Sequence Specific Force Curves Measured by Mechanically Opening the DNA Double Helix

1997 ◽  
Vol 489 ◽  
Author(s):  
U. Bockelmann ◽  
B. Essevaz-Roulet ◽  
F. Heslot
Keyword(s):  
Single Molecule ◽  
Double Helix ◽  
Force Sensor ◽  
Optical Microscope ◽  
Microscope Slide ◽  
Characteristic Variation ◽  
Force Curves ◽  
Dna Double Helix ◽  
Glass Microscope Slide ◽  
Glass Microscope

AbstractUsing techniques of molecular biology, we have designed a molecular construction which allows to attach the two complementary strands of one end of a single molecule of bacteriophage λ DNA separately to a glass microscope slide and a microscopic bead. A soft microneedle acting as a force sensor is chemically attached to the bead and its deflection is measured by an optical microscope. Keeping the base of the force lever fixed, the glass slide is displaced slowly, leading to a progressive opening of the double helix. The force measured during the opening process shows a characteristic variation which is related to the sequence of the bases along the DNA molecule. We present a brief summary of the present state of our work.

Hole Formation in Gold Films

1972 ◽  
Vol 30 ◽  
pp. 510-511
Author(s):  
R. W. Vook ◽  
R. Cook ◽  
R. Ziemer
Keyword(s):  
Deposition Rate ◽  
Quartz Crystal ◽  
Evaporation Rate ◽  
Gold Films ◽  
Hole Density ◽  
Hole Formation ◽  
Microscope Slide ◽  
Crystal Film ◽  
Glass Microscope Slide ◽  
Glass Microscope

During recent experiments on Au films, a qualitative correlation between hole formation and deposition rate was observed. These early studies were concerned with films 80 to 1000A thick deposited on glass at -185°C and annealed at 170°C. In the present studies this earlier work was made quantitative. Deposition rates varying between 5 and 700 A/min were used. The effects of deposition rate on hole density for two films 300 and 700A thick were investigated.Au was evaporated from an outgassed W filament located 10 cm from a glass microscope slide substrate and a quartz crystal film thickness monitor. A shutter separating the filament from the substrate and monitor made it possible to obtain a constant evaporation rate before initiating deposition. The pressure was reduced to less than 1 x 10-6 torr prior to cooling the substrate with liquid nitrogen. The substrate was cooled in 15 minutes during which the pressure continued to drop to the mid 10-7 torr range, where deposition was begun.

Droplet Spray Ionization from a Glass Microscope Slide: Real-Time Monitoring of Ethylene Polymerization

2015 ◽  
Vol 87 (16) ◽  
pp. 8057-8062 ◽  
Author(s):  
Jie Jiang ◽  
Hong Zhang ◽  
Ming Li ◽  
Maria T. Dulay ◽  
Andrew J. Ingram ◽  
...  
Keyword(s):  
Real Time ◽  
Ethylene Polymerization ◽  
Real Time Monitoring ◽  
Microscope Slide ◽  
Droplet Spray ◽  
Glass Microscope Slide ◽  
Glass Microscope

Planar Waveguide Genetic Assay Readout Device

2003 ◽  
Author(s):  
David R. Wulfman ◽  
Tracey L. Baas ◽  
Ronald C. McGlennen
Keyword(s):  
Planar Waveguide ◽  
Effective Means ◽  
Glass Slide ◽  
Microscope Slide ◽  
Excitation Light ◽  
Fluorescent Intensity ◽  
Sensing System ◽  
Glass Microscope Slide ◽  
Glass Microscope ◽  
Genetic Assay

A planar waveguide (PWG) device has been developed for the detection of fluorescently labeled nucleic acid sequences immobilized or hybridized to the surface of a planar waveguide. Unlike current technologies requiring image gathering and reading capabilities or specially textured waveguide surfaces, this instrument uses simple glass slide based arrays, providing a numerical output in proportion to the fluorescent intensity recorded. The system consists of an optical waveguide (a glass microscope slide), an excitation light source, a photo detector, filters for select fluorescent emissions and the positioning array cassette. A data analysis algorithm is presented for interpretation of two dimensionally organized arrays. Based on our experimental evaluations we conclude that this sensing system shows promise as a simple and effective means to read fluorescent microarrays.

