Single-Molecule View of Small RNA–Guided Target Search and Recognition

2018 ◽  
Vol 47 (1) ◽  
pp. 569-593 ◽  
Author(s):  
Viktorija Globyte ◽  
Sung Hyun Kim ◽  
Chirlmin Joo
Keyword(s):  
Single Molecule ◽  
Gene Expression Regulation ◽  
Weak Interactions ◽  
Three Dimensional ◽  
Cellular Level ◽  
Interacting Proteins ◽  
Search System ◽  
Recognition Mechanism ◽  
Target Search ◽  
Search And Recognition

Most everyday processes in life involve a necessity for an entity to locate its target. On a cellular level, many proteins have to find their target to perform their function. From gene-expression regulation to DNA repair to host defense, numerous nucleic acid–interacting proteins use distinct target search mechanisms. Several proteins achieve that with the help of short RNA strands known as guides. This review focuses on single-molecule advances studying the target search and recognition mechanism of Argonaute and CRISPR (clustered regularly interspaced short palindromic repeats) systems. We discuss different steps involved in search and recognition, from the initial complex prearrangement into the target-search competent state to the final proofreading steps. We focus on target search mechanisms that range from weak interactions, to one- and three-dimensional diffusion, to conformational proofreading. We compare the mechanisms of Argonaute and CRISPR with a well-studied target search system, RecA.

scholarly journals Advancing Drug Discovery for Neurological Disorders Using iPSC-Derived Neural Organoids

2021 ◽  
Vol 22 (5) ◽  
pp. 2659
Author(s):  
Gianluca Costamagna ◽  
Giacomo Pietro Comi ◽  
Stefania Corti
Keyword(s):  
Drug Discovery ◽  
Drug Screening ◽  
Neural Development ◽  
Neurological Disorders ◽  
Large Scale ◽  
Three Dimensional ◽  
Induced Pluripotent Stem Cell ◽  
Cellular Level ◽  
Complex Data ◽  
Complex Data Sets

In the last decade, different research groups in the academic setting have developed induced pluripotent stem cell-based protocols to generate three-dimensional, multicellular, neural organoids. Their use to model brain biology, early neural development, and human diseases has provided new insights into the pathophysiology of neuropsychiatric and neurological disorders, including microcephaly, autism, Parkinson’s disease, and Alzheimer’s disease. However, the adoption of organoid technology for large-scale drug screening in the industry has been hampered by challenges with reproducibility, scalability, and translatability to human disease. Potential technical solutions to expand their use in drug discovery pipelines include Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) to create isogenic models, single-cell RNA sequencing to characterize the model at a cellular level, and machine learning to analyze complex data sets. In addition, high-content imaging, automated liquid handling, and standardized assays represent other valuable tools toward this goal. Though several open issues still hamper the full implementation of the organoid technology outside academia, rapid progress in this field will help to prompt its translation toward large-scale drug screening for neurological disorders.

scholarly journals Weak Interactions in Cocrystals of Isoniazid with Glycolic and Mandelic Acids

Crystals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 328
Author(s):  
Raquel Álvarez-Vidaurre ◽  
Alfonso Castiñeiras ◽  
Antonio Frontera ◽  
Isabel García-Santos ◽  
Diego M. Gil ◽  
...  
Keyword(s):  
Density Functional ◽  
Glycolic Acid ◽  
Weak Interactions ◽  
Three Dimensional ◽  
Functional Theory ◽  
Molecular Systems ◽  
X Ray Crystallography ◽  
Hydroxycarboxylic Acids ◽  
Non Covalent Interactions ◽  
Covalent Interactions

