More Like this

1. Programming the Nucleation of DNA Brick Self‐Assembly with a Seeding Strand

   https://doi.org/10.1002/anie.201915063  

   Zhang, Yingwei ; Reinhardt, Aleks ; Wang, Pengfei ; Song, Jie ; Ke, Yonggang ( March 2020 , Angewandte Chemie International Edition)

   Recently, the DNA brick strategy has provided a highly modular and scalable approach for the construction of complex structures, which can be used as nanoscale pegboards for the precise organization of molecules and nanoparticles for many applications. Despite the dramatic increase of structural complexity provided by the DNA brick method, the assembly pathways are still poorly understood. Herein, we introduce a “seed” strand to control the crucial nucleation and assembly pathway in DNA brick assembly. Through experimental studies and computer simulations, we successfully demonstrate that the regulation of the assembly pathways through seeded growth can accelerate the assembly kinetics and increase the optimal temperature by circa 4–7 °C for isothermal assembly. By improving our understanding of the assembly pathways, we provide new guidelines for the design of programmable pathways to improve the self‐assembly of DNA nanostructures.

    

   more » « less
2. Programming the Nucleation of DNA Brick Self‐Assembly with a Seeding Strand

   https://doi.org/10.1002/ange.201915063  

   Zhang, Yingwei ; Reinhardt, Aleks ; Wang, Pengfei ; Song, Jie ; Ke, Yonggang ( March 2020 , Angewandte Chemie)

   Recently, the DNA brick strategy has provided a highly modular and scalable approach for the construction of complex structures, which can be used as nanoscale pegboards for the precise organization of molecules and nanoparticles for many applications. Despite the dramatic increase of structural complexity provided by the DNA brick method, the assembly pathways are still poorly understood. Herein, we introduce a “seed” strand to control the crucial nucleation and assembly pathway in DNA brick assembly. Through experimental studies and computer simulations, we successfully demonstrate that the regulation of the assembly pathways through seeded growth can accelerate the assembly kinetics and increase the optimal temperature by circa 4–7 °C for isothermal assembly. By improving our understanding of the assembly pathways, we provide new guidelines for the design of programmable pathways to improve the self‐assembly of DNA nanostructures.

    

   more » « less
3. Novo&Stitch: accurate reconciliation of genome assemblies via optical maps

   https://doi.org/10.1093/bioinformatics/bty255  

   Pan, Weihua ; Wanamaker, Steve I. ; Ah-Fong, Audrey M. V. ; Judelson, Howard S. ; Lonardi, Stefano ( June 2018 , Bioinformatics)

   De novo genome assembly is a challenging computational problem due to the high repetitive content of eukaryotic genomes and the imperfections of sequencing technologies (i.e. sequencing errors, uneven sequencing coverage and chimeric reads). Several assembly tools are currently available, each of which has strengths and weaknesses in dealing with the trade-off between maximizing contiguity and minimizing assembly errors (e.g. mis-joins). To obtain the best possible assembly, it is common practice to generate multiple assemblies from several assemblers and/or parameter settings and try to identify the highest quality assembly. Unfortunately, often there is no assembly that both maximizes contiguity and minimizes assembly errors, so one has to compromise one for the other.

   The concept of assembly reconciliation has been proposed as a way to obtain a higher quality assembly by merging or reconciling all the available assemblies. While several reconciliation methods have been introduced in the literature, we have shown in one of our recent papers that none of them can consistently produce assemblies that are better than the assemblies provided in input. Here we introduce Novo&Stitch, a novel method that takes advantage of optical maps to accurately carry out assembly reconciliation (assuming that the assembled contigs are sufficiently long to be reliably aligned to the optical maps, e.g. 50 Kbp or longer). Experimental results demonstrate that Novo&Stitch can double the contiguity (N50) of the input assemblies without introducing mis-joins or reducing genome completeness.

   Novo&Stitch can be obtained from https://github.com/ucrbioinfo/Novo_Stitch.

    

   more » « less
4. Precision Evaluation of Large Payload SCARA Robot for PCB Assembly

   https://doi.org/10.1115/msec2022-85534  

   Nimon, Andrew S. ; Sherehiy, Andriy ; Alqatamin, Moath ; Wei, Danming ; Popa, Dan O. ( June 2022 , ASME 2022 17th International Manufacturing Science and Engineering Conference)

   The placement of SMD components is usually performed with Cartesian type robots, a task known as pick-and-place (P&P). Small Selective Compliance Articulated Robot Arm (SCARA) robots are also growing in popularity for this use because of their quick and accurate performance. This paper describes the use of the Lean Robotic Micromanufacturing (LRM) framework applied on a large, 10kg payload, industrial SCARA robot for PCB assembly. The LRM framework guided the precision evaluation of the PCB assembly process and provided a prediction of the placement precision and yield. We experimentally evaluated the repeatability of the system, as well as the resulting collective errors during the assembly. Results confirm that the P&P task can achieve the required assembly tolerance of 200 microns without employing closed-loop visual servoing, therefore considerably decreasing the system complexity and assembly time.

    

   more » « less
5. Encoding hierarchical assembly pathways of proteins with DNA

   https://doi.org/10.1073/pnas.2106808118  

   Hayes, Oliver G. ; Partridge, Benjamin E. ; Mirkin, Chad A. ( September 2021 , Proceedings of the National Academy of Sciences)

   The structural and functional diversity of materials in nature depends on the controlled assembly of discrete building blocks into complex architectures via specific, multistep, hierarchical assembly pathways. Achieving similar complexity in synthetic materials through hierarchical assembly is challenging due to difficulties with defining multiple recognition areas on synthetic building blocks and controlling the sequence through which those recognition sites direct assembly. Here, we show that we can exploit the chemical anisotropy of proteins and the programmability of DNA ligands to deliberately control the hierarchical assembly of protein–DNA materials. Through DNA sequence design, we introduce orthogonal DNA interactions with disparate interaction strengths (“strong” and “weak”) onto specific geometric regions of a model protein, stable protein 1 (Sp1). We show that the spatial encoding of DNA ligands leads to highly directional assembly via strong interactions and that, by design, the first stage of assembly increases the multivalency of weak DNA–DNA interactions that give rise to an emergent second stage of assembly. Furthermore, we demonstrate that judicious DNA design not only directs assembly along a given pathway but can also direct distinct structural outcomes from a single pathway. This combination of protein surface and DNA sequence design allows us to encode the structural and chemical information necessary into building blocks to program their multistep hierarchical assembly. Our findings represent a strategy for controlling the hierarchical assembly of proteins to realize a diverse set of protein–DNA materials by design.

    

   more » « less