scholarly journals Stretching DNA origami: effect of nicks and Holliday junctions on the axial stiffness

2020 ◽  
Vol 48 (21) ◽  
pp. 12407-12414
Author(s):  
Wei-Hung Jung ◽  
Enze Chen ◽  
Remi Veneziano ◽  
Stavros Gaitanaros ◽  
Yun Chen
Keyword(s):  
Numerical Models ◽  
Double Helix ◽  
Single Particle Tracking ◽  
Holliday Junctions ◽  
Dna Origami ◽  
Axial Stiffness ◽  
Local Loss ◽  
Design Characteristics ◽  
Local Stiffness ◽  
Force Displacement

Abstract The axial stiffness of DNA origami is determined as a function of key nanostructural characteristics. Different constructs of two-helix nanobeams with specified densities of nicks and Holliday junctions are synthesized and stretched by fluid flow. Implementing single particle tracking to extract force–displacement curves enables the measurement of DNA origami stiffness values at the enthalpic elasticity regime, i.e. for forces larger than 15 pN. Comparisons between ligated and nicked helices show that the latter exhibit nearly a two-fold decrease in axial stiffness. Numerical models that treat the DNA helices as elastic rods are used to evaluate the local loss of stiffness at the locations of nicks and Holliday junctions. It is shown that the models reproduce the experimental data accurately, indicating that both of these design characteristics yield a local stiffness two orders of magnitude smaller than the corresponding value of the intact double-helix. This local degradation in turn leads to a macroscopic loss of stiffness that is evaluated numerically for multi-helix DNA bundles.

scholarly journals Correlations of three-dimensional motion of chromosomal loci in yeast revealed by the double-helix point spread function microscope

2014 ◽  
Vol 25 (22) ◽  
pp. 3619-3629 ◽  
Author(s):  
Mikael P. Backlund ◽  
Ryan Joyner ◽  
Karsten Weis ◽  
W. E. Moerner
Keyword(s):  
Point Spread Function ◽  
Double Helix ◽  
Dynamical Behavior ◽  
Three Dimensional ◽  
Mean Square Displacement ◽  
Single Particle Tracking ◽  
3D Tracking ◽  
Point Spread ◽  
Spread Function ◽  
Diploid Cells

Single-particle tracking has been applied to study chromatin motion in live cells, revealing a wealth of dynamical behavior of the genomic material once believed to be relatively static throughout most of the cell cycle. Here we used the dual-color three-dimensional (3D) double-helix point spread function microscope to study the correlations of movement between two fluorescently labeled gene loci on either the same or different budding yeast chromosomes. We performed fast (10 Hz) 3D tracking of the two copies of the GAL locus in diploid cells in both activating and repressive conditions. As controls, we tracked pairs of loci along the same chromosome at various separations, as well as transcriptionally orthogonal genes on different chromosomes. We found that under repressive conditions, the GAL loci exhibited significantly higher velocity cross-correlations than they did under activating conditions. This relative increase has potentially important biological implications, as it might suggest coupling via shared silencing factors or association with decoupled machinery upon activation. We also found that on the time scale studied (∼0.1–30 s), the loci moved with significantly higher subdiffusive mean square displacement exponents than previously reported, which has implications for the application of polymer theory to chromatin motion in eukaryotes.

Single Particle Tracking and Super-Resolution Imaging of Membrane-Assisted Stop-and-Go Diffusion and Lattice Assembly of DNA Origami

ACS Nano ◽  
2019 ◽  
Author(s):  
Susanne Kempter ◽  
Alena Khmelinskaia ◽  
Maximilian T. Strauss ◽  
Petra Schwille ◽  
Ralf Jungmann ◽  
...  
Keyword(s):  
Particle Tracking ◽  
Single Particle ◽  
Super Resolution ◽  
Single Particle Tracking ◽  
Dna Origami ◽  
Stop And Go ◽  
Resolution Imaging

scholarly journals The Art of Designing DNA Nanostructures with CAD Software

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2287
Author(s):  
Martin Glaser ◽  
Sourav Deb ◽  
Florian Seier ◽  
Amay Agrawal ◽  
Tim Liedl ◽  
...  
Keyword(s):  
Human Error ◽  
Dna Nanotechnology ◽  
Holliday Junctions ◽  
Dna Origami ◽  
Dna Nanostructures ◽  
Dna Structures ◽  
Current State ◽  
Software Packages ◽  
Wide Range ◽  
Time Required

