Acharya, A. | Search bioRxiv

bioRxiv2018

Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

In situ hybridization based on the mechanism of hybridization chain reaction (HCR) has addressed multi-decade challenges to imaging mRNA expression in diverse organisms, offering a unique combination of multiplexing, quantitation, sensitivity, resolution, and versatility. Here, with third-generation in situ HCR, we augment these capabilities using probes and amplifiers that combine to provide automatic background suppression throughout the protocol, ensuring that even if reagents bind non-specifically within the sample they will not generate amplified background. Automatic background suppression dramatically enhances performance and robustness, combining the benefits of higher signal-to-background with the convenience of using unoptimized probe sets for new targets and organisms. In situ HCR v3.0 enables multiplexed quantitative mRNA imaging with subcellular resolution in the anatomical context of whole-mount vertebrate embryos, multiplexed quantitative mRNA flow cytometry for high-throughput single-cell expression profiling, and multiplexed quantitative single-molecule mRNA imaging in thick autofluorescent samples.\n\nSUMMARYIn situ hybridization chain reaction (HCR) v3.0 exploits automatic background suppression to enable multiplexed quantitative mRNA imaging and flow cytometry with dramatically enhanced ease-of-use and performance.

developmental biology↗

bioRxiv2017

Functional Implications Of Disordered Terminal Regions Of Macrotyloma uniflorum Bowman-Birk Inhibitors: A Molecular Dynamics Study

Bowman-Birk Inhibitors (BBI) - a class of serine protease inhibitors is of considerable interest due to their anti-inflammatory and anti-carcinogenic properties. Recent efforts have focused on understanding the structure and dynamics of these inhibitors, and the molecular mechanism behind its bioactive properties. BBI derived from Horsegram seeds is an interesting member of the class that exists as a number of isoforms that differ in length at the C- and N-terminal disordered regions. Interestingly, the length (or conversely, truncation) of the terminal regions affect whether the protein exists as a dimer or monomer. Here, we have investigated the mechanism of dimerization in Horsegram BBI. A recent study has proposed that the dimerization occur via a C-terminal hook that forms a salt bridge with the opposite monomer and is pivotal to the dimerization process. We have employed long computational simulation methods to predict the stability of the proposed C-terminal hook; we show that the terminal regions are highly disordered and the salt bridges are significantly solvent exposed. Further, using Hamiltonian replica exchange method, we have sought to obtain the conformational ensemble of the disordered terminal regions and have identified a conformational state that provides an interaction hot-spot that aids in the dimerization of HGI. Our analysis predicts an alternate model of dimerization that largely agrees with previous experimental studies and yet again, highlights the importance of intrinsically disordered region in tailoring the protein function.

biochemistry↗