Constructing higher order DNA origami arrays using DNA junctions of anti-parallel/parallel double crossovers

Revealing the energy landscape for nucleosome association may contribute to the understanding of higher-order chromatin structures and their impact on genome regulation. We accomplish this in a direct measurement by integrating two nucleosomes into a DNA origami–based force spectrometer, which enabled subnanometer-resolution measurements of nucleosome-nucleosome distance frequencies via single-particle electron microscopy imaging. From the data, we derived the Boltzmann-weighted distance-dependent energy landscape for nucleosome pair interactions. We find a shallow but long-range (~6 nm) attractive nucleosome pair potential with a minimum of −1.6 kcal/mol close to direct contact distances. The relative nucleosome orientation had little influence, but histone H4 acetylation or removal of histone tails drastically decreased the interaction strength. Because of the weak and shallow pair potential, higher-order nucleosome assemblies will be compliant and experience dynamic shape fluctuations in the absence of additional cofactors. Our results contribute to a more accurate description of chromatin and our force spectrometer provides a powerful tool for the direct and high-resolution study of molecular interactions using imaging techniques.

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Molecular Behavior of DNA Origami in Higher-Order Self-Assembly

Journal of the American Chemical Society ◽

10.1021/ja106292x ◽

2010 ◽

Vol 132 (38) ◽

pp. 13545-13552 ◽

Cited By ~ 96

Author(s):

Zhe Li ◽

Minghui Liu ◽

Lei Wang ◽

Jeanette Nangreave ◽

Hao Yan ◽

...

Keyword(s):

Self Assembly ◽

Higher Order ◽

Dna Origami ◽

Molecular Behavior

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Single-stranded templates as railroad tracks for hierarchical assembly of DNA origami

Nanoscale ◽

10.1039/c8nr03185a ◽

2018 ◽

Vol 10 (29) ◽

pp. 13994-13999 ◽

Cited By ~ 2

Author(s):

Janane F. Rahbani ◽

John C. C. Hsu ◽

Pongphak Chidchob ◽

Hanadi F. Sleiman

Keyword(s):

Repetitive Sequences ◽

Higher Order ◽

Dna Origami ◽

Dna Nanostructures ◽

Hierarchical Assembly ◽

Railroad Tracks ◽

Dna Strands

Long DNA strands consisting of repetitive sequences are valuable tools to build organized DNA nanostructures. This approach produces higher-order origami structures with prescribed length and addressability and provides a unique platform for the modular re-organization of any of their parts.

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Design of DNA Origami Machines and Mechanisms

Volume 9: Micro- and Nano-Systems Engineering and Packaging, Parts A and B ◽

10.1115/imece2012-87848 ◽

2012 ◽

Author(s):

Alex E. Marras ◽

Haijun J. Su ◽

Carlos E. Castro

Keyword(s):

Self Assembly ◽

Degrees Of Freedom ◽

Higher Order ◽

Dna Origami ◽

Motion Path ◽

3D Structures ◽

Detail Design ◽

Macro Scale ◽

Viable Approach ◽

Kinematic Mechanisms

This research introduces DNA origami as a viable approach to design and fabricate nanoscale mechanisms and machines. DNA origami is a recently developed nanotechnology that has enabled the construction of objects with unprecedented nanoscale geometric complexity via self-assembly. These objects are made up of thousands of DNA base-pairs packed into 3D structures with typical dimensions of 10–100nm. The majority of DNA origami research to date focuses on assembly of static 2D or 3D structures. In this work, we aim to extend the scope of DNA origami to include design of objects with kinematically constrained moving parts. Borrowing concepts from macro-scale kinematic mechanisms, we propose the concept of DNA Origami Mechanisms and Machines (DOMM) comprised of multiple links connected by joints. The links are designed by bundling double stranded DNA (dsDNA) helices to achieve the desired geometry and stiffness. The joints are designed by combining links with strategic placement flexible single stranded DNA (ssDNA) to enable motion in specific degrees of freedom. We detail design approaches for links and common joints including revolute, prismatic, and spherical, and discuss their integration into higher order mechanisms. As a proof of concept, we built a nanoscale hinge (revolute joint) and integrated four of these hinges into a prototype DOMM, namely a Bennett 4-bar linkage, which can be completely folded into a closed bundle geometry and unfolded into an open square geometry with a specified kinematic motion path. A kinematic analysis shows that the DNA Bennett linkage closely follows the 3D motion path of the rigid body counterpart. Our results demonstrate that DNA origami has high potential for the design and assembly of nanoscale machines. The ultimate goal of this work is to develop a library of nanoscale DNA-based links and joints that can be widely used in the design and assembly of higher order mechanisms and machines. We anticipate that, in the future, these components can be used to build nanorobots for useful applications including drug delivery, nanomanufacturing, and biosensing.

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Design Features to Accelerate the Higher-Order Assembly of DNA Origami on Membranes

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.1c07694 ◽

2021 ◽

Author(s):

Yusuf Qutbuddin ◽

Jan-Hagen Krohn ◽

Gereon A. Brüggenthies ◽

Johannes Stein ◽

Svetozar Gavrilovic ◽

...

