scholarly journals In vivo cloning of artificial DNA nanostructures

2008 ◽  
Vol 105 (46) ◽  
pp. 17626-17631 ◽  
Author(s):  
Chenxiang Lin ◽  
Sherri Rinker ◽  
Xing Wang ◽  
Yan Liu ◽  
Nadrian C. Seeman ◽  
...  
Keyword(s):  
Dna Nanotechnology ◽  
Dna Nanostructures ◽  
Scientific Enterprise ◽  
Dna Nanostructure ◽  
Copy Numbers ◽  
Artificial Dna ◽  
Difficult Challenge ◽  
Endonuclease Vii

Mimicking nature is both a key goal and a difficult challenge for the scientific enterprise. DNA, well known as the genetic-information carrier in nature, can be replicated efficiently in living cells. Today, despite the dramatic evolution of DNA nanotechnology, a versatile method that replicates artificial DNA nanostructures with complex secondary structures remains an appealing target. Previous success in replicating DNA nanostructures enzymatically in vitro suggests that a possible solution could be cloning these nanostructures by using viruses. Here, we report a system where a single-stranded DNA nanostructure (Holliday junction or paranemic cross-over DNA) is inserted into a phagemid, transformed into XL1-Blue cells and amplified in vivo in the presence of helper phages. High copy numbers of cloned nanostructures can be obtained readily by using standard molecular biology techniques. Correct replication is verified by a number of assays including nondenaturing PAGE, Ferguson analysis, endonuclease VII digestion, and hydroxyl radical autofootprinting. The simplicity, efficiency, and fidelity of nature are fully reflected in this system. UV-induced psoralen cross-linking is used to probe the secondary structure of the inserted junction in infected cells. Our data suggest the possible formation of the immobile four-arm junction in vivo.

scholarly journals Genetically Encoding Ultra-Stable Virus-like Particles Encapsulating Functional DNA Nanostructures in Living Bacteria

2020 ◽  
Author(s):  
Shai Zilberzwige-Tal ◽  
Dan Alon ◽  
Danielle Gazit ◽  
Shahar Zachariah ◽  
Amit Hollander ◽  
...  
Keyword(s):  
Dna Nanotechnology ◽  
Nucleic Acid Content ◽  
Dna Nanostructures ◽  
Loss Of Function ◽  
Virus Like Particles ◽  
Bio Imaging ◽  
Functional Dna ◽  
Biological Environment

Abstract DNA nanotechnology is leading the field of in vitro molecular-scale device engineering, accumulating to a dazzling array of applications from zeolite-like catalysts to bio-imaging. However, while DNA nanostructures' function is robust under in vitro settings, their implementation in real-world conditions requires overcoming their rapid degradation and subsequent loss of function. Viruses are incredibly sophisticated supramolecular assemblies, able to protect their nucleic acid content in the relatively inhospitable biological environment. Inspired by this natural ability, we engineered both in vitro and in vivo technologies, enabling the encapsulation and protection of functional DNA nanostructures inside MS2 bacteriophage virus-like particles (VLPs). We demonstrate the ssDNA-VLPs nanocomposites (NCs) abilities to encapsulate single-stranded-DNA (ssDNA) of an unprecedented variety of sizes (200–1500 nucleotides (nt)), sequences, and structures while retaining their functionality. Moreover, by exposing these NCs to hostile biological conditions, such as human blood serum, we exhibit that the VLPs serves as an excellent protective shell. To the best of our knowledge, these engineered NCs pose key properties that are yet unattainable by current fabrication methods.

scholarly journals Engineering nucleosomes for generating diverse chromatin assemblies

2021 ◽  
Author(s):  
Zenita Adhireksan ◽  
Deepti Sharma ◽  
Phoi Leng Lee ◽  
Qiuye Bao ◽  
Sivaraman Padavattan ◽  
...  
Keyword(s):  
Dynamic Properties ◽  
Dna Nanostructures ◽  
Macromolecular Assemblies ◽  
Maximum Resolution ◽  
Different Types ◽  
Chromatin Structural ◽  
Dna Fragment

Abstract Structural characterization of chromatin is challenging due to conformational and compositional heterogeneity in vivo and dynamic properties that limit achievable resolution in vitro. Although the maximum resolution for solving structures of large macromolecular assemblies by electron microscopy has recently undergone profound increases, X-ray crystallographic approaches may still offer advantages for certain systems. One such system is compact chromatin, wherein the crystalline state recapitulates the crowded molecular environment within the nucleus. Here we show that nucleosomal constructs with cohesive-ended DNA can be designed that assemble into different types of circular configurations or continuous fibers extending throughout crystals. We demonstrate the utility of the method for characterizing nucleosome compaction and linker histone binding at near-atomic resolution but also advance its application for tackling further problems in chromatin structural biology and for generating novel types of DNA nanostructures. We provide a library of cohesive-ended DNA fragment expression constructs and a strategy for engineering DNA-based nanomaterials with a seemingly vast potential variety of architectures and histone chemistries.

scholarly journals Spatiotemporally programmable cascade hybridization of hairpin DNA in polymeric nanoframework for precise siRNA delivery

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Feng Li ◽  
Wenting Yu ◽  
Jiaojiao Zhang ◽  
Yuhang Dong ◽  
Xiaohui Ding ◽  
...  
Keyword(s):  
Steric Effect ◽  
Sirna Delivery ◽  
Dna Nanotechnology ◽  
Hybridization Chain Reaction ◽  
Dna Nanostructures ◽  
Chain Reaction ◽  
Dna Hairpins ◽  
In Vivo Experiments ◽  
Dna And Rna

