scholarly journals Simultaneous detection of small molecules, proteins and microRNAs using single molecule arrays

2020 ◽  
Vol 11 (30) ◽  
pp. 7896-7903 ◽  
Author(s):  
Xu Wang ◽  
David R. Walt
Keyword(s):  
Nucleic Acids ◽  
Small Molecules ◽  
Single Molecule ◽  
Simultaneous Detection ◽  
Multiplexed Detection ◽  
Measurement Methodology

The first example of multiplexed detection of proteins, nucleic acids, and small molecules using single molecule measurement methodology.

scholarly journals Shining a Spotlight on DNA: Single-Molecule Methods to Visualise DNA

Molecules ◽  
2019 ◽  
Vol 24 (3) ◽  
pp. 491 ◽  
Author(s):  
Gurleen Kaur ◽  
Jacob Lewis ◽  
Antoine van Oijen
Keyword(s):  
Mechanical Properties ◽  
Nucleic Acids ◽  
Small Molecules ◽  
Single Molecule ◽  
Single Molecules ◽  
Dna Molecules ◽  
Dna Interactions ◽  
Biochemical Reactions ◽  
Imaging Methods ◽  
Protein Dna Interactions

The ability to watch single molecules of DNA has revolutionised how we study biological transactions concerning nucleic acids. Many strategies have been developed to manipulate DNA molecules to investigate mechanical properties, dynamics and protein–DNA interactions. Imaging methods using small molecules and protein-based probes to visualise DNA have propelled our understanding of complex biochemical reactions involving DNA. This review focuses on summarising some of the methodological developments made to visualise individual DNA molecules and discusses how these probes have been used in single-molecule biophysical assays.

Role of Intercalation on Electrical Properties of Nucleic Acids for use in Molecular Electronics

2021 ◽  
Author(s):  
Hashem Mohammad ◽  
Busra Demir ◽  
Caglanaz Akin ◽  
Binquan Luan ◽  
Joshua Hihath ◽  
...  
Keyword(s):  
Electrical Properties ◽  
Nucleic Acids ◽  
Small Molecules ◽  
Molecular Electronics ◽  
Data Storage ◽  
Single Molecule ◽  
Essential Role ◽  
Transmission Probability ◽  
Electron Transmission

Intercalating ds-DNA/RNA with small molecules can play an essential role in controlling the electron transmission probability for molecular electronics applications such as biosensors, single-molecule transistors, and data storage. However, its...

scholarly journals Ultra-sensitive and rapid detection of nucleic acids and microorganisms in body fluids using single-molecule tethering

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Wen-Chih Cheng ◽  
Troy Horn ◽  
Maya Zayats ◽  
Georges Rizk ◽  
Samuel Major ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Single Molecule ◽  
Clinical Utility ◽  
Simultaneous Detection ◽  
High Sensitivity ◽  
Body Fluids ◽  
Dna Probes ◽  
Molecular Assay ◽  
Colony Forming Unit ◽  
Micron Size

Abstract Detection of microbial nucleic acids in body fluids has become the preferred method for rapid diagnosis of many infectious diseases. However, culture-based diagnostics that are time-consuming remain the gold standard approach in certain cases, such as sepsis. New culture-free methods are urgently needed. Here, we describe Single MOLecule Tethering or SMOLT, an amplification-free and purification-free molecular assay that can detect microorganisms in body fluids with high sensitivity without the need of culturing. The signal of SMOLT is generated by the displacement of micron-size beads tethered by DNA probes that are between 1 and 7 microns long. The molecular extension of thousands of DNA probes is determined with sub-micron precision using a robust and rapid optical approach. We demonstrate that SMOLT can detect nucleic acids directly in blood, urine and sputum at sub-femtomolar concentrations, and microorganisms in blood at 1 CFU mL−1 (colony forming unit per milliliter) threefold faster, with higher multiplexing capacity and with a more straight-forward protocol than amplified methodologies. SMOLT’s clinical utility is further demonstrated by developing a multiplex assay for simultaneous detection of sepsis-causing Candida species directly in whole blood.

scholarly journals Infrared nanospectroscopy reveals the molecular interaction fingerprint of an aggregation inhibitor with single Aβ42 oligomers

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Francesco Simone Ruggeri ◽  
Johnny Habchi ◽  
Sean Chia ◽  
Robert I. Horne ◽  
Michele Vendruscolo ◽  
...  
Keyword(s):  
Small Molecules ◽  
Single Molecule ◽  
Protein Misfolding ◽  
Molecular Mechanisms ◽  
Chemical Sensitivity ◽  
Incomplete Knowledge ◽  
Parkinson’S Diseases ◽  
Aggregation Inhibitor ◽  
Misfolding Diseases

