Fabrication of a new substrate for atomic force microscopic observation of DNA molecules from an ultrasmooth sapphire plate.

Abstract:

:A new stable substrate applicable to the observation of DNA molecules by atomic force microscopy (AFM) was fabricated from a ultrasmooth sapphire (alpha-Al2O3 single crystal) plate. The atomically ultrasmooth sapphire as obtained by high-temperature annealing has hydrophobic surfaces and could not be used for the AFM observation of DNA. However, sapphire treated with Na3PO4 aqueous solution exhibited a hydrophilic character while maintaining a smooth surface structure. The surface of the wet-treated sapphire was found by x-ray photoelectron spectroscopy and AFM to be approximately 0.3 nm. The hydrophilic surface character of the ultrasmooth sapphire plate made it easy for DNA molecules to adhere to the plate. Circular molecules of the plasmid DNA could be imaged by AFM on the hydrophilic ultrasmooth sapphire plate.

journal_name

Biophys J

journal_title

Biophysical journal

authors

Yoshida K,Yoshimoto M,Sasaki K,Ohnishi T,Ushiki T,Hitomi J,Yamamoto S,Sigeno M

doi

10.1016/S0006-3495(98)77878-6

subject

Has Abstract

pub_date

1998-04-01 00:00:00

pages

1654-7

issue

4

eissn

0006-3495

issn

1542-0086

pii

S0006-3495(98)77878-6

journal_volume

74

pub_type

杂志文章
  • Cholesterol effects on the phosphatidylcholine bilayer nonpolar region: a molecular simulation study.

    abstract::A 15-ns molecular dynamics (MD) simulation of the fully hydrated dimyristoylphosphatidylcholine-cholesterol (DMPC-Chol) bilayer in the liquid-crystalline state was carried out to investigate the effect of Chol on the hydrocarbon chain region of the bilayer. The last 8-ns fragment of the generated trajectory was used f...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(01)75867-5

    authors: Róg T,Pasenkiewicz-Gierula M

    更新日期:2001-10-01 00:00:00

  • Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy.

    abstract::Cryo-electron microscopy is rapidly emerging as a powerful technique to determine the structures of complex macromolecular systems elusive to other techniques. Because many of these systems are highly dynamical, characterizing their movements is also a crucial step to unravel their biological functions. To achieve thi...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2018.02.028

    authors: Bonomi M,Pellarin R,Vendruscolo M

    更新日期:2018-04-10 00:00:00

  • Phase-lifetime spectroscopy of photocycle processes: proton release and uptake kinetics of purple membrane.

    abstract::Phase-lifetime spectroscopy was used to measure the kinetics of light-driven proton transients and M intermediate decay of purple membrane. The kinetics were measured in distilled water and in 0.4 M KCl over the pH range of 5.3-8.8. The low ionic strength data showed results that were comparable to previous data. The ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(88)83077-7

    authors: Sinton MH,Dewey TG

    更新日期:1988-02-01 00:00:00

  • On the possibility of nonthermal biological effects of pulsed electromagnetic radiation.

    abstract::Two mechanisms for the interaction of alternating electrical fields with biological tissue are the development of heat, via i(2)R losses, and field-induced force effects, via differences in passive electrical properties. It has been shown that for continuous wave (CW) fields in media of physiologic electrical conducti...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(70)86346-9

    authors: Sher LD,Kresch E,Schwan HP

    更新日期:1970-10-01 00:00:00

  • Laser-Activated Polymeric Microcapsules for Ultrasound Imaging and Therapy: In Vitro Feasibility.

    abstract::Polymeric microcapsules with a light-absorbing dye incorporated in their shell can generate vapor microbubbles that can be spatiotemporally controlled by pulsed laser irradiation. These contrast agents of 6-8 μm in diameter can circulate through the vasculature, offering possibilities for ultrasound (molecular) imagin...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2017.03.033

    authors: Lajoinie G,van Rooij T,Skachkov I,Blazejewski E,Veldhuis G,de Jong N,Kooiman K,Versluis M

    更新日期:2017-05-09 00:00:00

  • The equation of motion for sperm flagella.