This work deals with the preparation of pyridine-3-carbohydrazide (isoniazid, inh) cocrystals with two α-hydroxycarboxylic acids. The interaction of glycolic acid (H2ga) or d,l-mandelic acid (H2ma) resulted in the formation of cocrystals or salts of composition (inh)·(H2ga) (1) and [Hinh]+[Hma]–·(H2ma) (2) when reacted with isoniazid. An N′-(propan-2-ylidene)isonicotinic hydrazide hemihydrate, (pinh)·1/2(H2O) (3), was also prepared by condensation of isoniazid with acetone in the presence of glycolic acid. These prepared compounds were well characterized by elemental analysis, and spectroscopic methods, and their three-dimensional molecular structure was determined by single crystal X-ray crystallography. Hydrogen bonds involving the carboxylic acid occur consistently with the pyridine ring N atom of the isoniazid and its derivatives. The remaining hydrogen-bonding sites on the isoniazid backbone vary based on the steric influences of the derivative group. These are contrasted in each of the molecular systems. Finally, Hirshfeld surface analysis and Density-functional theory (DFT) calculations (including NCIplot and QTAIM analyses) have been performed to further characterize and rationalize the non-covalent interactions.

scholarly journals Motional dynamics of single Patched1 molecules in cilia are controlled by Hedgehog and cholesterol

2019 ◽  
Vol 116 (12) ◽  
pp. 5550-5557 ◽  
Author(s):  
Lucien E. Weiss ◽  
Ljiljana Milenkovic ◽  
Joshua Yoon ◽  
Tim Stearns ◽  
W. E. Moerner
Keyword(s):  
Single Molecule ◽  
Hedgehog Signaling ◽  
Primary Cilia ◽  
Transmembrane Protein ◽  
Cellular Level ◽  
Live Cells ◽  
Cholesterol Depletion ◽  
Motional Dynamics ◽  
Directional Transport ◽  
Bulk Behavior

The Hedgehog-signaling pathway is an important target in cancer research and regenerative medicine; yet, on the cellular level, many steps are still poorly understood. Extensive studies of the bulk behavior of the key proteins in the pathway established that during signal transduction they dynamically localize in primary cilia, antenna-like solitary organelles present on most cells. The secreted Hedgehog ligand Sonic Hedgehog (SHH) binds to its receptor Patched1 (PTCH1) in primary cilia, causing its inactivation and delocalization from cilia. At the same time, the transmembrane protein Smoothened (SMO) is released of its inhibition by PTCH1 and accumulates in cilia. We used advanced, single molecule-based microscopy to investigate these processes in live cells. As previously observed for SMO, PTCH1 molecules in cilia predominantly move by diffusion and less frequently by directional transport, and spend a fraction of time confined. After treatment with SHH we observed two major changes in the motional dynamics of PTCH1 in cilia. First, PTCH1 molecules spend more time as confined, and less time freely diffusing. This result could be mimicked by a depletion of cholesterol from cells. Second, after treatment with SHH, but not after cholesterol depletion, the molecules that remain in the diffusive state showed a significant increase in the diffusion coefficient. Therefore, PTCH1 inactivation by SHH changes the diffusive motion of PTCH1, possibly by modifying the membrane microenvironment in which PTCH1 resides.

scholarly journals Phase-Separated Transcriptional Condensates Accelerate Target-Search Process Revealed by Live-Cell Single-Molecule Imaging

Cell Reports ◽  
2020 ◽  
Vol 33 (2) ◽  
pp. 108248 ◽  
Author(s):  
Samantha Kent ◽  
Kyle Brown ◽  
Chou-hsun Yang ◽  
Njood Alsaihati ◽  
Christina Tian ◽  
...  
Keyword(s):  
Single Molecule ◽  
Live Cell ◽  
Search Process ◽  
Single Molecule Imaging ◽  
Target Search

scholarly journals Parallel, linear, and subnanometric 3D tracking of microparticles with Stereo Darkfield Interferometry

