In silico modelling of DNA nanostructures

Kekić, Tadija; Barišić, Ivan

doi:10.1016/j.csbj.2020.05.016

Cited by 17 publications

(19 citation statements)

References 55 publications

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“…With the advance of in silico design tools such as caDNAno, Tiamat, CanDo, and DAEDALUS, the design of such DNA nanostructures is now a relatively fast and well-developed process 23 . To start simulation, we use caDNAno to design DNA nanotubes as the input structure for coarse grained model simulation on oxDNA platform 24 . According to previous study, such DNA nanotube has the diameter with an average of 13.5 nm, the circumference contains 14 DNA tiles (Figure 1, Figure S1) 24,25 .…”

Section: Resultsmentioning

confidence: 99%

Forecasting the Reaction of DNA Modifying Enzymes on DNA Nanostructures by Coarse Grained Model for Stimuli-Responsive Drug Delivery

Deng¹,

Tan²,

Zhang³

et al. 2021

Preprint

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The reactivity of DNA modifying enzymes on their natural nucleic acid substrates has been fully understood. However, their reactivity on self-assembled nanostructures of nucleic acid is complicated and unpredictable. Here, we employed the molecular dynamic simulation to forecast the reactivity of tumor biomarker enzymes on DNA nanotubes by coarse grained model. It is found that the enzyme accessibility and the potential energy of the reaction products co-determine the structural change of DNA nanotubes. The reactivity can be regulated by the position of enzyme recognition site. According to the simulation results, stimuli-responsive drug nanocarrier with superior sensitivity and selectivity was developed. Drug payloads released in cancer cells is 3.7~5.5-fold higher than that in normal cells. The DNA nanocarrier equipped with cancer-specific aptamer AS1411 is used to deliver doxorubicin (DOX) to tumor-bearing mice not only effectively inhibiting tumor growth but also protecting major organs from drug-caused damage. This work provides new insights into the enzymatic reactivity of DNA nanostructures enriching the library of DNA-based reactions and heralding broad applications in nanomedicine.

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Section: Resultsmentioning

confidence: 99%

Forecasting the Reaction of DNA Modifying Enzymes on DNA Nanostructures by Coarse Grained Model for Stimuli-Responsive Drug Delivery

Deng¹,

Tan²,

Zhang³

et al. 2021

Preprint

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“…Here, our main focus is on the different robotic mechanisms and their intriguing applications, so the readers are suggested to refer to other sources for multiple DNA design and simulation software options. Both modeling and validation methods have been recently reviewed in ref ( 62 ), and in more detail, for the design of the DNA nanostructures, see, e.g. , ref ( 14 ) (various approaches) or ref ( 17 ) (wireframe constructions), and for the simulation software, see, e.g.…”

Section: Principles Of Mechanical Movement and Characterization Of Momentioning

confidence: 99%

Robotic DNA Nanostructures

et al. 2020

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Over the past decade, DNA nanotechnology has spawned a broad variety of functional nanostructures tailored toward the enabled state at which applications are coming increasingly in view. One of the branches of these applications is in synthetic biology, where the intrinsic programmability of the DNA nanostructures may pave the way for smart task-specific molecular robotics. In brief, the synthesis of the user-defined artificial DNA nano-objects is based on employing DNA molecules with custom lengths and sequences as building materials that predictably assemble together by obeying Watson–Crick base pairing rules. The general workflow of creating DNA nanoshapes is getting more and more straightforward, and some objects can be designed automatically from the top down. The versatile DNA nano-objects can serve as synthetic tools at the interface with biology, for example, in therapeutics and diagnostics as dynamic logic-gated nanopills, light-, pH-, and thermally driven devices. Such diverse apparatuses can also serve as optical polarizers, sensors and capsules, autonomous cargo-sorting robots, rotary machines, precision measurement tools, as well as electric and magnetic-field directed robotic arms. In this review, we summarize the recent progress in robotic DNA nanostructures, mechanics, and their various implementations.

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“…[27,28] These programmable DNA nanostructures with uniform sizes and shapes can be achieved by the tile-assembly approach, en-zymaticR CA-based procedure, non-enzymatic HCR-involved procedure, DNA origami technique, and so on ( Figure 1). [29] Tile-based DNA assemblies Self-assembled DNA nanotechnology was initiated with the construction of tile-based junctionsa nd lattices. [1] Additionally, the tile-based DNA nanostructures represent am ajor research topic in this emerging research field in the first two decades.…”

Section: Construction Of Elemental Dna Nanostructuresmentioning

confidence: 99%

Construction of Smart Stimuli‐Responsive DNA Nanostructures for Biomedical Applications

Wang

Luo

Wang

et al. 2020

Chemistry A European J

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DNA nanostructures have recently attracted increasing interest in biological and biomedical applications by virtue of their uniquep roperties, such as structuralp rogrammability, multi-functionality,s timuli-responsive behaviors, and excellentb iocompatibility.I np articular,t he intelligent responsivenesso fs mart DNA nanostructures to specific stimuli hasf acilitated their extensive developmenti nt he field of high-performance biosensing and controllable drug delivery.T his minireview begins with different self-assembly strategies for the construction of various DNA nanostructures, followed by the introduction of av ariety of stimuli-responsive functional DNA nanostructures for assembling metastable soft materials and for facilitating amplified biosensing.T he recent achievements of smartD NA nanostructures for controllable drug delivery are highlighted. Finally, the current challenges and possible developments of this promising research are discussed in the fields of intelligent nanomedicine.

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In silico modelling of DNA nanostructures

Cited by 17 publications

References 55 publications

Forecasting the Reaction of DNA Modifying Enzymes on DNA Nanostructures by Coarse Grained Model for Stimuli-Responsive Drug Delivery

Forecasting the Reaction of DNA Modifying Enzymes on DNA Nanostructures by Coarse Grained Model for Stimuli-Responsive Drug Delivery

Robotic DNA Nanostructures

Construction of Smart Stimuli‐Responsive DNA Nanostructures for Biomedical Applications

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