scholarly journals DNA sequence-dependent ionic currents in ultra-small solid-state nanopores

Nanoscale ◽  
2016 ◽  
Vol 8 (18) ◽  
pp. 9600-9613 ◽  
Author(s):  
Jeffrey Comer ◽  
Aleksei Aksimentiev
Keyword(s):  
Solid State ◽  
Dna Sequence ◽  
Ionic Current ◽  
Ionic Currents ◽  
Atomic Resolution ◽  
Sequence Dependent ◽  
Dna Strand

Atomic resolution simulations elucidate the effect of DNA sequence and conformation on the ionic current blockades produced by the presence of a DNA strand in an ultra-small solid-state nanopore.

scholarly journals Progress toward Ultrafast DNA Sequencing Using Solid-State Nanopores

2007 ◽  
Vol 53 (11) ◽  
pp. 1996-2001 ◽  
Author(s):  
Gautam V Soni ◽  
Amit Meller
Keyword(s):  
Solid State ◽  
Dna Sequencing ◽  
Dna Sequence ◽  
Large Scale ◽  
Optical Detection ◽  
Ionic Current ◽  
Molecular Beacons ◽  
Single Nucleotide ◽  
Dual Color ◽  
Target Dna

Abstract Background: Measurements of the ionic current flowing through nanometer-scale pores (nanopores) have been used to analyze single DNA and RNA molecules, with the ultimate goal of achieving ultrafast DNA sequencing. However, attempts at purely electronic measurements have not achieved the signal contrast required for single nucleotide differentiation. In this report we propose a novel method of optical detection of DNA sequence translocating through a nanopore. Methods: Each base of the target DNA sequence is 1st mapped onto a 2-unit code, 2 10-bp nucleotide sequence, by biochemical conversion into Designed DNA Polymers. These 2-unit codes are then hybridized to complementary, fluorescently labeled, and self-quenching molecular beacons. As the molecular beacons are sequentially unzipped during translocation through a <2-nm-wide nanopore, their fluorescent tags are unquenched and are detected by a custom-built dual-color total internal reflection fluorescence (TIRF) microscope. The 2-color optical signal is then correlated to the target DNA sequence. Results: A dual-color TIRFM microscope with single-molecule resolution was constructed, and controlled fabrication of 1-dimensional and 2-dimensional arrays of solid-state nanopores was performed. A nanofluidic cell assembly was constructed for TIRF-based optical detection of voltage-driven DNA translocation through a nanopore. Conclusions: We present a novel nanopore-based DNA sequencing technique that uses an optical readout of DNA translocating unzipping through a nanopore. Our technique offers better single nucleotide differentiation in sequence readout, as well as the possibility of large-scale parallelism using nanopore arrays.

Electric-Field Effects on Reactions Between Oxides

1997 ◽  
Vol 481 ◽  
Author(s):  
Matthew T. Johnson ◽  
Shelley R. Gilliss ◽  
C. Barry Carter
Keyword(s):  
Solid State ◽  
Electric Field ◽  
Elevated Temperatures ◽  
Ionic Current ◽  
Reaction Rates ◽  
Solid State Reactions ◽  
Interfacial Stability ◽  
Electric Field Effects ◽  
Thin Film Diffusion ◽  
Microscopy Techniques

ABSTRACTThin films of In2O3 and Fe2O3 have been deposited on (001) MgO using pulsed-laser deposition (PLD). These thin-film diffusion couples were then reacted in an applied electric field at elevated temperatures. In this type of solid-state reaction, both the reaction rate and the interfacial stability are affected by the transport properties of the reacting ions. The electric field provides a very large external driving force that influences the diffusion of the cations in the constitutive layers. This induced ionic current causes changes in the reaction rates, interfacial stability and distribution of the phases. Through the use of electron microscopy techniques the reaction kinetics and interface morphology have been investigated in these spinel-forming systems, to gain a better understanding of the influence of an electric field on solid-state reactions.

scholarly journals DNA Sequence-dependent Differences in TATA-binding Protein-induced DNA Bending in Solution Are Highly Sensitive to Osmolytes