Direct Single-Molecule Observations of Local Denaturation of a DNA Double Helix under a Negative Supercoil State

2015 ◽  
Vol 87 (6) ◽  
pp. 3490-3497 ◽  
Author(s):  
Shunsuke Takahashi ◽  
Shinya Motooka ◽  
Tomohiro Usui ◽  
Shohei Kawasaki ◽  
Hidefumi Miyata ◽  
...  
Keyword(s):  
Single Molecule ◽  
Double Helix ◽  
Dna Double Helix

scholarly journals Mechanism of RPA-Facilitated Processive DNA Unwinding by the Eukaryotic CMG Helicase

2019 ◽  
Author(s):  
Hazal B. Kose ◽  
Sherry Xie ◽  
George Cameron ◽  
Melania S. Strycharska ◽  
Hasan Yardimci
Keyword(s):  
Single Molecule ◽  
Replication Fork ◽  
Double Helix ◽  
Dna Unwinding ◽  
Helicase Activity ◽  
Replicative Helicase ◽  
Double Stranded Dna ◽  
Order Of Magnitude ◽  
Dna Strand ◽  
Dna Double Helix

AbstractThe DNA double helix is unwound by the Cdc45/Mcm2-7/GINS (CMG) complex at the eukaryotic replication fork. While isolated CMG unwinds duplex DNA very slowly, its fork unwinding rate is stimulated by an order of magnitude by single-stranded DNA binding protein, RPA. However, the molecular mechanism by which RPA enhances CMG helicase activity remained elusive. Here, we demonstrate that engagement of CMG with parental double-stranded DNA (dsDNA) at the replication fork impairs its helicase activity, explaining the slow DNA unwinding by isolated CMG. Using single-molecule and ensemble biochemistry, we show that binding of RPA to the excluded DNA strand prevents duplex engagement by the helicase and speeds up CMG-mediated DNA unwinding. When stalled due to dsDNA interaction, DNA rezipping-induced helicase backtracking re-establishes productive helicase-fork engagement underscoring the significance of plasticity in helicase action. Together, our results elucidate the dynamics of CMG at the replication fork and reveal how other replisome components can mediate proper DNA engagement by the replicative helicase to achieve efficient fork progression.

Bulk and Single-Molecule Fluorescence Studies of the Saturation of the DNA Double Helix Using YOYO-3 Intercalator Dye

2012 ◽  
Vol 116 (38) ◽  
pp. 11561-11569 ◽  
Author(s):  
Sergio G. Lopez ◽  
Maria J. Ruedas-Rama ◽  
Salvador Casares ◽  
Jose M. Alvarez-Pez ◽  
Angel Orte
Keyword(s):  
Single Molecule ◽  
Double Helix ◽  
Single Molecule Fluorescence ◽  
Fluorescence Studies ◽  
Dna Double Helix

Stretched, Twisted, Supercoiled and Braided DNA

1996 ◽  
Vol 463 ◽  
Author(s):  
John F. Marko
Keyword(s):  
Single Molecule ◽  
Double Helix ◽  
Persistence Length ◽  
Thermal Fluctuations ◽  
Internal Dynamics ◽  
Flexible Polymer ◽  
Bending Elasticity ◽  
Polymer Elasticity ◽  
Dna Double Helix ◽  
Semi Flexible Polymer

ABSTRACTThe DNA double helix is a semi-flexible polymer with twist rigidity. Its bending elasticity gives rise to entropie polymer elasticity, which can be precisely studied in single-molecule experiments. DNA's twist rigidity causes it to wrap around itself, or ‘supercoil’, when it is sufficiently twisted; thermal fluctuations destabilize supercoiling for DNAs twisted fewer than once per twist persistence length. Twisted DNAs under tension, braided DNAs, and the internal dynamics of supercoiled DNAs are discussed. The interplay between braiding and supercoiling free energy is argued to be important for the decatenation of duplicated DNAs in prokaryote cells.

scholarly journals II.—Nathorst's use of Collodion Imprints in the Study of Fossil Plants

