Oligonucleotide (oligo)-based FISH has emerged as an important tool for the study of chromosome organization and gene expression and has been empowered by the commercial availability of highly complex pools of oligos. However, a dedicated bioinformatic design utility has yet to be created spec... Read more
Encryption is a useful tool to protect data confidentiality. Yet it is still challenging to hide the very presence of encrypted, secret data from a powerful adversary. This paper presents a new technique to hide data in flash by manipulating the voltage level of pseudo …
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DNA performs diverse functional roles in biology, nanotechnology and biotechnology, but current methods for autonomously synthesizing arbitrary single-stranded DNA are limited. Here, we introduce the concept of primer exchange reaction (PER) cascades, which grow nascent single-stranded DNA wit... Read more
A natural feature of molecular systems is their inherent stochastic behavior. A fundamental challenge related to the programming of molecular information processing systems is to develop a circuit architecture that controls the stochastic states of individual molecular events. Here we present ... Read more
This paper gives a focussed summary of good practice taken primarily from engineers who are responsible for teaching topics related to systems and control. This engineering specialisation allows the paper to give some degree of focus in the discussions around …
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For decades, in situ hybridization methods have been essential tools for studies of vertebrate development and disease, as they enable qualitative analyses of mRNA expression in an anatomical context. Quantitative mRNA analyses typically sacrifice the …
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Efforts in programming DNA and other biological molecules have recently focused on general schemes to physically implement arbitrary Chemical Reaction Networks. Errors in some of the proposed schemes have driven a desire for formal verification methods. By …
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Chemistries exhibiting complex dynamics-from inorganic oscillators to gene regulatory networks-have been long known but either cannot be reprogrammed at will or rely on the sophisticated enzyme chemistry underlying the central dogma. Can simpler molecular mechanisms, designed from scratch, exh... Read more
Self-folding of an information-carrying polymer into a defined structure is foundational to biology and offers attractive potential as a synthetic strategy. Although multicomponent self-assembly has produced complex synthetic nanostructures, unimolecular folding has seen limited progress. We d... Read more
This book contains information obtained from authentic and highly regarded sources. Reprinted material is quoted with permission, and sources are indicated. A wide variety of references are listed. Reasonable efforts have been made to publish reliable data and …
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For the synthesis of correct-by-construction control policies from temporal logic specifications the scalability of the synthesis algorithms is often a bottle- neck. In this paper, we parallelize synthesis from specifications in the GR(1) frag- ment of linear temporal logic by introducing a hi... Read more
Chemical clocks usually achieve well-defined temporal delays through concentration thresholding coupled to the production, degradation, activation, or inhibition of downstream effectors. In this way, the stochastic dynamics of many individual molecules yield essentially deterministic bulk beha... Read more
Single-molecule localization microscopy (SMLM) can visualize biological targets on the nanoscale, but complex hardware is required to perform SMLM in thick samples. Here, we combine 3D DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) with spinning disk confocal (SDC) har... Read more
DNA nanostructures are a set of materials with well-defined physical, chemical, and biological properties that can be used on their own or incorporated with other materials for many applications. Herein, the practical aspects of utilizing DNA nanostructures (structural …
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DNA nanotechnology is a materials design paradigm in which synthetic nucleic acids are used to program the structure and dynamics of nanometer-scale devices and materials. Driven by the convergence of decreasing DNA synthesis costs, advanced yet easy-to-use …
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Self-assembled DNA nanostructures enable nanometre-precise patterning that can be used to create programmable molecular machines and arrays of functional materials. DNA origami is particularly versatile in this context because each DNA strand in the origami nanostructure occupies a unique posi... Read more
DNA nanotechnology, in particular DNA origami, enables the bottom-up self-assembly of micrometre-scale, three-dimensional structures with nanometre-precise features1,2,3,4,5,6,7,8,9,10,11,12. These structures are customizable in that they can be site-specifically functionalized13 or constructe... Read more
Nucleic acids (DNA and RNA) are widely used to construct nanometre-scale structures with ever increasing complexity, with possible application in fields such as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with ea... Read more
Neural networks are highly sensitive to adversarial examples, which cause large output deviations with only small input perturbations. However, little is known quantitatively about the distribution and prevalence of such adversarial examples. To address this issue, we propose a rigorous search... Read more
Our ability to predict protein expression from DNA sequence alone remains poor, reflecting our limited understanding of cis-regulatory grammar and hampering the design of engineered genes for synthetic biology applications. Here, we generate a model that predicts the protein expression of the ... Read more
Genetic engineering technology has become sophisticated enough to allow precise manipulation of bacterial genetic material. Engineering efforts with these technologies have created modified bacteria for various medical, industrial, and environmental purposes, but organisms designed for specifi... Read more
Evolution has been used to address many engineering problems. Within the context of metabolic engineering and synthetic biology, directed evolution has natural applications. However, most research concerning optimizing microbial evolution has been focused on library generation and screening, w... Read more
Our ability to predict protein expression from DNA sequence alone remains poor, reflecting our limited understanding of cis-regulatory grammar and hampering the design of engineered genes for synthetic biology applications. Here, we generate a model that predicts the protein expression of the ... Read more
High-throughput methods for screening protein-protein interactions enable the rapid characterization of engineered binding proteins and interaction networks. While existing approaches are powerful, none allow quantitative library-on-library characterization of protein interactions in a modifia... Read more
The emerging fields of genetic engineering, synthetic biology, DNA computing, DNA nanotechnology, and molecular programming herald the birth of a new information technology that acquires information by directly sensing molecules within a chemical …
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