2001 ◽  
Vol 276 (18) ◽  
pp. 14623-14627 ◽  
Author(s):  
Jiong Wu ◽  
Kay M. Parkhurst ◽  
Robyn M. Powell ◽  
Lawrence J. Parkhurst
Keyword(s):  
Dna Sequence ◽  
Binding Protein ◽  
Dna Bending ◽  
Tata Binding Protein ◽  
Sequence Dependent ◽  
Highly Sensitive

scholarly journals FEI Titan 80-300 TEM

2016 ◽  
Vol 2 ◽  
Author(s):  
Andreas Thust ◽  
Juri Barthel ◽  
Karsten Tillmann
Keyword(s):  
Electron Microscope ◽  
Solid State ◽  
Spherical Aberration ◽  
Atomic Scale ◽  
Atomic Resolution ◽  
Lens System ◽  
Stage Design ◽  
Precise Positioning ◽  
Transmission Electron ◽  
Wide Range

The FEI Titan 80-300 TEM is a high-resolution transmission electron microscope equipped with a field emission gun and a corrector for the spherical aberration (<em>C</em><sub>S</sub>) of the imaging lens system. The instrument is designed for the investigation of a wide range of solid state phenomena taking place on the atomic scale, which requires true atomic resolution capabilities. Under optimum optical settings of the image <em>C</em><sub>S</sub>-corrector (CEOS CETCOR) the point-resolution is extended up to the information limit of well below 100 pm with 200 keV and 300 keV electrons. A special piezo-stage design allows ultra-precise positioning of the specimen in all 3 dimensions. Digital images are acquired with a Gatan 2k x 2k slow-scan charged coupled device camera.

scholarly journals Atomic-resolution structure of cytoskeletal bactofilin by solid-state NMR

2015 ◽  
Vol 1 (11) ◽  
pp. e1501087 ◽  
Author(s):  
Chaowei Shi ◽  
Pascal Fricke ◽  
Lin Lin ◽  
Veniamin Chevelkov ◽  
Melanie Wegstroth ◽  
...  
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
Caulobacter Crescentus ◽  
Heavy Atom ◽  
Cytoskeletal Proteins ◽  
Atomic Resolution ◽  
Hydrophobic Core ◽  
X Ray Crystallography ◽  
Wide Range ◽  
Resolution Structure

Bactofilins are a recently discovered class of cytoskeletal proteins of which no atomic-resolution structure has been reported thus far. The bacterial cytoskeleton plays an essential role in a wide range of processes, including morphogenesis, cell division, and motility. Among the cytoskeletal proteins, the bactofilins are bacteria-specific and do not have a eukaryotic counterpart. The bactofilin BacA of the speciesCaulobacter crescentusis not amenable to study by x-ray crystallography or solution nuclear magnetic resonance (NMR) because of its inherent noncrystallinity and insolubility. We present the atomic structure of BacA calculated from solid-state NMR–derived distance restraints. We show that the core domain of BacA forms a right-handed β helix with six windings and a triangular hydrophobic core. The BacA structure was determined to 1.0 Å precision (heavy-atom root mean square deviation) on the basis of unambiguous restraints derived from four-dimensional (4D) HN-HN and 2D C-C NMR spectra.

scholarly journals Anoctamin 5/TMEM16E facilitates muscle precursor cell fusion

2018 ◽  
Vol 150 (11) ◽  
pp. 1498-1509 ◽  
Author(s):  
Jarred M. Whitlock ◽  
Kuai Yu ◽  
Yuan Yuan Cui ◽  
H. Criss Hartzell
Keyword(s):  
Cell Fusion ◽  
Ionic Current ◽  
Ionic Currents ◽  
Muscle Physiology ◽  
Muscle Repair ◽  
Hek 293 ◽  
293 Cells ◽  
Phospholipid Scrambling ◽  
Muscle Precursor Cell

