Antagonistic effects of natural osmolyte mixtures and hydrostatic pressure on the conformational dynamics of a DNA hairpin probed at the single-molecule level

2018 ◽  
Vol 20 (19) ◽  
pp. 13159-13170 ◽  
Author(s):  
Satyajit Patra ◽  
Christian Anders ◽  
Paul Hendrik Schummel ◽  
Roland Winter
Keyword(s):  
Hydrostatic Pressure ◽  
Nucleic Acids ◽  
Single Molecule ◽  
Deep Sea ◽  
Conformational Dynamics ◽  
Dna Hairpin ◽  
Antagonistic Effects ◽  
Single Molecule Level

Osmolyte mixtures from deep sea organisms are able to rescue nucleic acids from pressure-induced unfolding.

Ultra-high-density 3D DNA arrays within nanoporous biocompatible membranes for single-molecule-level detection and purification of circulating nucleic acids

Nanoscale ◽  
2015 ◽  
Vol 7 (14) ◽  
pp. 5998-6006 ◽  
Author(s):  
M. Aramesh ◽  
O. Shimoni ◽  
K. Fox ◽  
T. J. Karle ◽  
A. Lohrmann ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Single Molecule ◽  
High Density ◽  
Single Molecule Detection ◽  
Diamond Like Carbon ◽  
Dna Arrays ◽  
Single Molecule Level ◽  
Circulating Nucleic Acids ◽  
Carbon Coated ◽  
Oxide Membranes

Single-molecule-detection, selectivity, broad-range detection and biocompatibility are achieved using nanoporous diamond-like carbon coated oxide membranes.

scholarly journals Nucleic acid-based nanoengineering: novel structures for biomedical applications

2011 ◽  
Vol 1 (5) ◽  
pp. 702-724 ◽  
Author(s):  
Hanying Li ◽  
Thomas H. LaBean ◽  
Kam W. Leong
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Single Molecule ◽  
Biomedical Applications ◽  
Three Dimensional ◽  
Base Pairs ◽  
Single Molecule Level ◽  
Stimulus Responsive ◽  
Bioactive Agents ◽  
Novel Structures

Nanoengineering exploits the interactions of materials at the nanometre scale to create functional nanostructures. It relies on the precise organization of nanomaterials to achieve unique functionality. There are no interactions more elegant than those governing nucleic acids via Watson–Crick base-pairing rules. The infinite combinations of DNA/RNA base pairs and their remarkable molecular recognition capability can give rise to interesting nanostructures that are only limited by our imagination. Over the past years, creative assembly of nucleic acids has fashioned a plethora of two-dimensional and three-dimensional nanostructures with precisely controlled size, shape and spatial functionalization. These nanostructures have been precisely patterned with molecules, proteins and gold nanoparticles for the observation of chemical reactions at the single molecule level, activation of enzymatic cascade and novel modality of photonic detection, respectively. Recently, they have also been engineered to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The future of nucleic acid-based nanoengineering is bright and exciting. In this review, we will discuss the strategies to control the assembly of nucleic acids and highlight the recent efforts to build functional nucleic acid nanodevices for nanomedicine.

Single-molecule insights into the temperature and pressure dependent conformational dynamics of nucleic acids in the presence of crowders and osmolytes

2019 ◽  
Vol 251 ◽  
pp. 106190 ◽  
Author(s):  
Loana Arns ◽  
Jim-Marcel Knop ◽  
Satyajit Patra ◽  
Christian Anders ◽  
Roland Winter
Keyword(s):  
Nucleic Acids ◽  
Single Molecule ◽  
Conformational Dynamics ◽  
Temperature And Pressure

scholarly journals Exploring the effects of cosolutes and crowding on the volumetric and kinetic profile of the conformational dynamics of a poly dA loop DNA hairpin: a single-molecule FRET study

2018 ◽  
Vol 47 (2) ◽  
pp. 981-996 ◽  
Author(s):  
Satyajit Patra ◽  
Vitor Schuabb ◽  
Irena Kiesel ◽  
Jim-Marcel Knop ◽  
Rosario Oliva ◽  
...  
Keyword(s):  
Single Molecule ◽  
Conformational Dynamics ◽  
Dna Hairpin ◽  
Single Molecule Fret ◽  
Kinetic Profile

scholarly journals Conformational Dynamics of a DNA Polymerase At the Single-Molecule Level

2010 ◽  
Vol 98 (3) ◽  
pp. 63a
Author(s):  
Joshua Gill ◽  
David Millar
Keyword(s):  
Dna Polymerase ◽  
Single Molecule ◽  
Conformational Dynamics ◽  
Single Molecule Level

scholarly journals Structural titration of receptor ion channel GLIC gating by HS-AFM

