scholarly journals Research on DNA Nanostructures Based on the Hybrid Chain Reaction for the Assignment Problem

2021 ◽  
Vol 2021 ◽  
pp. 1-6
Author(s):  
Risheng Wang ◽  
Zhixiang Yin ◽  
Jing Yang ◽  
Xinmu Yang ◽  
Zhen Tang
Keyword(s):  
Information Processing ◽  
Assignment Problem ◽  
Feasible Solution ◽  
Optimal Solution ◽  
Dna Origami ◽  
Hairpin Structure ◽  
Dna Nanostructures ◽  
Chain Reaction ◽  
Light Emitting ◽  
Starting Point

Nanostructures with information processing play an important role in many fields. It is an excellent approach to the application that DNA nanostructures represented by DNA origami molecules combine with the hybrid chain reaction. In this paper, the assignment problem is mapped to a combinatorial graph on the DNA origami substrate. The graph has several modules corresponding to the time efficiency matrix of the assignment problem. The starting chain of the corresponding module is hybridized with the hairpin structure of the starting point, and the corresponding module is opened to emit light. The feasible solution to the problem can be obtained by observing the light-emitting fluorescent numbers of the opened modules. The fluorescent numbers of all the opened modules are added up on the same origami substrate, then different opening methods in different test tubes are compared, and the optimal solution is obtained.

scholarly journals DNA Origami Model for Simple Image Decoding

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Risheng Wang ◽  
Zhixiang Yin ◽  
Jianzhong Cui ◽  
Jing Yang ◽  
Zhen Tang ◽  
...  
Keyword(s):  
Self Assembly ◽  
Molecular Beacon ◽  
Important Application ◽  
Dna Origami ◽  
Hairpin Structure ◽  
Hybridization Chain Reaction ◽  
Chain Reaction ◽  
Reaction Solution ◽  
Application Methods ◽  
Image Decoding

DNA origami is the application of self-assembly in nanotechnology. The combination of DNA origami and hybridization chain reaction is one of the important application methods of DNA origami. In this paper, DNA origami is used to design the cipher pattern on the base of origami. The cipher chain, which is put into the reaction solution, hybridizes with the molecular beacon and the hairpin structure that form the cipher pattern to build a DNA origami model that can decode the pattern. The cipher chain consists of the starting chain and the intermediate chain. When the cipher is correct, the cipher chain can open the molecular beacon and the hairpin structure to display the cipher pattern on the origami base in the solution.

scholarly journals On the Simplex Algorithm Initializing

2012 ◽  
Vol 2012 ◽  
pp. 1-15 ◽  
Author(s):  
Nebojša V. Stojković ◽  
Predrag S. Stanimirović ◽  
Marko D. Petković ◽  
Danka S. Milojković
Keyword(s):  
Feasible Solution ◽  
Numerical Test ◽  
Optimal Solution ◽  
Simplex Algorithm ◽  
Initial Solution ◽  
Test Problems ◽  
Basic Feasible Solution ◽  
Cpu Time ◽  
Starting Point ◽  
Number Of Iterations

This paper discusses the importance of starting point in the simplex algorithm. Three different methods for finding a basic feasible solution are compared throughout performed numerical test examples. We show that our two methods on theNetlibtest problems have better performances than the classical algorithm for finding initial solution. The comparison of the introduced optimization softwares is based on the number of iterative steps and on the required CPU time. It is pointed out that on average it takes more iterations to determine the starting point than the number of iterations required by the simplex algorithm to find the optimal solution.

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.

Computationally Simple and Efficient Method for Solving Real-Life Mixed Intuitionistic Fuzzy 3D Assignment Problems

2022 ◽  
Vol 14 (1) ◽  
pp. 0-0
Keyword(s):  
Assignment Problem ◽  
Graphical Representation ◽  
Real Life ◽  
Optimal Solution ◽  
Future Research ◽  
Assignment Problems ◽  
3 Dimensional ◽  
Intuitionistic Fuzzy ◽  
Comparison Results ◽  
Future Research Directions