Limb-girdle muscular dystrophy type 2L (LGMD2L) is a myopathy arising from mutations in ANO5; however, information about the contribution of ANO5 to muscle physiology is lacking. To explain the role of ANO5 in LGMD2L, we previously hypothesized that ANO5-mediated phospholipid scrambling facilitates cell–cell fusion of mononucleated muscle progenitor cells (MPCs), which is required for muscle repair. Here, we show that heterologous overexpression of ANO5 confers Ca2+-dependent phospholipid scrambling to HEK-293 cells and that scrambling is associated with the simultaneous development of a nonselective ionic current. MPCs isolated from adult Ano5−/− mice exhibit defective cell fusion in culture and produce muscle fibers with significantly fewer nuclei compared with controls. This defective fusion is associated with a decrease of Ca2+-dependent phosphatidylserine exposure on the surface of Ano5−/− MPCs and a decrease in the amplitude of Ca2+-dependent outwardly rectifying ionic currents. Viral introduction of ANO5 in Ano5−/− MPCs restores MPC fusion competence, ANO5-dependent phospholipid scrambling, and Ca2+-dependent outwardly rectifying ionic currents. ANO5-rescued MPCs produce myotubes having numbers of nuclei similar to wild-type controls. These data suggest that ANO5-mediated phospholipid scrambling or ionic currents play an important role in muscle repair.

Vacuum‐UV and Low‐Energy Electron‐Induced DNA Strand Breaks – Influence of the DNA Sequence and Substrate

ChemPhysChem ◽  
2019 ◽  
Vol 20 (6) ◽  
pp. 823-830 ◽  
Author(s):  
Stefanie Vogel ◽  
Kenny Ebel ◽  
Robin M. Schürmann ◽  
Christian Heck ◽  
Till Meiling ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dna Strand Breaks ◽  
Low Energy ◽  
Energy Electron ◽  
Strand Breaks ◽  
Low Energy Electron ◽  
Dna Strand ◽  
Vacuum Uv

scholarly journals Differential Inhibitory Actions of Multitargeted Tyrosine Kinase Inhibitors on Different Ionic Current Types in Cardiomyocytes

2020 ◽  
Vol 21 (5) ◽  
pp. 1672 ◽  
Author(s):  
Wei-Ting Chang ◽  
Ping-Yen Liu ◽  
Kaisen Lee ◽  
Yin-Hsun Feng ◽  
Sheng-Nan Wu
Keyword(s):  
Tyrosine Kinase ◽  
Tyrosine Kinase Inhibitors ◽  
Kinase Inhibitors ◽  
Ionic Current ◽  
Small Animal ◽  
Ionic Currents ◽  
Neonatal Rat ◽  
Delayed Rectifier ◽  
Qtc Prolongation ◽  
The Impact

Lapatinib (LAP) and sorafenib (SOR) are multitargeted tyrosine kinase inhibitors (TKIs) with antineoplastic properties. In clinical observations, LAP and SOR may contribute to QTc prolongation, but the detailed mechanism for this has been largely unexplored. In this study, we investigated whether LAP and SOR affect the activities of membrane ion channels. Using a small animal model and primary cardiomyocytes, we studied the impact of LAP and SOR on Na+ and K+ currents. We found that LAP-induced QTc prolongation in mice was reversed by isoproterenol. LAP or SOR suppressed the amplitude of the slowly activating delayed-rectifier K+ current (IK(S)) in H9c2 cells in a time- and concentration-dependent fashion. The LAP-mediated inhibition of IK(S) was reversed by adding isoproterenol or meclofenamic acid, but not by adding diazoxide. The steady-state activation curve of IK(S) during exposure to LAP or SOR was shifted toward a less negative potential, with no change in the gating charge required to activate the current. LAP shortened the recovery from IK(S) deactivation. As rapid repetitive stimuli, the IK(S) amplitude decreased; however; the LAP-induced inhibition of IK(S) remained effective. LAP or SOR alone also suppressed inwardly rectifying K+ and voltage-gated Na+ current in neonatal rat ventricular myocytes. The inhibition of ionic currents during exposure to TKIs could be an important mechanism underlying changes in QTc intervals.

scholarly journals The B cell coactivator Bob1 shows DNA sequence-dependent complex formation with Oct-1/Oct-2 factors, leading to differential promoter activation.

1996 ◽  
Vol 15 (11) ◽  
pp. 2781-2790 ◽  
Author(s):  
M. Gstaiger ◽  
O. Georgiev ◽  
H. van Leeuwen ◽  
P. van der Vliet ◽  
W. Schaffner
Keyword(s):  
Complex Formation ◽  
B Cell ◽  
Dna Sequence ◽  
Promoter Activation ◽  
Sequence Dependent
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