Since the arrival of DNA nanotechnology nearly 40 years ago, the field has progressed from its beginnings of envisioning rather simple DNA structures having a branched, multi-strand architecture into creating beautifully complex structures comprising hundreds or even thousands of unique strands, with the possibility to exactly control the positions down to the molecular level. While the earliest construction methodologies, such as simple Holliday junctions or tiles, could reasonably be designed on pen and paper in a short amount of time, the advent of complex techniques, such as DNA origami or DNA bricks, require software to reduce the time required and propensity for human error within the design process. Where available, readily accessible design software catalyzes our ability to bring techniques to researchers in diverse fields and it has helped to speed the penetration of methods, such as DNA origami, into a wide range of applications from biomedicine to photonics. Here, we review the historical and current state of CAD software to enable a variety of methods that are fundamental to using structural DNA technology. Beginning with the first tools for predicting sequence-based secondary structure of nucleotides, we trace the development and significance of different software packages to the current state-of-the-art, with a particular focus on programs that are open source.

scholarly journals Tracking single particles for hours via continuous DNA-mediated fluorophore exchange

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Florian Stehr ◽  
Johannes Stein ◽  
Julian Bauer ◽  
Christian Niederauer ◽  
Ralf Jungmann ◽  
...  
Keyword(s):  
Particle Tracking ◽  
Fusion Proteins ◽  
Organic Dyes ◽  
Single Particle Tracking ◽  
Dna Origami ◽  
Single Particles ◽  
Inherent Limitation ◽  
Cellular Processes ◽  
Fluorescently Labeled Oligonucleotides ◽  
Observation Times

AbstractMonitoring biomolecules in single-particle tracking experiments is typically achieved by employing fixed organic dyes or fluorescent fusion proteins linked to a target of interest. However, photobleaching typically limits observation times to merely a few seconds, restricting downstream statistical analysis and observation of rare biological events. Here, we overcome this inherent limitation via continuous fluorophore exchange using DNA-PAINT, where fluorescently-labeled oligonucleotides reversibly bind to a single-stranded DNA handle attached to the target molecule. Such versatile and facile labeling allows uninterrupted monitoring of single molecules for extended durations. We demonstrate the power of our approach by observing DNA origami on membranes for tens of minutes, providing perspectives for investigating cellular processes on physiologically relevant timescales.

scholarly journals Metasurface integrated with double-helix point spread function and metalens for three-dimensional imaging

Nanophotonics ◽  
2019 ◽  
Vol 8 (3) ◽  
pp. 451-458 ◽  
Author(s):  
Chunqi Jin ◽  
Jihua Zhang ◽  
Chunlei Guo
Keyword(s):  
Particle Tracking ◽  
Point Spread Function ◽  
Double Helix ◽  
Three Dimensional ◽  
Super Resolution ◽  
Single Particle Tracking ◽  
Point Sources ◽  
Phase Mask ◽  
Point Spread ◽  
Spread Function

AbstractMetasurfaces are two-dimensional arrangements of antennas that control the propagation of electromagnetic waves with a subwavelength thickness and resolution. Previously, metasurfaces have been mostly used to obtain the function of a single optical element. Here, we demonstrate a plasmonic metasurface that represents the combination of a phase mask generating a double-helix point spread function (DH-PSF) and a metalens for imaging. DH-PSF has been widely studied in three-dimensional (3D) super-resolution imaging, biomedical imaging, and particle tracking, but the current DH-PSFs are inefficient, bulky, and difficult to integrate. The multielement metasurface, which we label as DH-metalens, enables a DH-PSF with transfer efficiency up to 70.3% and an ultrahigh level of optical system integration, three orders of magnitude smaller than those realized by conventional phase elements. Moreover, the demonstrated DH-metalens can work in broadband visible wavelengths and in multiple incident polarization states. Finally, we demonstrate the application of the DH-metalens in 3D imaging of point sources. These results pave ways for realizing integrated DH-PSFs, which have applications in 3D super-resolution microscopy, single particle tracking/imaging, and machine vision.

scholarly journals Response Modification Factor of RC Frames Strengthened with RC Haunches

2020 ◽  
Vol 2020 ◽  
pp. 1-18
Author(s):  
Junaid Akbar ◽  
Naveed Ahmad ◽  
Muhammad Rizwan ◽  
Sairash Javed ◽  
Bashir Alam
Keyword(s):  
Reinforced Concrete ◽  
Numerical Models ◽  
Lateral Force ◽  
Roof Displacement ◽  
Response Modification Factor ◽  
Capacity Curves ◽  
Displacement Capacity ◽  
Rc Frames ◽  
Modification Factor ◽  
Force Displacement

