scholarly journals Synthetic Biology Parts for the Storage of Increased Genetic Information in Cells

2017 ◽  
Vol 6 (10) ◽  
pp. 1834-1840 ◽  
Author(s):  
Sydney E. Morris ◽  
Aaron W. Feldman ◽  
Floyd E. Romesberg
Keyword(s):  
Synthetic Biology ◽  
Genetic Information ◽  
In Cells

scholarly journals Properties of alternative microbial hosts used in synthetic biology: towards the design of a modular chassis

2016 ◽  
Vol 60 (4) ◽  
pp. 303-313 ◽  
Author(s):  
Juhyun Kim ◽  
Manuel Salvador ◽  
Elizabeth Saunders ◽  
Jaime González ◽  
Claudio Avignone-Rossa ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Genetic Information ◽  
Essential Element ◽  
Model Organisms ◽  
Biotechnological Applications ◽  
Cell Models ◽  
Genetic Circuits ◽  
Metabolic Diversity ◽  
Translational Machinery ◽  
Metabolic Fluxes

The chassis is the cellular host used as a recipient of engineered biological systems in synthetic biology. They are required to propagate the genetic information and to express the genes encoded in it. Despite being an essential element for the appropriate function of genetic circuits, the chassis is rarely considered in their design phase. Consequently, the circuits are transferred to model organisms commonly used in the laboratory, such as Escherichia coli, that may be suboptimal for a required function. In this review, we discuss some of the properties desirable in a versatile chassis and summarize some examples of alternative hosts for synthetic biology amenable for engineering. These properties include a suitable life style, a robust cell wall, good knowledge of its regulatory network as well as of the interplay of the host components with the exogenous circuits, and the possibility of developing whole-cell models and tuneable metabolic fluxes that could allow a better distribution of cellular resources (metabolites, ATP, nucleotides, amino acids, transcriptional and translational machinery). We highlight Pseudomonas putida, widely used in many different biotechnological applications as a prominent organism for synthetic biology due to its metabolic diversity, robustness and ease of manipulation.

scholarly journals Engineering polymerases for applications in synthetic biology

2020 ◽  
Vol 53 ◽  
Author(s):  
Ali Nikoomanzar ◽  
Nicholas Chim ◽  
Eric J. Yik ◽  
John C. Chaput
Keyword(s):  
Cell Division ◽  
Synthetic Biology ◽  
Substrate Specificity ◽  
Physicochemical Properties ◽  
Genetic Information ◽  
Biomedical Applications ◽  
Dna Polymerases ◽  
Enzyme Engineering ◽  
Practical Applications ◽  
Naturally Occurring

Abstract DNA polymerases play a central role in biology by transferring genetic information from one generation to the next during cell division. Harnessing the power of these enzymes in the laboratory has fueled an increase in biomedical applications that involve the synthesis, amplification, and sequencing of DNA. However, the high substrate specificity exhibited by most naturally occurring DNA polymerases often precludes their use in practical applications that require modified substrates. Moving beyond natural genetic polymers requires sophisticated enzyme-engineering technologies that can be used to direct the evolution of engineered polymerases that function with tailor-made activities. Such efforts are expected to uniquely drive emerging applications in synthetic biology by enabling the synthesis, replication, and evolution of synthetic genetic polymers with new physicochemical properties.

Establishment of order in the flow of genetic information in cells

1999 ◽  
Vol 30 (1) ◽  
pp. 35-70 ◽  
Author(s):  
Ram S. Bandyopadhyay ◽  
Douglas V. Faller
Keyword(s):  
Genetic Information ◽  
In Cells

scholarly journals Bioinspired genotype–phenotype linkages: mimicking cellular compartmentalization for the engineering of functional proteins

2015 ◽  
Vol 5 (4) ◽  
pp. 20150035 ◽  
Author(s):  
Liisa D. van Vliet ◽  
Pierre-Yves Colin ◽  
Florian Hollfelder
Keyword(s):  
Synthetic Biology ◽  
Directed Evolution ◽  
Enzyme Catalysis ◽  
Darwinian Evolution ◽  
Oil Droplets ◽  
Shell Beads ◽  
Cellular Compartmentalization ◽  
In Cells

The idea of compartmentalization of genotype and phenotype in cells is key for enabling Darwinian evolution. This contribution describes bioinspired systems that use in vitro compartments—water-in-oil droplets and gel-shell beads—for the directed evolution of functional proteins. Technologies based on these principles promise to provide easier access to protein-based therapeutics, reagents for processes involving enzyme catalysis, parts for synthetic biology and materials with biological components.

The Structure of DNA Taking Into Account the Higher Dimension of Its Components

2021 ◽  
pp. 730-747
Author(s):  
Gennadiy Vladimirovich Zhizhin
Keyword(s):  
Phosphoric Acid ◽  
Genetic Information ◽  
Higher Dimension ◽  
Dna Molecules ◽  
Dna Molecule ◽  
First Time ◽  
In Cells

The process of formation of spirals (right and left) in the DNA molecule is described for the first time. Representations of the higher dimensionality of the constituent DNA molecules (D-ribose and phosphoric acid ion), developed in the previous works of the author, are used. Images of a DNA molecule with elements of higher dimension are presented. The higher dimensionality of the constituent DNA molecules, which allows to describe mathematically the structure of DNA, requires reconsidering the issues of tight packing of DNA molecules in cells, viruses and bacteria, provided that the DNA chains necessary for the preservation and transfer of genetic information are complementary.