2018 ◽  
Vol 115 (41) ◽  
pp. 10333-10338 ◽  
Author(s):  
Yi Ruan ◽  
Kevin Kao ◽  
Solène Lefebvre ◽  
Arin Marchesi ◽  
Pierre-Jean Corringer ◽  
...  
Keyword(s):  
Ion Channel ◽  
Single Molecule ◽  
Conformational Changes ◽  
Protein Interactions ◽  
High Speed ◽  
Conformational Dynamics ◽  
Protein Protein Interactions ◽  
Ion Conductance ◽  
Single Molecule Level ◽  
Selective Channel

Gloeobacter violaceus ligand-gated ion channel (GLIC), a proton-gated, cation-selective channel, is a prokaryotic homolog of the pentameric Cys-loop receptor ligand-gated ion channel family. Despite large changes in ion conductance, small conformational changes were detected in X-ray structures of detergent-solubilized GLIC at pH 4 (active/desensitized state) and pH 7 (closed state). Here, we used high-speed atomic force microscopy (HS-AFM) combined with a buffer exchange system to perform structural titration experiments to visualize GLIC gating at the single-molecule level under native conditions. Reference-free 2D classification revealed channels in multiple conformational states during pH gating. We find changes of protein–protein interactions so far elusive and conformational dynamics much larger than previously assumed. Asymmetric pentamers populate early stages of activation, which provides evidence for an intermediate preactivated state.

scholarly journals Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy: Concepts and Applications

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2972 ◽  
Author(s):  
Takuhiro Otosu ◽  
Shoichi Yamaguchi
Keyword(s):  
Single Molecule ◽  
Fluorescence Lifetime ◽  
Fluorescence Correlation Spectroscopy ◽  
Conformational Dynamics ◽  
Correlation Spectroscopy ◽  
Two Dimensional ◽  
Single Molecule Level ◽  
Fluorescence Correlation ◽  
Promising Tool ◽  
Molecular Ruler

We review the basic concepts and recent applications of two-dimensional fluorescence lifetime correlation spectroscopy (2D FLCS), which is the extension of fluorescence correlation spectroscopy (FCS) to analyze the correlation of fluorescence lifetime in addition to fluorescence intensity. Fluorescence lifetime is sensitive to the microenvironment and can be a “molecular ruler” when combined with FRET. Utilization of fluorescence lifetime in 2D FLCS thus enables us to quantify the inhomogeneity of the system and the interconversion dynamics among different species with a higher time resolution than other single-molecule techniques. Recent applications of 2D FLCS to various biological systems demonstrate that 2D FLCS is a unique and promising tool to quantitatively analyze the microsecond conformational dynamics of macromolecules at the single-molecule level.

scholarly journals KERA: Analysis Tool for Multi-Process, Multi-State Single-Molecule Data

2021 ◽  
Author(s):  
Joseph Tibbs ◽  
Mohamed Ghoneim ◽  
Colleen C. Caldwell ◽  
Troy Buzynski ◽  
Wayne Bowie ◽  
...  
Keyword(s):  
Single Molecule ◽  
Molecular Interactions ◽  
Conformational Dynamics ◽  
Software Tool ◽  
Underlying Mechanism ◽  
Temporal Organization ◽  
Analysis Tool ◽  
Time Data ◽  
Single Molecule Level ◽  
Complex Architectures

ABSTRACTMolecular machines within cells dynamically assemble, disassemble, and reorganize. Molecular interactions between their components can be observed at the single-molecule level and quantified using colocalization single-molecule spectroscopy (CoSMoS), in which individual labeled molecules are seen transiently associating with a surface-tethered partner, or other total internal reflection fluorescence microscopy (TIRFM) approaches in which the interactions elicit changes in fluorescence in the labeled surface-tethered partner. When multiple interacting partners can form ternary, quaternary and higher order complexes, the types of spatial and temporal organization of these complexes can be deduced from the order of appearance and reorganization of the components. Time evolution of complex architectures can be followed by changes in the fluorescence behavior in multiple channels. Here, we describe the kinetic event resolving algorithm (KERA), a software tool for organizing and sorting the discretized fluorescent trajectories from a range of single-molecule experiments. KERA organizes the data in groups by transition patterns, and displays exhaustive dwell-time data for each interaction sequence. Enumerating and quantifying sequences of molecular interactions provides important information regarding the underlying mechanism of the assembly, dynamics and architecture of the macromolecular complexes. We demonstrate KERA’s utility by analyzing conformational dynamics of two DNA binding proteins: RPA and XPD helicase.

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