AbstractSignificant efforts have been devoted in the last twenty years to developing compounds that can interfere with the aggregation pathways of proteins related to misfolding disorders, including Alzheimer’s and Parkinson’s diseases. However, no disease-modifying drug has become available for clinical use to date for these conditions. One of the main reasons for this failure is the incomplete knowledge of the molecular mechanisms underlying the process by which small molecules interact with protein aggregates and interfere with their aggregation pathways. Here, we leverage the single molecule morphological and chemical sensitivity of infrared nanospectroscopy to provide the first direct measurement of the structure and interaction between single Aβ42 oligomeric and fibrillar species and an aggregation inhibitor, bexarotene, which is able to prevent Aβ42 aggregation in vitro and reverses its neurotoxicity in cell and animal models of Alzheimer’s disease. Our results demonstrate that the carboxyl group of this compound interacts with Aβ42 aggregates through a single hydrogen bond. These results establish infrared nanospectroscopy as a powerful tool in structure-based drug discovery for protein misfolding diseases.

Structural Insights into the Recognition of DNA Defects by Small Molecules

2021 ◽  
Author(s):  
David Dayanidhi Paul Elisa Sundar ◽  
Vaidyanathan Ganesan
Keyword(s):  
Nucleic Acids ◽  
Metal Complexes ◽  
Small Molecules ◽  
Chemical Properties ◽  
Biological Applications ◽  
Binding Interaction ◽  
Structural Insights

Studies on the binding interaction of small molecules and nucleic acids have been explored for their biological applications. With excellent photophysical/chemical properties, numerous metal complexes have been studied as structural...

scholarly journals Fluorinated molecular beacons as functional DNA nanomolecules for cellular imaging

2017 ◽  
Vol 8 (10) ◽  
pp. 7082-7086 ◽  
Author(s):  
Cheng Jin ◽  
Ting Fu ◽  
Ruowen Wang ◽  
Hui Liu ◽  
Jianmei Zou ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Small Molecules ◽  
Cellular Imaging ◽  
Molecular Beacons ◽  
Functional Dna

Molecular beacons (MBs) are simple, but practical, fluorescent nanoprobes widely used to detect small molecules, nucleic acids and proteins.

Probing Adsorption Configurations of Small Molecules on Surfaces by Single-Molecule Tip-Enhanced Raman Spectroscopy

ChemPhysChem ◽  
2018 ◽  
Vol 20 (1) ◽  
pp. 37-41 ◽  
Author(s):  
Yao Zhang ◽  
Rui Zhang ◽  
Song Jiang ◽  
Yang Zhang ◽  
Zhen-Chao Dong
Keyword(s):  
Raman Spectroscopy ◽  
Small Molecules ◽  
Single Molecule ◽  
Tip Enhanced Raman Spectroscopy

scholarly journals Protocell Arrays for Simultaneous Detection of Diverse Analytes

2021 ◽  
Author(s):  
Yan Zhang ◽  
Taisuke Kojima ◽  
Ge-Ah Kim ◽  
Monica P. McNerney ◽  
Shuichi Takayama ◽  
...  
Keyword(s):  
Small Molecules ◽  
Simultaneous Detection ◽  
Sample Volume ◽  
Free Expression ◽  
Phase System ◽  
Two Phase ◽  
Complex Decision Making ◽  
Multiple Analytes ◽  
Complex Decision ◽  
Analyte Detection

AbstractSimultaneous detection of multiple analytes from a single sample (multiplexing), particularly when at the point of need, can guide complex decision-making without increasing the required sample volume or cost per test. Despite recent advances, multiplexing still typically faces the critical limitation of measuring only one type of molecule per assay platform – for example, only small molecules or only nucleic acids. In this work, we address this bottleneck with a customizable platform that integrates cell-free expression (CFE) with a polymer-based aqueous two-phase system (ATPS) to produce membrane-less “protocells” containing transcription and translation machinery used for analyte detection. Multiple protocells are arrayed in microwells where each protocell droplet performs distinct reactions to detect chemically diverse targets including small molecules, minerals, and nucleic acid sequences, all from the same sample. We demonstrate that these protocell arrays can measure analytes in a human biofluid matrix, maintain function after lyophilization and rehydration, and produce visually interpretable readouts, illustrating its potential for application as a minimal-equipment, field-deployable, multi-analyte detection tool.

scholarly journals Preparation of Mycobacterium smegmatis porin A (MspA) nanopores for single molecule sensing of nucleic acids

2021 ◽  
Vol 7 (5) ◽  
pp. 355-364
Author(s):  
Wang Yuqin ◽  
◽  
Fan Pingping ◽  
Zhang Shanyu ◽  
Yan Shuanghong ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Single Molecule ◽  
Mycobacterium Smegmatis
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