DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning

The overwinding and underwinding of duplex segments between junctions have been used in designing both left-handed and right-handed DNA origami nanostructures. For a variety of DNA tubes obtained from self-assembled tiles, only a theoretical approach of the intrinsic curvature of the DNA tile (specified as the intrinsic tile curvature) has been previously used to explain their formation. Details regarding the quantitative and structural descriptions of the tile curvature and its evolution in DNA tubes by the coupling of the twist of the inter-tile arm (specified as the arm twist) have never been addressed. In this work, we designed three types of tile cores built around a circular 128 nucleotide scaffold by using longitudinal weaving (LW), bridged longitudinal weaving (bLW) and transverse weaving (TW). Joining the tiles with inter-tile arms having the length of an odd number of DNA half-turns (termed O-tiling) almost resulted into planar 2D lattices, whereas joining the tiles with the arms having the length of an even number of DNA half-turns (termed E-tiling) nearly generated tubes. Streptavidin bound to biotin was used as a labeling technique to characterize the inside and outside surfaces of the E-tiling tubes and thereby the conformations of their component tiles with addressable concave and convex curvatures. When the arms have the normal winding at the relaxed B-form of DNA, the intrinsic tile curvature deter-mines the chirality of the E-tiling tubes. By regulating the arm length and the sticky end length of the bLW-Ep/q (E-tiling of the bLW cores with the arm length of p-bp and the sticky end length of q-nt) assemblies, the arm can be overwound, resulting in a left-handed twist, and can also be underwound, resulting in a right-handed twist. Chiral bLW-Ep/q tubes with either a right-handed curvature or a left-handed curvature can also be formed by the coupling of the intrinsic tile curvature and the arm twist. We were able to assign the chiral indices (n,m) to each tube using high-resolution AFM images, and therefore were able to estimate the tile curvature using a regular polygon model that approximated the transverse section of the tube. A deeper understanding of the integrated actions of dif-ferent types of twisting forces on the DNA tubes will be extremely helpful in engineering more elaborate DNA nanostructures in the future.

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Nanoscale pattern extraction from relative positions of sparse 3D localisations

10.1101/2020.02.13.947135 ◽

2020 ◽

Cited By ~ 1

Author(s):

Alistair P. Curd ◽

Joanna Leng ◽

Ruth E. Hughes ◽

Alexa J. Cleasby ◽

Brendan Rogers ◽

...

Keyword(s):

Pattern Recognition ◽

High Resolution ◽

Protein Detection ◽

Dna Origami ◽

Nuclear Pore ◽

Pattern Extraction ◽

Heterogeneous Samples ◽

Microscopy Data ◽

Localisation Microscopy ◽

2D And 3D

AbstractWe present a method for extracting high-resolution ordered features from localisation microscopy data by analysis of relative molecular positions in 2D or 3D. This approach allows pattern recognition at sub-1% protein detection efficiencies, in large and heterogeneous samples, and in 2D and 3D datasets. We used this method to infer ultrastructure of the nuclear pore, the cardiomyocyte Z-disk, DNA origami structures and the centriole.

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Protein patterning by a DNA origami framework

Nanoscale ◽

10.1039/c6nr03199d ◽

2016 ◽

Vol 8 (33) ◽

pp. 15233-15240 ◽

Cited By ~ 5

Author(s):

Hüsnü Aslan ◽

Abhichart Krissanaprasit ◽

Flemming Besenbacher ◽

Kurt V. Gothelf ◽

Mingdong Dong

Keyword(s):

Dna Origami ◽

Protein Patterning

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Observations of the spatial structure of interstellar hydrogen

Symposium - International Astronomical Union ◽

10.1017/s007418090010066x ◽

1967 ◽

Vol 31 ◽

pp. 45-46

Author(s):

Carl Heiles

Keyword(s):

High Resolution ◽

Spatial Structure ◽

Velocity Dispersion ◽

Temperature Variations

High-resolution 21-cm line observations in a region aroundlII= 120°,b11= +15°, have revealed four types of structure in the interstellar hydrogen: a smooth background, large sheets of density 2 atoms cm-3, clouds occurring mostly in groups, and ‘Cloudlets’ of a few solar masses and a few parsecs in size; the velocity dispersion in the Cloudlets is only 1 km/sec. Strong temperature variations in the gas are in evidence.

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Combining integrated systems-biology approaches with intervention-based experimental design provides a higher-resolution path forward for microbiome research

Behavioral and Brain Sciences ◽

10.1017/s0140525x18002911 ◽

2019 ◽

Vol 42 ◽

Author(s):

J. Alfredo Blakeley-Ruiz ◽

Carlee S. McClintock ◽

Ralph Lydic ◽

Helen A. Baghdoyan ◽

James J. Choo ◽

...

Keyword(s):

Systems Biology ◽

High Resolution ◽

Experimental Design ◽

Integrated Systems ◽

Microbiome Research ◽

Constructive Criticism

Abstract The Hooks et al. review of microbiota-gut-brain (MGB) literature provides a constructive criticism of the general approaches encompassing MGB research. This commentary extends their review by: (a) highlighting capabilities of advanced systems-biology “-omics” techniques for microbiome research and (b) recommending that combining these high-resolution techniques with intervention-based experimental design may be the path forward for future MGB research.

