Allostery of DNA nanostructures controlled by enzymatic modifications

Abstract Allostery is comprehensively studied for natural macromolecules, such as proteins and nucleic acids. Here, we present controllable allostery of synthetic DNA nanostructure–enzyme systems. Rational designs of the synthetic allosteric systems are based on an in-depth understanding of allosteric sites with several types of strand placements, whose varying stacking strengths determine the local conformation and ultimately lead to a gradient level of allosteric transition. When enzymes in a molecular cloning toolbox such as DNA polymerase, exonuclease and ligase are applied to treat the allosteric sites, the resulting local conformational changes propagate through the entire structure for a global allosteric transition.

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Biophysical characterization of DNA origami nanostructures reveals inaccessibility to intercalation binding sites

10.1101/845420 ◽

2019 ◽

Author(s):

Helen L. Miller ◽

Sonia Contera ◽

Adam J.M. Wollman ◽

Adam Hirst ◽

Katherine E. Dunn ◽

...

Keyword(s):

Drug Delivery ◽

Single Molecule ◽

Targeted Drug Delivery ◽

Binding Sites ◽

Dna Origami ◽

Target Cells ◽

Dna Nanostructures ◽

Synthetic Dna ◽

Drug Molecules ◽

Targeted Drug

AbstractIntercalation of drug molecules into synthetic DNA nanostructures formed through self-assembled origami has been postulated as a valuable future method for targeted drug delivery. This is due to the excellent biocompatibility of synthetic DNA nanostructures, and high potential for flexible programmability including facile drug release into or near to target cells. Such favourable properties may enable high initial loading and efficient release for a predictable number of drug molecules per nanostructure carrier, important for efficient delivery of safe and effective drug doses to minimise non-specific release away from target cells. However, basic questions remain as to how intercalation-mediated loading depends on the DNA carrier structure. Here we use the interaction of dyes YOYO-1 and acridine orange with a tightly-packed 2D DNA origami tile as a simple model system to investigate intercalation-mediated loading. We employed multiple biophysical techniques including single-molecule fluorescence microscopy, atomic force microscopy, gel electrophoresis and controllable damage using low temperature plasma on synthetic DNA origami samples. Our results indicate that not all potential DNA binding sites are accessible for dye intercalation, which has implications for future DNA nanostructures designed for targeted drug delivery.

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An electrochemical aptasensor based on cocoon-like DNA nanostructure signal amplification for the detection of Escherichia coli O157:H7

The Analyst ◽

10.1039/d0an01258k ◽

2020 ◽

Vol 145 (22) ◽

pp. 7340-7348

Author(s):

Huasong Bai ◽

Shengjun Bu ◽

Wensen Liu ◽

Chengyu Wang ◽

Zhongyi Li ◽

...

Keyword(s):

Escherichia Coli ◽

Signal Amplification ◽

Selective Detection ◽

Escherichia Coli O157 ◽

Dna Nanostructures ◽

Electrochemical Aptasensor ◽

Dna Nanostructure ◽

Highly Sensitive

We developed an electrochemical aptasensor based on cocoon-like DNA nanostructures as signal tags for highly sensitive and selective detection of Escherichia coli O157:H7.

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DNA nanostructures coordinate gene silencing in mature plants

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1818290116 ◽

2019 ◽

Vol 116 (15) ◽

pp. 7543-7548 ◽

Cited By ~ 34

Author(s):

Huan Zhang ◽

Gozde S. Demirer ◽

Honglu Zhang ◽

Tianzheng Ye ◽

Natalie S. Goh ◽

...

Keyword(s):

Cell Wall ◽

Gene Silencing ◽

Plant Cell ◽

Mammalian Cells ◽

Plant Cell Wall ◽

Plant Cells ◽

Design Parameters ◽

Dna Nanostructures ◽

Dna Nanostructure ◽

The Impact

Delivery of biomolecules to plants relies onAgrobacteriuminfection or biolistic particle delivery, the former of which is amenable only to DNA delivery. The difficulty in delivering functional biomolecules such as RNA to plant cells is due to the plant cell wall, which is absent in mammalian cells and poses the dominant physical barrier to biomolecule delivery in plants. DNA nanostructure-mediated biomolecule delivery is an effective strategy to deliver cargoes across the lipid bilayer of mammalian cells; however, nanoparticle-mediated delivery without external mechanical aid remains unexplored for biomolecule delivery across the cell wall in plants. Herein, we report a systematic assessment of different DNA nanostructures for their ability to internalize into cells of mature plants, deliver siRNAs, and effectively silence a constitutively expressed gene inNicotiana benthamianaleaves. We show that nanostructure internalization into plant cells and corresponding gene silencing efficiency depends on the DNA nanostructure size, shape, compactness, stiffness, and location of the siRNA attachment locus on the nanostructure. We further confirm that the internalization efficiency of DNA nanostructures correlates with their respective gene silencing efficiencies but that the endogenous gene silencing pathway depends on the siRNA attachment locus. Our work establishes the feasibility of biomolecule delivery to plants with DNA nanostructures and both details the design parameters of importance for plant cell internalization and also assesses the impact of DNA nanostructure geometry for gene silencing mechanisms.