    abstract::The equation of motion for sperm flagella, in which the elastic bending moment and the active contractile moment are balanced by the moment from the viscous resistance of the surrounding fluid, is solved for a wave solution that superimposes partial solutions. Substitution of the expression for the wave solution into ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(78)85442-3

    authors: Rikmenspoel R

    更新日期:1978-08-01 00:00:00

  • A mathematical description of miniature postsynaptic current generation at central nervous system synapses.

    abstract::Variation in the amplitude of miniature postsynaptic currents (mPSCs) generated by individual quanta of neurotransmitter is a major contributor to the variance of evoked synaptic responses. Here we explore the possible origins of this variability by developing a mathematical description of mPSC generation and consider...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(96)79325-6

    authors: Uteshev VV,Pennefather PS

    更新日期:1996-09-01 00:00:00

  • Direct visualization of the action of Triton X-100 on giant vesicles of erythrocyte membrane lipids.

    abstract::The raft hypothesis proposes that microdomains enriched in sphingolipids, cholesterol, and specific proteins are transiently formed to accomplish important cellular tasks. Equivocally, detergent-resistant membranes were initially assumed to be identical to membrane rafts, because of similarities between their composit...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2014.04.039

    authors: Casadei BR,Domingues CC,de Paula E,Riske KA

    更新日期:2014-06-03 00:00:00

  • Computer modelling of glycolipids at membrane surfaces.

    abstract::Interactions of membrane anchored molecules such as glycolipids with a membrane surface are important in determining headgroup conformation. It is therefore essential to represent these membrane surface interactions in molecular modeling studies of glycolipids and other membrane bound molecules. We introduce here an e...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(92)81729-0

    authors: Ram P,Kim E,Thomson DS,Howard KP,Prestegard JH

    更新日期:1992-12-01 00:00:00

  • Theoretical analysis of membrane tension in moving cells.

    abstract::Lateral tension in cell plasma membranes plays an essential role in regulation of a number of membrane-related intracellular processes and cell motion. Understanding the physical factors generating the lateral tension and quantitative determination of the tension distribution along the cell membrane is an emerging top...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2013.11.009

    authors: Schweitzer Y,Lieber AD,Keren K,Kozlov MM

    更新日期:2014-01-07 00:00:00

  • Diffraction rings obtained from a suspension of skeletal myofibrils by laser light illumination. Study of internal structure of sarcomeres.

    abstract::Diffraction rings corresponding to the first, second, and third order were obtained by laser light illumination from a suspension of rabbit glycerinated psoas myofibrils (diameter, 1-2 microns; average length of the straight region, 44 microns; average sarcomere length, 2.2-2.6 microns) of which the optical thickness ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(89)82759-6

    authors: Ishiwata S,Okamura N

    更新日期:1989-12-01 00:00:00

  • Stoichiometry and apparent dissociation constant of the calcium-arsenazo III reaction under physiological conditions.

    abstract::In vitro and in situ tests have been run to characterize the reaction of the mettalochromic indicator, arsenazo III, with calcium. Job plots as well as plots of indicator absorbance vs. [Ca2+] at different indicator concentrations show a 1:1 reaction stoichiometry. Equilibrium analysis and analysis using Adair's equat...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(80)85025-9

    authors: Ahmed Z,Kragie L,Connor JA

    更新日期:1980-12-01 00:00:00

  • Nonstationary fluctuation analysis of the delayed rectifier K channel in cardiac Purkinje fibers. Actions of norepinephrine on single-channel current.

    abstract::We have studied the large increase in macroscopic potassium channel current caused by catecholamines in mammalian cardiac cells. An increase in macroscopic K current could result from either an increase in the single-channel current or by an increase in the number of channels that are open. Therefore, we have measured...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(89)82872-3

    authors: Bennett PB,Kass R,Begenisich T

    更新日期:1989-04-01 00:00:00

  • Systematic size study of an insect antifreeze protein and its interaction with ice.

    abstract::Because of their remarkable ability to depress the freezing point of aqueous solutions, antifreeze proteins (AFPs) play a critical role in helping many organisms survive subzero temperatures. The beta-helical insect AFP structures solved to date, consisting of multiple repeating circular loops or coils, are perhaps th...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.104.051169

    authors: Liu K,Jia Z,Chen G,Tung C,Liu R

    更新日期:2005-02-01 00:00:00

  • Swelling of skinned muscle fibers of the frog. Experimental observations.