2021 ◽  
Vol 7 (6) ◽  
pp. eabe3902
Author(s):  
Martin Rieu ◽  
Thibault Vieille ◽  
Gaël Radou ◽  
Raphaël Jeanneret ◽  
Nadia Ruiz-Gutierrez ◽  
...  
Keyword(s):  
High Precision ◽  
High Throughput ◽  
Single Molecule ◽  
Particle Tracking ◽  
Focal Plane ◽  
Tracking System ◽  
Three Dimensional ◽  
3D Tracking ◽  
Single Molecule Force Spectroscopy ◽  
A New Technique

While crucial for force spectroscopists and microbiologists, three-dimensional (3D) particle tracking suffers from either poor precision, complex calibration, or the need of expensive hardware, preventing its massive adoption. We introduce a new technique, based on a simple piece of cardboard inserted in the objective focal plane, that enables simple 3D tracking of dilute microparticles while offering subnanometer frame-to-frame precision in all directions. Its linearity alleviates calibration procedures, while the interferometric pattern enhances precision. We illustrate its utility in single-molecule force spectroscopy and single-algae motility analysis. As with any technique based on back focal plane engineering, it may be directly embedded in a commercial objective, providing a means to convert any preexisting optical setup in a 3D tracking system. Thanks to its precision, its simplicity, and its versatility, we envision that the technique has the potential to enhance the spreading of high-precision and high-throughput 3D tracking.

scholarly journals Synthesis, Crystal Structure, and Properties of a New Coordination Polymer Built from N/O-Donor Mixed Ligands

Crystals ◽  
2018 ◽  
Vol 8 (10) ◽  
pp. 372
Author(s):  
Mei-An Zhu ◽  
Shuai-Shuai Han ◽  
Feng Deng ◽  
Jia-Le Li ◽  
Shui-Sheng Chen
Keyword(s):  
Coordination Polymer ◽  
Weak Interactions ◽  
Three Dimensional ◽  
Luminescent Properties ◽  
Tridentate Ligand ◽  
Supramolecular Polymer ◽  
X Ray Diffraction ◽  
X Ray ◽  
Mixed Ligands ◽  
Benzenedicarboxylic Acid

The coordination polymer, namely, [Cd(H2L)(nobda)]n (1) was prepared by the reaction of Cd(NO3)2·4H2O with 4-amino-1,2-benzenedicarboxylic acid (H2nobda) and 1,4-di(1H-imidazol-4-yl)benzene (H2L), and characterized by single-crystal X-ray diffraction, elemental analysis, infrared (IR) spectroscopy, thermogravimetric analysis, and powder X-ray diffraction (PXRD). The carboxylic acid of H2nobda ligands was completely deprotonated to be nobda2− anions, which act as tridentate ligand to connect the Cd2+ to form two-dimensional (2D) network, while the neutral H2L ligands serve as a linear didentate bridge to connect two adjacent Cd2+ ions upper and down the 2D layer. The adjacent 2D layers were further linked into the three-dimensional (3D) supramolecular polymer by the weak interactions such as hydrogen bonds and π−π stacking interactions. The ultraviolet-visible (UV-vis) absorption spectra and luminescent properties in the solid state at room temperature have been investigated.

scholarly journals 3D DNA structural barcode copying and random access

2020 ◽  
Author(s):  
Filip Bošković ◽  
Alexander Ohmann ◽  
Ulrich F. Keyser ◽  
Kaikai Chen
Keyword(s):  
Data Storage ◽  
Single Molecule ◽  
Self Assembly ◽  
Large Scale ◽  
Three Dimensional ◽  
Random Access ◽  
Scale Production ◽  
Digital Information ◽  
Dna Nanostructures ◽  
Large Scale Production