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A method for the specific Inhibition of poly[d(A-T)] synthesis using the A-T specific quinoxaline antibiotic TANDEM

Canadian Journal of Biochemistry ◽

10.1139/o82-018 ◽

1982 ◽

Vol 60 (2) ◽

pp. 131-136 ◽

Cited By ~ 7

Author(s):

D. H. Evans ◽

J. S. Lee ◽

A. R. Morgan ◽

R. K. Olsen

Keyword(s):

Escherichia Coli ◽

Dna Polymerase ◽

Thermal Denaturation ◽

Strong Preference ◽

Specific Inhibition ◽

Dna Polymerase I ◽

Synthetic Dna ◽

Polymerase I

A serious problem in the replication of repeating-sequence DNA polymers using Escherichia coli DNA polymerase I arises from the fact that this polymerase has a very strong preference for the replication of poly[d(A-T)]. Thus reactions primed with DNA containing small amounts of contaminating poly[d(A-T)] will eventually result in complete domination of the synthesis by poly[d(A-T)]. This problem can be overcome by the addition to the reaction mixture of the synthetic quinoxaline antibiotic TANDEM which binds specifically to poly[d(A-T)] completely inhibiting its replication. Using thermal denaturation experiments it can be shown that TANDEM does not bind to most other synthetic DNA polymers (e.g., poly(dA)∙poly(dT) and poly[d(A-T-C)]∙poly[d(G-A-T)]) and therefore their replication is not inhibited. The only exception we have encountered is poly[d(T-A-C)]∙poly[d(G-T-A)] which does bind TANDEM and therefore the drug cannot be used during the synthesis of this polymer. The fact that poly[d(T-A-C)]-poly[d(G-T-A)] does bind TANDEM while poly [d(A-T-C)]-poly[d(G-A-T)] does not, suggests that the drug recognizes T-A rather than A-T sequences.

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Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms

Theoretical Chemistry Accounts ◽

10.1007/s00214-012-1287-7 ◽

2012 ◽

Vol 131 (12) ◽

Cited By ~ 29

Author(s):

Tamar Schlick ◽

Karunesh Arora ◽

William A. Beard ◽

Samuel H. Wilson

Keyword(s):

Dna Polymerase ◽

Conformational Changes

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Probing Conformational Changes of Human DNA Polymerase λ using Mass Spectrometry-Based Protein Footprinting

Journal of Molecular Biology ◽

10.1016/j.jmb.2009.05.037 ◽

2009 ◽

Vol 390 (3) ◽

pp. 368-379 ◽

Cited By ~ 11

Author(s):

Jason D. Fowler ◽

Jessica A. Brown ◽

Mamuka Kvaratskhelia ◽

Zucai Suo

Keyword(s):

Mass Spectrometry ◽

Dna Polymerase ◽

Conformational Changes ◽

Protein Footprinting ◽

Human Dna ◽

Dna Polymerase Λ

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FOLDNA, a Web Server for Self-Assembled DNA Nanostructure Autoscaffolds and Autostaples

Journal of Nanotechnology ◽

10.1155/2012/453953 ◽

2012 ◽

Vol 2012 ◽

pp. 1-5 ◽

Cited By ~ 3

Author(s):

Chensheng Zhou ◽

Heng Luo ◽

Xiaolu Feng ◽

Xingwang Li ◽

Jie Zhu ◽

...

Keyword(s):

Drug Delivery ◽

Dna Sequences ◽

Self Assembly ◽

Web Server ◽

Automatic Design ◽

Dna Nanostructures ◽

Complementary Dna ◽

Dna Nanostructure ◽

Comprehensive Information ◽

Self Assembled

DNA self-assembly is a nanotechnology that folds DNA into desired shapes. Self-assembled DNA nanostructures, also known as origami, are increasingly valuable in nanomaterial and biosensing applications. Two ways to use DNA nanostructures in medicine are to form nanoarrays, and to work as vehicles in drug delivery. The DNA nanostructures perform well as a biomaterial in these areas because they have spatially addressable and size controllable properties. However, manually designing complementary DNA sequences for self-assembly is a technically demanding and time consuming task, which makes it advantageous for computers to do this job instead. We have developed a web server, FOLDNA, which can automatically design 2D self-assembled DNA nanostructures according to custom pictures and scaffold sequences provided by the users. It is the first web server to provide an entirely automatic design of self-assembled DNA nanostructure, and it takes merely a second to generate comprehensive information for molecular experiments including: scaffold DNA pathways, staple DNA directions, and staple DNA sequences. This program could save as much as several hours in the designing step for each DNA nanostructure. We randomly selected some shapes and corresponding outputs from our server and validated its performance in molecular experiments.

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5′-(CGA) n sequence-assisted pH-controlled assembly of supramolecular DNA nanostructure

Royal Society Open Science ◽

10.1098/rsos.180123 ◽

2018 ◽

Vol 5 (8) ◽

pp. 180123

Author(s):

Yuting Yan ◽

Yanwei Cao ◽

Chunsheng Xiao ◽

Yang Li ◽

Xiaoxuan Xiang ◽

...

Keyword(s):

Dna Nanostructures ◽

Controlled Assembly ◽

Dna Nanostructure ◽

Ph Values ◽

Dna Strands ◽

The Stability ◽

Size Controlled ◽

Ph Controlled

Herein, the DNA strands containing 5′-(CGA) n and consecutive guanines are used to construct supramolecular DNA nanostructures that are size-controlled by pH values. Additionally, the introduction of thymine linkers within DNA nanostructures is necessary to maintain the stability of long-sized nanostructures. This work also demonstrates a method for accurately building DNA nanostructures.

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