1907 ◽  
Vol 4 (10) ◽  
pp. 437-440 ◽  
Author(s):  
F. A. Bathee
Keyword(s):  
Thin Film ◽  
Fossil Plants ◽  
Microscope Slide ◽  
Cover Slip ◽  
Sharp Knife ◽  
Glass Microscope Slide ◽  
Glass Microscope

The following note is based on two papers by Professor A. G. Nathorst and on further details which he has kindly communicated by letter. For the loan of the block (Fig. 1) thanks are due to Dr. H. Munthe, Secretary of Geologiska Föreningen i Stockholm.By the term ‘collodion imprint’ is meant the impression of any surface on a thin film of collodion. Such an impression is obtained by letting a drop or two of collodion dissolved in ether fall on the surface to be copied. The ether evaporates rapidly, so that in two or three minutes the film is hard. If it does not of its own accord come loose at the corners, it is easily raised by a needle or sharp knife. It is then lifted on to a glass microscope-slide and preserved dry under a cover-slip held in position by gummed strips of paper or by Canada balsam. When the imprint is very sharp, the film can, if desired, be preserved in glycerine-jelly without its distinctness being greatly affected. Some films may be less successful than others, and some may curl too much, so that it is as well to take more than one imprint. In any case it is advisable to throw away the first made, since it usually retains some dust from the surface of the object, whereas following films will be free from this. If the collodion solution is too thick it may be thinned by the addition of ether or of ether and alcohol.

A non-fatal method of sex determination for patellacean gastropods

1979 ◽  
Vol 59 (3) ◽  
pp. 803-803 ◽  
Author(s):  
W. G. Wright ◽  
D. R. lindberg
Keyword(s):  
Body Wall ◽  
The Body ◽  
Hypodermic Needle ◽  
Microscope Slide ◽  
Posterior Portion ◽  
Sudden Decrease ◽  
Reproductive Cycles ◽  
Glass Microscope Slide ◽  
Glass Microscope

During our studies of the reproductive cycles in limpets (family Acmaeidae) we have been confronted by the lack of a method to determine sex without killing the animals. Previous studies have relied upon dissection or histological sectioning to determine sex. This note describes a technique which allows the determination of sex in patellacean limpets without killing the animal.The tools needed are a syringe (1 cc) with a hypodermic needle (we have found that a 26 gauge, 16 mm needle works well with specimens larger than 10 mm in length), and a glass microscope slide. After removing the limpet from the substratum the shell is held with the aperture down. As the animal extends its foot downward it exposes and stretches the sides of the body wall. When the posterior portion of the body wall is fully exposed the needle is inserted approximately one third of the way up the body wall towards the shell attachment muscle. The orientation of the needle should be in line with the plane of the aperture. Penetration of the gonad can be felt by a ‘breaking through’ or sudden decrease in resistance to the progress of the needle. Care should be taken to avoid penetrating further than necessary because other organs can be easily damaged. Drawing the sample requires more force and time (approximately 10 s) than one would expect. When withdrawing the needle constant tension on the syringe plunger is necessary to keep the sample in the needle. The contents of the needle are then emptied on to the glass slide.

scholarly journals The Dip-Slide: a modified dip-inoculum transport medium for the laboratory diagnosis of infections of the urinary tract

1967 ◽  
Vol 65 (3) ◽  
pp. 367-371 ◽  
Author(s):  
G. R. E. Naylor ◽  
Dennis Guttmann
Keyword(s):  
General Practice ◽  
Urinary Tract ◽  
Laboratory Diagnosis ◽  
Microscope Slide ◽  
Bacterial Concentration ◽  
Tract Infections ◽  
Urine Specimens ◽  
Glass Microscope Slide ◽  
Glass Microscope ◽  
Fresh Urine

The dip-slide, consisting of a glass microscope slide coated with nutrient medium and inoculated by dipping in freshly voided urine, provides a simple measure of the bacterial concentration in fresh urine. This is a useful supplement to the usual microscopy and culture of urine in the diagnosis of urinary tract infections in general practice, when specimens cannot be delivered to a laboratory within several hours of collection, particularly when urine specimens have to travel by post. Dip-slides are also useful as the sole test in screening for symptomless bacteriuria.

Sign in / Sign up

Export Citation Format

Share Document