AbstractDNA nanostructures have been demonstrated as promising carriers for gene delivery. In the carrier design, spatiotemporally programmable assembly of DNA under nanoconfinement is important but has proven highly challenging due to the complexity–scalability–error of DNA. Herein, a DNA nanotechnology-based strategy via the cascade hybridization chain reaction (HCR) of DNA hairpins in polymeric nanoframework has been developed to achieve spatiotemporally programmable assembly of DNA under nanoconfinement for precise siRNA delivery. The nanoframework is prepared via precipitation polymerization with Acrydite-DNA as cross-linker. The potential energy stored in the loops of DNA hairpins can overcome the steric effect in the nanoframework, which can help initiate cascade HCR of DNA hairpins and achieve efficient siRNA loading. The designer tethering sequence between DNA and RNA guarantees a triphosadenine triggered siRNA release specifically in cellular cytoplasm. Nanoframework provides stability and ease of functionalization, which helps address the complexity–scalability–error of DNA. It is exemplified that the phenylboronate installation on nanoframework enhanced cellular uptake and smoothed the lysosomal escape. Cellular results show that the siRNA loaded nanoframework down-regulated the levels of relevant mRNA and protein. In vivo experiments show significant therapeutic efficacy of using siPLK1 loaded nanoframework to suppress tumor growth.

A Molecular Hero Suit for In Vitro and In Vivo DNA Nanostructures

Small ◽  
2019 ◽  
Vol 15 (26) ◽  
pp. 1805386 ◽  
Author(s):  
Megan E. Kizer ◽  
Robert J. Linhardt ◽  
Arun Richard Chandrasekaran ◽  
Xing Wang
Keyword(s):  
Dna Nanostructures

scholarly journals Addressing the Stability of Polygonal DNA Nanostructures In Vitro and In Vivo

2018 ◽  
Vol 114 (3) ◽  
pp. 693a ◽  
Author(s):  
Christina Kolonelou ◽  
Alessandro Bosco ◽  
Björn Högberg ◽  
Ana Teixeira
Keyword(s):  
Dna Nanostructures ◽  
The Stability

A smart ATP-responsive chemotherapy drug-free delivery system using a DNA nanostructure for synergistic treatment of breast cancer in vitro and in vivo

2020 ◽  
Vol 28 (7-8) ◽  
pp. 852-859 ◽  
Author(s):  
Khalil Abnous ◽  
Noor Mohammad Danesh ◽  
Mohammad Ramezani ◽  
Mona Alibolandi ◽  
Amirhossein Bahreyni ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Delivery System ◽  
Chemotherapy Drug ◽  
Dna Nanostructure ◽  
Drug Free

Extended-spectrum resistance to β-lactams/β-lactamase inhibitors (ESRI) evolved from low-level resistant Escherichia coli

2019 ◽  
Author(s):  
Ángel Rodríguez-Villodres ◽  
María Luisa Gil-Marqués ◽  
Rocío Álvarez-Marín ◽  
Rémy A Bonnin ◽  
María Eugenia Pachón-Ibáñez ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Clavulanic Acid ◽  
Genomic Analysis ◽  
E Coli ◽  
Extended Spectrum ◽  
Copy Numbers ◽  
Resistance Patterns ◽  
Amoxicillin Clavulanic Acid

Abstract Objectives Escherichia coli is characterized by three resistance patterns to β-lactams/β-lactamase inhibitors (BLs/BLIs): (i) resistance to ampicillin/sulbactam and susceptibility to amoxicillin/clavulanic acid and piperacillin/tazobactam (RSS); (ii) resistance to ampicillin/sulbactam and amoxicillin/clavulanic acid, and susceptibility to piperacillin/tazobactam (RRS); and (iii) resistance to ampicillin/sulbactam, amoxicillin/clavulanic acid and piperacillin/tazobactam (RRR). These resistance patterns are acquired consecutively, indicating a potential risk of developing resistance to piperacillin/tazobactam, but the precise mechanism of this process is not completely understood. Methods Clinical isolates incrementally pressured by piperacillin/tazobactam selection in vitro and in vivo were used. We determined the MIC of piperacillin/tazobactam in the presence and absence of piperacillin/tazobactam pressure. We deciphered the role of the blaTEM genes in the new concept of extended-spectrum resistance to BLs/BLIs (ESRI) using genomic analysis. The activity of β-lactamase was quantified in these isolates. Results We show that piperacillin/tazobactam resistance is induced in E. coli carrying blaTEM genes. This resistance is due to the increase in copy numbers and transcription levels of the blaTEM gene, thus increasing β-lactamase activity and consequently increasing piperacillin/tazobactam MICs. Genome sequencing of two blaTEM-carrying representative isolates showed that piperacillin/tazobactam treatment produced two types of duplications of blaTEM (8 and 60 copies, respectively). In the clinical setting, piperacillin/tazobactam treatment of patients infected by E. coli carrying blaTEM is associated with a risk of therapeutic failure. Conclusions This study describes for the first time the ESRI in E. coli. This new concept is very important in the understanding of the mechanism involved in the acquisition of resistance to BLs/BLIs.

Cellular processing and destinies of artificial DNA nanostructures

2016 ◽  
Vol 45 (15) ◽  
pp. 4199-4225 ◽  
Author(s):  
Di Sheng Lee ◽  
Hang Qian ◽  
Chor Yong Tay ◽  
David Tai Leong
Keyword(s):  
Dna Nanotechnology ◽  
Dna Nanostructures ◽  
Panoramic View ◽  
Artificial Dna ◽  
Cellular Processing ◽  
Mechanistic Understanding ◽  
The Many ◽  
In Cells

This review gives a panoramic view of the many DNA nanotechnology applications in cells, mechanistic understanding of how and where their interactions occur and their subsequent outcomes.

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