This paper presents experimental and numerical studies carried out on two-story reinforced concrete (RC) frames having weaker beam-column joints, which were retrofitted with reinforced concrete haunches to avoid joint panel damage under seismic actions. The design philosophy of the retrofit solution is to allow beam-column members to deform inelastically and dissipate seismic energy. Shake table tests were performed on three 1 : 3 reduced scale two-story RC frame models, including one model incorporating construction deficiencies common in developing countries, which was retrofitted with two retrofit schemes using RC haunches. The focus of the experimental study was to understand the seismic behaviour of both as-built and retrofitted models and obtain the seismic response properties, i.e., lateral force-displacement capacity curves and time histories of model response displacement. The derived capacity curves were used to quantify overstrength and ductility factors of both as-built and retrofitted frames. Finite element- (FE-) based software SeismoStruct was used to develop representative numerical models, which were calibrated with the experimental data in simulating the time history response of structure roof displacement and in predicting peak roof-displacement and peak base shear force. Moreover, the FE-based numerical models were subjected to a suite of spectrum natural accelerograms, linearly scaled to multiple intensity levels for performing incremental dynamic analysis. Lateral force-displacement capacity and response curves were developed, which were analyzed to calculate the structure ductility and overstrength factors. The structure R factor is the product of ductility and overstrength factors, which exhibited substantial increase due to the proposed retrofitting technique. A case study was presented for the seismic performance assessment of RC frames with/without RC haunches in various seismic zones using the static force procedure given in seismic code and using response modification factor quantified in the present research.

scholarly journals Regulation of 2D DNA Nanostructures by the Coupling of Tile Curvatures and Arm Twists

2021 ◽  
Author(s):  
Chuan Jiang ◽  
Biao Lu ◽  
Wei Zhang ◽  
Yoel P. Ohayon ◽  
Caihong Ni ◽  
...  
Keyword(s):  
Transverse Section ◽  
Regular Polygon ◽  
Holliday Junctions ◽  
Dna Origami ◽  
Dna Nanostructures ◽  
Base Pairs ◽  
Left Handed ◽  
Different Types ◽  
Sticky End ◽  
Structural Descriptions

DNA overwinding and underwinding between adjacent Holliday junctions have been applied in DNA origami constructs to design both left-handed and right-handed nanostructures. For a variety of DNA tubes assembled from small tiles, only a theoretical approach of the intrinsic tile curvature was previously used to explain their formation. Details regarding the quantitative and structural descriptions of the intrinsic tile curvature and its evolution in DNA tubes by coupling with arm twists were missing. In this work, we designed three types of tile cores from a circular 128 nucleotide scaffold by longitudinal weaving (LW), bridging longitudinal weaving (bLW), and transverse weaving (TW) and assembled their 2D planar or tubular nanostructures via inter-tile arms with a distance of an odd or even number of DNA half-turns. The biotin/streptavidin (SA) labeling technique was applied to define the tube configuration with addressable inside and outside surfaces and thus their component tile conformation with addressable concave and convex curvatures. Both chiral tubes possessing left-handed and right-handed curvatures could be generated by finely tuning p and q in bLW-E<sub>p/q</sub> designs (bLW tile cores joined together by inter-tile arms of an even number of half-turns with the arm length of p base pairs (bp) and the sticky end length of q nucleotides (nt)). We were able to assign the chiral indices (n,m) to each specific tube from the high-resolution AFM images, and thus estimated the tile curvature angle with a regular polygon model that approximates each tube’s transverse section. We attribute the curvature evolution of bLW-E<sub>p/q</sub> tubes composed of the same tile core to the coupling of the intrinsic tile curvature and different arm twists. A better understanding of the integrated actions of different types of twisting forces on DNA tubes will be much more helpful in engineering DNA nanostructures in the future.

scholarly journals Validation of Stainless-Steel CHS Columns Finite Element Models

Materials ◽  
2021 ◽  
Vol 14 (7) ◽  
pp. 1785
Author(s):  
Daniel Jindra ◽  
Zdeněk Kala ◽  
Jiří Kala
Keyword(s):  
Stainless Steel ◽  
Cross Sections ◽  
Numerical Models ◽  
Initial Imperfection ◽  
Material Model ◽  
Nonlinear Material ◽  
Geometric Imperfection ◽  
Local Loss ◽  
Aesthetic Appearance ◽  
Wide Range

Stainless-steel elements are increasingly used in a wide range of load-bearing structures due to their strength, minimal maintenance requirements, and aesthetic appearance. Their response differs from standard steels; therefore, it is necessary to choose a different procedure when creating a correct computational model. Seven groups of numerical models differing in the used formulation of elements integration, mesh density localization, nonlinear material model, and initial geometric imperfection were calibrated. The results of these advanced simulations were validated with published results obtained by an extensive experimental approach on circular hollow sections columns. With regard to the different slenderness of the cross-sections, the influence of the initial imperfection in the form of global and local loss of stability on the response was studied. Responses of all models were validated by comparing the averaged normalized ultimate loads and the averaged normalized deflections with experimentally obtained results.

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