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Very High Resolution Analysis of the Dynamics of a Coronal Plasmoid

International Astronomical Union Colloquium ◽

10.1017/s0252921100026117 ◽

1994 ◽

Vol 144 ◽

pp. 593-596

Author(s):

O. Bouchard ◽

S. Koutchmy ◽

L. November ◽

J.-C. Vial ◽

J. B. Zirker

Keyword(s):

High Resolution ◽

Solar Eclipse ◽

Total Solar Eclipse ◽

Field Of View ◽

Small Field ◽

High Resolution Analysis ◽

Ccd Observations ◽

Resolution Analysis ◽

Very High ◽

Small Field Of View

AbstractWe present the results of the analysis of a movie taken over a small field of view in the intermediate corona at a spatial resolution of 0.5“, a temporal resolution of 1 s and a spectral passband of 7 nm. These CCD observations were made at the prime focus of the 3.6 m aperture CFHT telescope during the 1991 total solar eclipse.

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FeXIV Line Emission Polarization of the July 11, 1991 Solar Corona

International Astronomical Union Colloquium ◽

10.1017/s0252921100026002 ◽

1994 ◽

Vol 144 ◽

pp. 541-547

Author(s):

J. Sýkora ◽

J. Rybák ◽

P. Ambrož

Keyword(s):

High Resolution ◽

Solar Corona ◽

Emission Line ◽

Solar Eclipse ◽

White Light ◽

Preliminary Analysis ◽

Line Emission ◽

Total Solar Eclipse ◽

Degree Of Polarization ◽

High Resolution Images

AbstractHigh resolution images, obtained during July 11, 1991 total solar eclipse, allowed us to estimate the degree of solar corona polarization in the light of FeXIV 530.3 nm emission line and in the white light, as well. Very preliminary analysis reveals remarkable differences in the degree of polarization for both sets of data, particularly as for level of polarization and its distribution around the Sun’s limb.

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Microcalorimeters for X-Ray Spectroscopy

International Astronomical Union Colloquium ◽

10.1017/s0252921100107365 ◽

1988 ◽

Vol 102 ◽

pp. 41

Author(s):

E. Silver ◽

C. Hailey ◽

S. Labov ◽

N. Madden ◽

D. Landis ◽

...

Keyword(s):

High Resolution ◽

High Efficiency ◽

Thermal Response ◽

Low Noise ◽

High Resolution Spectroscopy ◽

Superconducting Transition ◽

Sapphire Substrates ◽

Laboratory Plasmas ◽

Adiabatic Demagnetization ◽

Theoretical Predictions

The merits of microcalorimetry below 1°K for high resolution spectroscopy has become widely recognized on theoretical grounds. By combining the high efficiency, broadband spectral sensitivity of traditional photoelectric detectors with the high resolution capabilities characteristic of dispersive spectrometers, the microcalorimeter could potentially revolutionize spectroscopic measurements of astrophysical and laboratory plasmas. In actuality, however, the performance of prototype instruments has fallen short of theoretical predictions and practical detectors are still unavailable for use as laboratory and space-based instruments. These issues are currently being addressed by the new collaborative initiative between LLNL, LBL, U.C.I., U.C.B., and U.C.D.. Microcalorimeters of various types are being developed and tested at temperatures of 1.4, 0.3, and 0.1°K. These include monolithic devices made from NTD Germanium and composite configurations using sapphire substrates with temperature sensors fabricated from NTD Germanium, evaporative films of Germanium-Gold alloy, or material with superconducting transition edges. A new approache to low noise pulse counting electronics has been developed that allows the ultimate speed of the device to be determined solely by the detector thermal response and geometry. Our laboratory studies of the thermal and resistive properties of these and other candidate materials should enable us to characterize the pulse shape and subsequently predict the ultimate performance. We are building a compact adiabatic demagnetization refrigerator for conveniently reaching 0.1°K in the laboratory and for use in future satellite-borne missions. A description of this instrument together with results from our most recent experiments will be presented.

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Radiation Damage, Contrast and Statistics in High Resolution Biological Electron Microscopy

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100068291 ◽

1970 ◽

Vol 28 ◽

pp. 260-261

Author(s):

Robert M. Glaeser

Keyword(s):

High Resolution ◽

Particle Flux ◽

Unit Area ◽

Signal To Noise ◽

Resolution Image ◽

High Resolution Image ◽

Pass Through ◽

Counting Statistics ◽

The Relationship ◽

Picture Element

It is well known that a large flux of electrons must pass through a specimen in order to obtain a high resolution image while a smaller particle flux is satisfactory for a low resolution image. The minimum particle flux that is required depends upon the contrast in the image and the signal-to-noise (S/N) ratio at which the data are considered acceptable. For a given S/N associated with statistical fluxtuations, the relationship between contrast and “counting statistics” is s131_eqn1, where C = contrast; r2 is the area of a picture element corresponding to the resolution, r; N is the number of electrons incident per unit area of the specimen; f is the fraction of electrons that contribute to formation of the image, relative to the total number of electrons incident upon the object.

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