Recursive DNA Assembly Using Protected Oligonucleotide Duplex Assisted Cloning (PODAC)

2017 ◽  
Vol 6 (6) ◽  
pp. 943-949 ◽  
Author(s):  
Bob Van Hove ◽  
Chiara Guidi ◽  
Lien De Wannemaeker ◽  
Jo Maertens ◽  
Marjan De Mey
Keyword(s):  
Dna Assembly ◽  
Oligonucleotide Duplex

DNA assembly creates 3D superconducting nanostructures

Nano Today ◽  
2021 ◽  
Vol 36 ◽  
pp. 101071
Author(s):  
Cordelia Sealy
Keyword(s):  
Dna Assembly

scholarly journals DNA-Guided Assembly for Fibril Proteins

Mathematics ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 404
Author(s):  
Alexandru Amărioarei ◽  
Frankie Spencer ◽  
Gefry Barad ◽  
Ana-Maria Gheorghe ◽  
Corina Iţcuş ◽  
...  
Keyword(s):  
Computational Model ◽  
Structural Properties ◽  
Self Assembly ◽  
Structural Characteristics ◽  
Computational Modelling ◽  
Shape Reconstruction ◽  
Raw Material ◽  
Dna Assembly ◽  
Mesh Structure ◽  
Elementary Fibril

Current advances in computational modelling and simulation have led to the inclusion of computer scientists as partners in the process of engineering of new nanomaterials and nanodevices. This trend is now, more than ever, visible in the field of deoxyribonucleic acid (DNA)-based nanotechnology, as DNA’s intrinsic principle of self-assembly has been proven to be highly algorithmic and programmable. As a raw material, DNA is a rather unremarkable fabric. However, as a way to achieve patterns, dynamic behavior, or nano-shape reconstruction, DNA has been proven to be one of the most functional nanomaterials. It would thus be of great potential to pair up DNA’s highly functional assembly characteristics with the mechanic properties of other well-known bio-nanomaterials, such as graphene, cellulos, or fibroin. In the current study, we perform projections regarding the structural properties of a fibril mesh (or filter) for which assembly would be guided by the controlled aggregation of DNA scaffold subunits. The formation of such a 2D fibril mesh structure is ensured by the mechanistic assembly properties borrowed from the DNA assembly apparatus. For generating inexpensive pre-experimental assessments regarding the efficiency of various assembly strategies, we introduced in this study a computational model for the simulation of fibril mesh assembly dynamical systems. Our approach was based on providing solutions towards two main circumstances. First, we created a functional computational model that is restrictive enough to be able to numerically simulate the controlled aggregation of up to 1000s of elementary fibril elements yet rich enough to provide actionable insides on the structural characteristics for the generated assembly. Second, we used the provided numerical model in order to generate projections regarding effective ways of manipulating one of the the key structural properties of such generated filters, namely the average size of the openings (gaps) within these meshes, also known as the filter’s aperture. This work is a continuation of Amarioarei et al., 2018, where a preliminary version of this research was discussed.

scholarly journals CRIMoClo plasmids for modular assembly and orthogonal chromosomal integration of synthetic circuits in Escherichia coli

2019 ◽  
Vol 13 (1) ◽  
Author(s):  
Stefano Vecchione ◽  
Georg Fritz
Keyword(s):  
Escherichia Coli ◽  
Synthetic Biology ◽  
Integrated Circuits ◽  
High Efficiency ◽  
Genetic Circuit ◽  
Dna Assembly ◽  
Chromosomal Integration ◽  
Golden Gate ◽  
Genetic Circuits ◽  
E Coli

Abstract Background Synthetic biology heavily depends on rapid and simple techniques for DNA engineering, such as Ligase Cycling Reaction (LCR), Gibson assembly and Golden Gate assembly, all of which allow for fast, multi-fragment DNA assembly. A major enhancement of Golden Gate assembly is represented by the Modular Cloning (MoClo) system that allows for simple library propagation and combinatorial construction of genetic circuits from reusable parts. Yet, one limitation of the MoClo system is that all circuits are assembled in low- and medium copy plasmids, while a rapid route to chromosomal integration is lacking. To overcome this bottleneck, here we took advantage of the conditional-replication, integration, and modular (CRIM) plasmids, which can be integrated in single copies into the chromosome of Escherichia coli and related bacteria by site-specific recombination at different phage attachment (att) sites. Results By combining the modularity of the MoClo system with the CRIM plasmids features we created a set of 32 novel CRIMoClo plasmids and benchmarked their suitability for synthetic biology applications. Using CRIMoClo plasmids we assembled and integrated a given genetic circuit into four selected phage attachment sites. Analyzing the behavior of these circuits we found essentially identical expression levels, indicating orthogonality of the loci. Using CRIMoClo plasmids and four different reporter systems, we illustrated a framework that allows for a fast and reliable sequential integration at the four selected att sites. Taking advantage of four resistance cassettes the procedure did not require recombination events between each round of integration. Finally, we assembled and genomically integrated synthetic ECF σ factor/anti-σ switches with high efficiency, showing that the growth defects observed for circuits encoded on medium-copy plasmids were alleviated. Conclusions The CRIMoClo system enables the generation of genetic circuits from reusable, MoClo-compatible parts and their integration into 4 orthogonal att sites into the genome of E. coli. Utilizing four different resistance modules the CRIMoClo system allows for easy, fast, and reliable multiple integrations. Moreover, utilizing CRIMoClo plasmids and MoClo reusable parts, we efficiently integrated and alleviated the toxicity of plasmid-borne circuits. Finally, since CRIMoClo framework allows for high flexibility, it is possible to utilize plasmid-borne and chromosomally integrated circuits simultaneously. This increases our ability to permute multiple genetic modules and allows for an easier design of complex synthetic metabolic pathways in E. coli.