Ribozymes and aptamers in the RNA world, and in synthetic biology

2016 ◽  
Author(s):  
◽  
Raghav Raj Poudyal
Keyword(s):  
Synthetic Biology ◽  
Genetic Information ◽  
Rna World ◽  
Information Storage ◽  
Rna Aptamers ◽  
Darwinian Evolution ◽  
University Of Missouri ◽  
Biologically Relevant ◽  
Functional Rnas

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] The RNA world hypothesis postulates that Ribonucleic Acids (RNA) may have provided functions of catalysis and genetic information storage during the origin of life on earth. An RNA based life is hypothesized to have undergone Darwinian evolution to ultimately lead into extant biology, where DNA is used as the repository for genetic information and proteins are used as biological catalysts. The discovery of functional RNAs such as catalytic RNAs, regulatory RNAs, and ligand-binding RNA aptamers further strengthen this hypothesis. These functional RNAs are also used as tools for synthetic biology and therapeutics. This work highlights strategies used by RNA enzymes (Ribozymes) for catalysis of chemical reactions, and explores new chemistries catalyzed by ribozymes. We also engineered an in vitro evolved ribozyme to control activities of other functional RNA molecules. Finally, this work explores innovative approaches to discover new RNA enzymes that catalyze biologically relevant reactions. Findings from these studies have revealed potential roles of RNA enzymes during the primordial earth, and also opened doors to build RNA-based tools that regulate biological processes.

scholarly journals Biocomputing and Synthetic Biology in Cells: Cells Special Issue

Cells ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 2459
Author(s):  
Feifei Cui ◽  
Quan Zou
Keyword(s):  
Synthetic Biology ◽  
Special Issue ◽  
In Cells

Biocomputing and synthetic biology have been two of the most exciting emerging fields in recent years [...]

scholarly journals Analog synthetic biology

2014 ◽  
Vol 372 (2012) ◽  
pp. 20130110 ◽  
Author(s):  
R. Sarpeshkar
Keyword(s):  
Synthetic Biology ◽  
Feedback Linearization ◽  
Dynamic Range ◽  
Analog Computation ◽  
Digital Computation ◽  
Use Of Resources ◽  
Time Space ◽  
Gene And Protein Expression ◽  
Pros And Cons ◽  
In Cells

We analyse the pros and cons of analog versus digital computation in living cells. Our analysis is based on fundamental laws of noise in gene and protein expression, which set limits on the energy, time, space, molecular count and part-count resources needed to compute at a given level of precision. We conclude that analog computation is significantly more efficient in its use of resources than deterministic digital computation even at relatively high levels of precision in the cell. Based on this analysis, we conclude that synthetic biology must use analog, collective analog, probabilistic and hybrid analog–digital computational approaches; otherwise, even relatively simple synthetic computations in cells such as addition will exceed energy and molecular-count budgets. We present schematics for efficiently representing analog DNA–protein computation in cells. Analog electronic flow in subthreshold transistors and analog molecular flux in chemical reactions obey Boltzmann exponential laws of thermodynamics and are described by astoundingly similar logarithmic electrochemical potentials. Therefore, cytomorphic circuits can help to map circuit designs between electronic and biochemical domains. We review recent work that uses positive-feedback linearization circuits to architect wide-dynamic-range logarithmic analog computation in Escherichia coli using three transcription factors, nearly two orders of magnitude more efficient in parts than prior digital implementations.

Crystal structures of deprotonated nucleobases from an expanded DNA alphabet

2016 ◽  
Vol 72 (12) ◽  
pp. 952-959 ◽  
Author(s):  
Mariko F. Matsuura ◽  
Hyo-Joong Kim ◽  
Daisuke Takahashi ◽  
Khalil A. Abboud ◽  
Steven A. Benner
Keyword(s):  
Crystal Structure ◽  
Information System ◽  
Hydrogen Bonding ◽  
Synthetic Biology ◽  
Genetic Information ◽  
Hydrogen Bonding Pattern ◽  
Artificial Dna ◽  
Donor Acceptor ◽  
Crystallization Conditions ◽  
New Form

Reported here is the crystal structure of a heterocycle that implements a donor–donor–acceptor hydrogen-bonding pattern, as found in theZcomponent [6-amino-5-nitropyridin-2(1H)-one] of an artificially expanded genetic information system (AEGIS). AEGIS is a new form of DNA from synthetic biology that has six replicable nucleotides, rather than the four found in natural DNA. Remarkably,Zcrystallizes from water as a 1:1 complex of its neutral and deprotonated forms, and forms a `skinny' pyrimidine–pyrimidine pair in this structure. The pair resembles the known intercalated cytosine pair. The formation of the same pair in two different salts, namely poly[[aqua(μ6-2-amino-6-oxo-3-nitro-1,6-dihydropyridin-1-ido)sodium]–6-amino-5-nitropyridin-2(1H)-one–water (1/1/1)], denoted Z-Sod, {[Na(C5H4N3O3)(H2O)]·C5H5N3O3·H2O}n, and ammonium 2-amino-6-oxo-3-nitro-1,6-dihydropyridin-1-ide–6-amino-5-nitropyridin-2(1H)-one–water (1/1/1), denoted Z-Am, NH4+·C5H4N3O3−·C5H5N3O3·H2O, under two different crystallization conditions suggests that the pair is especially stable. Implications of this structure for the use of this heterocycle in artificial DNA are discussed.

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