This article addresses the 3-dimensional mixed intuitionistic fuzzy assignment problems (3D-MIFAPs). In this article, firstly, the author formulates an assignment problem (AP) and assumes the parameters are in uncertainty with hesitation. Secondly, based on the nature of the parameter the author defines various types of solid assignment problem (SAP) in uncertain environment. Thirdly, to solve 3D-MIFAP the PSK method for finding an optimal solution of fully intuitionistic fuzzy assignment problem (FIFAP) is extended by the author. Fourthly, the author presents the proofs of the proposed theorems and corollary. Fifthly, the proposed approach is illustrated with three numerical examples and the optimal objective value of 3D-MIFAP is obtained in the form of intuitionistic fuzzy number and the solution is checked with MATLAB and their coding are also given by the author. Sixthly, the author presents the comparison results and their graphical representation, merits and demerits of the proposed and existing methods and finally the author presents conclusion and future research directions.

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

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.

scholarly journals Dendrites enable a robust mechanism for neuronal stimulus selectivity

2015 ◽  
Author(s):  
Romain D. Cazé ◽  
Sarah Jarvis ◽  
Amanda J. Foust ◽  
Simon R. Schultz
Keyword(s):  
Spatial Distribution ◽  
Information Processing ◽  
Linear Model ◽  
Cortical Neurons ◽  
General Mechanism ◽  
Starting Point ◽  
Dendritic Processing ◽  
Non Linear ◽  
Equivalent Linear Model ◽  
Preferred Stimulus

AbstractHearing, vision, touch-underlying all of these senses is stimulus selectivity, a robust information processing operation in which cortical neurons respond more to some stimuli than to others. Previous models assume that these neurons receive the highest weighted input from an ensemble encoding the preferred stimulus, but dendrites enable other possibilities. Non-linear dendritic processing can produce stimulus selectivity based on the spatial distribution of synapses, even if the total preferred stimulus weight does not exceed that of non-preferred stimuli. Using a multi-subunit non-linear model, we demonstrate that stimulus selectivity can arise from the spatial distribution of synapses. We propose this as a general mechanism for information processing by neurons possessing dendritic trees. Moreover, we show that this implementation of stimulus selectivity increases the neuron's robustness to synaptic and dendritic failure. Importantly, our model can maintain stimulus selectivity for a larger range of synapses or dendrites loss than an equivalent linear model. We then use a layer 2/3 biophysical neuron model to show that our implementation is consistent with two recent experimental observations: (1) one can observe a mixture of selectivities in dendrites, that can differ from the somatic selectivity, and (2) hyperpolarization can broaden somatic tuning without affecting dendritic tuning. Our model predicts that an initially non-selective neuron can become selective when depolarized. In addition to motivating new experiments, the model's increased robustness to synapses and dendrites loss provides a starting point for fault-resistant neuromorphic chip development.

scholarly journals DNA Origami Nanomachines

Molecules ◽  
2018 ◽  
Vol 23 (7) ◽  
pp. 1766 ◽  
Author(s):  
Masayuki Endo ◽  
Hiroshi Sugiyama
Keyword(s):  
Dna Sequences ◽  
Molecular Motors ◽  
Molecular Machines ◽  
Dna Origami ◽  
Dna Nanostructures ◽  
Molecular Systems ◽  
Nanoscale Structures ◽  
Research Fields ◽  
Dna Strands ◽  
External Stimuli

DNA can assemble various molecules and nanomaterials in a programmed fashion and is a powerful tool in the nanotechnology and biology research fields. DNA also allows the construction of desired nanoscale structures via the design of DNA sequences. Structural nanotechnology, especially DNA origami, is widely used to design and create functionalized nanostructures and devices. In addition, DNA molecular machines have been created and are operated by specific DNA strands and external stimuli to perform linear, rotational, and reciprocating movements. Furthermore, complicated molecular systems have been created on DNA nanostructures by arranging multiple molecules and molecular machines precisely to mimic biological systems. Currently, DNA nanomachines, such as molecular motors, are operated on DNA nanostructures. Dynamic DNA nanostructures that have a mechanically controllable system have also been developed. In this review, we describe recent research on new DNA nanomachines and nanosystems that were built on designed DNA nanostructures.

Sign in / Sign up

Export Citation Format

Share Document