scholarly journals DNA Assembly in 3D Printed Fluidics

PLoS ONE ◽  
2015 ◽  
Vol 10 (12) ◽  
pp. e0143636 ◽  
Author(s):  
William G. Patrick ◽  
Alec A. K. Nielsen ◽  
Steven J. Keating ◽  
Taylor J. Levy ◽  
Che-Wei Wang ◽  
...  
Keyword(s):  
Dna Assembly ◽  
3D Printed

A DNAzyme-catalyzed label-free aptasensor based on multifunctional dendrimer-like DNA assembly for sensitive detection of carcinoembryonic antigen

2021 ◽  
Vol 194 ◽  
pp. 113618
Author(s):  
Xiao-Jing Zhai ◽  
Qiong-Lin Wang ◽  
Hui-Fang Cui ◽  
Xiaojie Song ◽  
Qi-Yan Lv ◽  
...  
Keyword(s):  
Carcinoembryonic Antigen ◽  
Sensitive Detection ◽  
Dna Assembly ◽  
Label Free

Spectral and cyclic voltammetric characterization of self-assembled monolayers on gold of pyrene end-labeled oligonucleotide duplexes

1999 ◽  
Vol 77 (5-6) ◽  
pp. 1077-1084 ◽  
Author(s):  
R Scott Reese ◽  
Marye Anne Fox
Keyword(s):  
Gold Surface ◽  
Self Assembled Monolayers ◽  
Self Assembled Monolayer ◽  
Surface Emission ◽  
Assembled Monolayers ◽  
Oligonucleotide Duplex ◽  
Self Assembled ◽  
Duplex Formation

Self-assembled monolayers of sulfur-terminated oligonucleotide duplexes were formed on flat gold surfaces, either by exposure of a self-assembled monolayer bearing one oligonucleotide strand to the complementary strand or by preformation of a oligonucleotide duplex that was then deposited on a fresh gold surface. Virtually identical spectral behavior was observed whether the duplex was produced before deposition or by in situ complementary association. With a duplex bearing an appropriate pyrene end-label, the resulting thin film was photoresponsive. Surface emission measurements show no evidence for pyrene aggregation on the modified surfaces. The polarity of the photocurrent, reflecting photoinduced electron transfer initiated by photoexcitation of pyrene, is opposite that expected from the oligonucleotide-mediated reduction of the appended pyrene excited state.Key words: oligonucleotide, self-assembled monolayer, duplex formation, photoelectrochemistry, surface emission.

scholarly journals Erratum to: No training required: experimental tests support homology-based DNA assembly as a best practice in synthetic biology

2016 ◽  
Vol 10 (1) ◽  
Author(s):  
Afnan Azizi ◽  
Wilson Lam ◽  
Hilary Phenix ◽  
Lioudmila Tepliakova ◽  
Ian J. Roney ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Best Practice ◽  
Experimental Tests ◽  
Dna Assembly

scholarly journals Direct requirement for Xmus101 in ATR-mediated phosphorylation of Claspin bound Chk1 during checkpoint signaling

2006 ◽  
Vol 173 (2) ◽  
pp. 181-186 ◽  
Author(s):  
Shan Yan ◽  
Howard D. Lindsay ◽  
W. Matthew Michael
Keyword(s):  
Sperm Chromatin ◽  
Checkpoint Control ◽  
Direct Role ◽  
Checkpoint Activation ◽  
Replication Checkpoint ◽  
Checkpoint Signaling ◽  
Checkpoint Response ◽  
Egg Extracts ◽  
Oligonucleotide Duplex ◽  
Stalled Replication Forks

TopBP1-like proteins, which include Xenopus laevis Xmus101, are required for DNA replication and have been linked to replication checkpoint control. A direct role for TopBP1/Mus101 in checkpoint control has been difficult to prove, however, because of the requirement for replication in generating the DNA structures that activate the checkpoint. Checkpoint activation occurs in X. laevis egg extracts upon addition of an oligonucleotide duplex (AT70). We show that AT70 bypasses the requirement for replication in checkpoint activation. We take advantage of this replication-independent checkpoint system to determine the role of Xmus101 in the checkpoint. We find that Xmus101 is essential for AT70-mediated checkpoint signaling and that it functions to promote phosphorylation of Claspin bound Chk1 by the ataxia-telangiectasia and Rad-3–related (ATR) protein kinase. We also identify a separation-of-function mutant of Xmus101. In extracts expressing this mutant, replication of sperm chromatin occurs normally; however, the checkpoint response to stalled replication forks fails. These data demonstrate that Xmus101 functions directly during signal relay from ATR to Chk1.

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