    abstract::Frog skeletal muscle fibers, mechanically skinned under water-saturated silicone oil, swell upon transfer to aqueous relaxing medium (60 mM KCl; 3 mM MgCl(2); 3 mM ATP; 4 mM EGTA; 20 mM Tris maleate; pH = 7.0; ionic strength 0.15 M). Their cross-sectional areas, estimated with an elliptical approximation, increase 2.3...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(77)85573-2

    authors: Godt RE,Maughan DW

    更新日期:1977-08-01 00:00:00

  • Effects of hydrophobic surfactant proteins on collapse of pulmonary surfactant monolayers.

    abstract::To determine if hydrophobic surfactant proteins affect the stability of pulmonary surfactant monolayers at an air/water interface, the studies reported here compared the kinetics of collapse for the complete set of lipids in calf surfactant with and without the proteins. Monomolecular films spread at the surface of ca...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.107.111823

    authors: Lhert F,Yan W,Biswas SC,Hall SB

    更新日期:2007-12-15 00:00:00

  • Bending free energy from simulation: correspondence of planar and inverse hexagonal lipid phases.

    abstract::Simulations of two distinct systems, one a planar bilayer, the other the inverse hexagonal phase, indicate consistent mechanical properties and curvature preferences, with single DOPE leaflets having a spontaneous curvature, R0 = -26 Å (experimentally ~ -29.2 Å) and DOPC leaflets preferring to be approximately flat (R...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2013.03.048

    authors: Sodt AJ,Pastor RW

    更新日期:2013-05-21 00:00:00

  • Protein-induced membrane curvature investigated through molecular dynamics flexible fitting.

    abstract::In the photosynthetic purple bacterium Rhodobacter (Rba.) sphaeroides, light is absorbed by membrane-bound light-harvesting (LH) proteins LH1 and LH2. LH1 directly surrounds the reaction center (RC) and, together with PufX, forms a dimeric (RC-LH1-PufX)2 protein complex. In LH2-deficient Rba. sphaeroides mutants, RC-L...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2009.04.031

    authors: Hsin J,Gumbart J,Trabuco LG,Villa E,Qian P,Hunter CN,Schulten K

    更新日期:2009-07-08 00:00:00

  • Kinetics and thermodynamics of association of a phospholipid derivative with lipid bilayers in liquid-disordered and liquid-ordered phases.

    abstract::We have measured the rates of insertion into, desorption from, and spontaneous interlayer translocation (flip-flop) in liquid-disordered and liquid-ordered phase lipid bilayer membranes, of the fluorescent phospholipid derivative NBD-dimyristoylphosphatidyl ethanolamine. This study made use of a recently described met...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.104.040576

    authors: Abreu MS,Moreno MJ,Vaz WL

    更新日期:2004-07-01 00:00:00

  • Macromolecular assemblies of myosin.

    abstract::The self-assembly of myosin into filamentous structures is a highly cooperative and rapid process. Nevertheless, the presence of nonequivalent bonding interactions within the filament permits differential stabilization of several macromolecular assemblies of myosin under well-controlled ionic conditions in citrate/Tri...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(86)83646-3

    authors: Reisler E,Cheung P,Borochov N

    更新日期:1986-01-01 00:00:00

  • Flexibility of ras lipid modifications studied by 2H solid-state NMR and molecular dynamics simulations.

    abstract::Human posttranslationally modified N-ras oncogenes are known to be implicated in numerous human cancers. Here, we applied a combination of experimental and computational techniques to determine structural and dynamical details of the lipid chain modifications of an N-ras heptapeptide in 1,2-dimyristoyl-sn-glycero-3-ph...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.107.104562

    authors: Vogel A,Tan KT,Waldmann H,Feller SE,Brown MF,Huster D

    更新日期:2007-10-15 00:00:00

  • Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness.

    abstract::Two mechanisms have been proposed to account for solute permeation of lipid bilayers. Partitioning into the hydrophobic phase of the bilayer, followed by diffusion, is accepted by many for the permeation of water and other small neutral solutes, but transient pores have also been proposed to account for both water and...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(96)79575-9

    authors: Paula S,Volkov AG,Van Hoek AN,Haines TH,Deamer DW

    更新日期:1996-01-01 00:00:00

  • Refinement of the solution structure of a branched DNA three-way junction.