AbstractThree-dimensional (3D) DNA nanostructures built via DNA self-assembly have established recent applications in multiplexed biosensing and storing digital information. However, a key challenge is that 3D DNA structures are not easily copied which is of vital importance for their large-scale production and for access to desired molecules by target-specific amplification. Here, we build 3D DNA structural barcodes and demonstrate the copying and random access of the barcodes from a library of molecules using a modified polymerase chain reaction (PCR). The 3D barcodes were assembled by annealing a single-stranded DNA scaffold with complementary short oligonucleotides containing 3D protrusions at defined locations. DNA nicks in these structures are ligated to facilitate barcode copying using PCR. To randomly access a target from a library of barcodes, we employ a non-complementary end in the DNA construct that serves as a barcode-specific primer template. Readout of the 3D DNA structural barcodes was performed with nanopore measurements. Our study provides a roadmap for convenient production of large quantities of self-assembled 3D DNA nanostructures. In addition, this strategy offers access to specific targets, a crucial capability for multiplexed single-molecule sensing and for DNA data storage.

scholarly journals Comparative analysis of the coordinated motion of Hsp70s from different organelles observed by single-molecule three-color FRET

2021 ◽  
Vol 118 (33) ◽  
pp. e2025578118
Author(s):  
Lena Voith von Voithenberg ◽  
Anders Barth ◽  
Vanessa Trauschke ◽  
Benjamin Demarco ◽  
Swati Tyagi ◽  
...  
Keyword(s):  
Single Molecule ◽  
Structural Changes ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Conformational Space ◽  
Distribution Analysis ◽  
Nucleotide Exchange ◽  
Nucleotide Analogs ◽  
Recognition Mechanism ◽  
Substrate Peptide

Cellular function depends on the correct folding of proteins inside the cell. Heat-shock proteins 70 (Hsp70s), being among the first molecular chaperones binding to nascently translated proteins, aid in protein folding and transport. They undergo large, coordinated intra- and interdomain structural rearrangements mediated by allosteric interactions. Here, we applied a three-color single-molecule Förster resonance energy transfer (FRET) combined with three-color photon distribution analysis to compare the conformational cycle of the Hsp70 chaperones DnaK, Ssc1, and BiP. By capturing three distances simultaneously, we can identify coordinated structural changes during the functional cycle. Besides the known conformations of the Hsp70s with docked domains and open lid and undocked domains with closed lid, we observed additional intermediate conformations and distance broadening, suggesting flexibility of the Hsp70s in adopting the states in a coordinated fashion. Interestingly, the difference of this distance broadening varied between DnaK, Ssc1, and BiP. Study of their conformational cycle in the presence of substrate peptide and nucleotide exchange factors strengthened the observation of additional conformational intermediates, with BiP showing coordinated changes more clearly compared to DnaK and Ssc1. Additionally, DnaK and BiP were found to differ in their selectivity for nucleotide analogs, suggesting variability in the recognition mechanism of their nucleotide-binding domains for the different nucleotides. By using three-color FRET, we overcome the limitations of the usual single-distance approach in single-molecule FRET, allowing us to characterize the conformational space of proteins in higher detail.

scholarly journals Mechanochemical Synthesis of a Mercury(II) Metal-Organic Framework Reveals a Two-Dimensional Polymorph Stabilized by Weak Interactions

2019 ◽  
Author(s):  
Isaiah R. Speight ◽  
Igor Huskić ◽  
Mihails Arhangelskis ◽  
Hatem M. Titi ◽  
Robin Stein ◽  
...  
Keyword(s):  
Density Functional ◽  
Weak Interactions ◽  
Metal Organic Framework ◽  
Three Dimensional ◽  
Density Functional Theory Calculations ◽  
Dimensional Structure ◽  
Reaction Monitoring ◽  
Two Dimensional ◽  
Functional Theory ◽  
Metal Organic

Solid-state mechanochemistry revealed a novel polymorph of the mercury(II) imidazolate framework, based on square-grid (sql) topology layers. Reaction monitoring and periodic density functional theory calculations show that the sql-structure is of higher stability than the previously reported three-dimensional structure, with the unexpected stabilization of a lower dimensionality structure explained by contributions of weak interactions, which include short C-H···Hg contacts.

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