between the NPs and the dispersion medium. The Q10 NPs stabilized by SDS and C12E5, respectively, are small (down to 19.9 nm) and stable (for at least 16 months) even when no stabilizer is used. The SDS-stabilized Q10 NPs reported here, are therewith, to the best of our knowledge, the smallest organic NPs which have been reported to be prepared by AP so far. In particular, these NPs exhibit a core–shell structure consisting of an amorphous Q10 core and a surrounding shell, which is mainly composed of oriented Q10 molecules and aligned SDS molecules. This structure suggests a significant amphiphilic behavior and a rather unexpected stabilizing role of Q10 molecules

A novel experimental approach for nanostructure analysis: simultaneous small-angle X-ray and neutron scattering

Exploiting small-angle X-ray and neutron scattering (SAXS/SANS) on the same sample volume at the same time provides complementary nanoscale structural information in two different contrast situations. Unlike an independent experimental approach, the truly combined SAXS/SANS experimental approach ensures the exactness of the probed samples, particularly for in situ studies. Here, an advanced portable SAXS system that is dimensionally suitable for installation in the D22 zone of ILL is introduced. The SAXS apparatus is based on a Rigaku switchable copper/molybdenum microfocus rotating-anode X-ray generator and a DECTRIS detector with a changeable sample-to-detector distance of up to 1.6 m in a vacuum chamber. A case study is presented to demonstrate the uniqueness of the newly established method. Temporal structural rearrangements of both the organic stabilizing agent and organically capped gold colloidal particles during gold nanoparticle growth are simultaneously probed, enabling the immediate acquisition of correlated structural information. The new nano-analytical method will open the way for real-time investigations of a wide range of innovative nanomaterials and will enable comprehensive in situ studies on biological systems. The potential development of a fully automated SAXS/SANS system with a common control environment and additional sample environments, permitting a continual and efficient operation of the system by ILL users, is also introduced