    abstract::We have refined the structure of the DNA Three-Way Junction complex, TWJ-TC, described in the companion paper by quantitative analysis of two 2D NOESY spectra (mixing times 60 and 200 ms) obtained in D2O solution. NOESY crosspeak intensities extracted from these spectra were used in two kinds of refinement procedure: ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(95)80183-9

    authors: Ouporov IV,Leontis NB

    更新日期:1995-01-01 00:00:00

  • Equilibrium dynamics of spermine-induced plasmid DNA condensation revealed by fluorescence lifetime correlation spectroscopy.

    abstract::The spermine-induced DNA condensation is a first-order phase transition. Here, we apply a novel technique fluorescence lifetime correlation spectroscopy to analyze this transition in a greater detail. We show that the method allows for the observation of the condensed and uncondensed molecules simultaneously based sol...

    journal_title:Biophysical journal

    pub_type: 信件

    doi:10.1529/biophysj.107.122408

    authors: Humpolícková J,Benda A,Sýkora J,Machán R,Kral T,Gasinska B,Enderlein J,Hof M

    更新日期:2008-02-01 00:00:00

  • Asymmetrical membranes and surface tension.

    abstract::The (31)P-nuclear magnetic resonance chemical shift of phosphatidic acid in a membrane is sensitive to the lipid head group packing and can report qualitatively on membrane lateral compression near the aqueous interface. We have used high-resolution (31)P-nuclear magnetic resonance to evaluate the lateral compression ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(02)73915-5

    authors: Traïkia M,Warschawski DE,Lambert O,Rigaud JL,Devaux PF

    更新日期:2002-09-01 00:00:00

  • Quantitative measurement of cAMP concentration using an exchange protein directly activated by a cAMP-based FRET-sensor.

    abstract::Förster resonance energy transfer (FRET)-based biosensors for the quantitative analysis of intracellular signaling, including sensors for monitoring cyclic adenosine monophosphate (cAMP), are of increasing interest. The measurement of the donor/acceptor emission ratio in tandem biosensors excited at the donor excitati...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.107.125666

    authors: Salonikidis PS,Zeug A,Kobe F,Ponimaskin E,Richter DW

    更新日期:2008-12-01 00:00:00

  • Effects of lipid interactions on model vesicle engulfment by alveolar macrophages.

    abstract::The engulfment function of macrophages relies on complex molecular interactions involving both lipids and proteins. In particular, the clearance of apoptotic bodies (efferocytosis) is enabled by externalization on the cell target of phosphatidylserine lipids, which activate receptors on macrophages, suggesting that (l...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2013.12.036

    authors: Justice MJ,Petrusca DN,Rogozea AL,Williams JA,Schweitzer KS,Petrache I,Wassall SR,Petrache HI

    更新日期:2014-02-04 00:00:00

  • Fusion Pore Expansion and Contraction during Catecholamine Release from Endocrine Cells.

    abstract::Amperometry recording reveals the exocytosis of catecholamine from individual vesicles as a sequential process, typically beginning slowly with a prespike foot, accelerating sharply to initiate a spike, reaching a peak, and then decaying. This complex sequence reflects the interplay between diffusion, flux through a f...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2020.06.001

    authors: Jackson MB,Hsiao YT,Chang CW

    更新日期:2020-07-07 00:00:00

  • Interruptions in single strands of the DNA in slime mold and other organisms.

    abstract::The molecular weight of single-stranded DNA from the slime mold Physarum polycephalum has been determined by alkaline gradient centrifugation. The average molecular weight during DNA synthesis ( approximately 1.5 x 10(7) D) is less than that observed in nonsynthetic periods ( approximately 4 x 10(7) D). On the basis o...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(67)86590-1

    authors: McGrath RA,Williams RW

    更新日期:1967-05-01 00:00:00

  • Force microscopy of nonadherent cells: a comparison of leukemia cell deformability.

    abstract::Atomic force microscopy (AFM) has become an important tool for quantifying mechanical properties of biological materials ranging from single molecules to cells and tissues. Current AFM techniques for measuring elastic and viscoelastic properties of whole cells are based on indentation of cells firmly adhered to a subs...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.105.067496

    authors: Rosenbluth MJ,Lam WA,Fletcher DA

    更新日期:2006-04-15 00:00:00