Keyword(s):

Higher Order ◽

Dna Origami ◽

Design Features

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A DNA-based synthetic apoptosome

10.1101/660183 ◽

2019 ◽

Author(s):

Bas J.H.M. Rosier ◽

Albert J. Markvoort ◽

Berta Gumí-Audenis ◽

Job A.L. Roodhuizen ◽

Anniek den Hamer ◽

...

Keyword(s):

Protein Interactions ◽

Intracellular Signaling ◽

Spatial Organization ◽

Higher Order ◽

Dna Origami ◽

Caspase 9 ◽

Signaling Complex ◽

Synthetic Dna ◽

Modular Platform

AbstractLiving cells are able to regulate key cellular processes by physically assembling signaling components on dedicated molecular platforms. The spatial organization of proteins in these higher-order signaling complexes facilitates proximity-driven activation and inhibition events, allowing tight regulation of the flow of information. Here, we employ the programmability and modularity of DNA origami as a controllable molecular platform for studying protein-protein interactions involved in intracellular signaling. Specifically, we engineer a synthetic, DNA origami-based version of the apoptosome, a large multi-protein signaling complex that regulates apoptosis by co-localization of multiple caspase-9 monomers. Our in vitro characterization using both wildtype caspase-9 monomers and inactive mutants tethered to a DNA origami platform directly demonstrates that enzymatic activity is induced by proximity-driven dimerization with asymmetric, half-of-sites reactivity. Additionally, experimental results supported by a detailed thermodynamic model reveal a multivalent activity enhancement in tethered caspase-9 oligomers of three and four enzymes, partly originating from a statistical increase in the number of active catalytic units in higher-order enzyme clusters. Our results offer fundamental insights in caspase-9 activity regulation and demonstrate that DNA origami provides a modular platform to construct and characterize higher-order signaling complexes. The engineered DNA-based protein assembly platform has the potential to be broadly applied to inform the function of other important multi-enzyme assemblies involved in inflammation, innate immunity, and necrosis.

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DNA Origami: Scaffolds for Creating Higher Order Structures

Chemical Reviews ◽

10.1021/acs.chemrev.6b00825 ◽

2017 ◽

Vol 117 (20) ◽

pp. 12584-12640 ◽

Cited By ~ 376

Author(s):

Fan Hong ◽

Fei Zhang ◽

Yan Liu ◽

Hao Yan

Keyword(s):

Higher Order ◽

Dna Origami ◽

Order Structures

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Dual systems for all: Higher-order, role-based relational reasoning as a uniquely derived feature of human cognition

Behavioral and Brain Sciences ◽

10.1017/s0140525x19000451 ◽

2019 ◽

Vol 42 ◽

Author(s):

Daniel J. Povinelli ◽

Gabrielle C. Glorioso ◽

Shannon L. Kuznar ◽

Mateja Pavlic

Keyword(s):

Temporal Reasoning ◽

Higher Order ◽

Important Case ◽

Human Cognition ◽

Relational Reasoning ◽

Dual Systems ◽

First Order ◽

Reasoning System ◽

Role Based

Abstract Hoerl and McCormack demonstrate that although animals possess a sophisticated temporal updating system, there is no evidence that they also possess a temporal reasoning system. This important case study is directly related to the broader claim that although animals are manifestly capable of first-order (perceptually-based) relational reasoning, they lack the capacity for higher-order, role-based relational reasoning. We argue this distinction applies to all domains of cognition.

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Quantitative EPMA of nitrogen : A tricky element in the electron-probe microanalyzer

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100132741 ◽

1992 ◽

Vol 50 (2) ◽

pp. 1622-1623

Author(s):

G.F. Bastin ◽

H.J.M. Heijligers

Keyword(s):

Background Subtraction ◽

Electron Probe ◽

Detection System ◽

Higher Order ◽

Light Elements ◽

Strong Suppression ◽

Electron Probe Microanalyzer ◽

Quantitative Epma ◽

Peak Count ◽

Lead Stearate

Among the ultra-light elements B, C, N, and O nitrogen is the most difficult element to deal with in the electron probe microanalyzer. This is mainly caused by the severe absorption that N-Kα radiation suffers in carbon which is abundantly present in the detection system (lead-stearate crystal, carbonaceous counter window). As a result the peak-to-background ratios for N-Kα measured with a conventional lead-stearate crystal can attain values well below unity in many binary nitrides . An additional complication can be caused by the presence of interfering higher-order reflections from the metal partner in the nitride specimen; notorious examples are elements such as Zr and Nb. In nitrides containing these elements is is virtually impossible to carry out an accurate background subtraction which becomes increasingly important with lower and lower peak-to-background ratios. The use of a synthetic multilayer crystal such as W/Si (2d-spacing 59.8 Å) can bring significant improvements in terms of both higher peak count rates as well as a strong suppression of higher-order reflections.

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