3.8 Review

Synthetic Biology: Major Principles and Current Trends of Development in Russia

Related references

Note: Only part of the references are listed.
Review Chemistry, Multidisciplinary

DNA synthesis technologies to close the gene writing gap

Alex Hoose et al.

Summary: The demand for synthetic DNA is growing in various research and commercial fields. If DNA can be provided at scale and low cost, it will accelerate developments in engineering biology, therapy, data storage, and nanotechnology. Although DNA synthesis is already a thriving industry, synthesizing sequences longer than 200 base pairs remains expensive. To address this issue, alternative technologies such as molecular assembly, cloning methods, enzymatic synthesis, microarray, and rolling circle amplification have been developed. This article reviews the progress and commercialization of these technologies, discusses their pros and cons, the need for oversight and regulatory policies, and presents an overview of DNA synthesis business models.

NATURE REVIEWS CHEMISTRY (2023)

Review Biochemistry & Molecular Biology

RNA-Dependent RNA Targeting by CRISPR-Cas Systems: Characterizations and Applications

Natalia Gunitseva et al.

Summary: The currently available genome editing technologies have a significant impact on various fields such as molecular biology, medicine, and biotechnology. The use of RNA-targeting systems in genome editing provides a promising alternative for controlling gene expression without complete elimination. The innovative CRISPR-Cas RNA-targeting systems have revolutionized biosensing systems and opened up possibilities for various applications including genomic editing, virus diagnostics, biomarkers, and transcription regulations. This review discusses the state-of-the-art of specific CRISPR-Cas systems that bind and cleave RNA substrates, and summarizes the potential applications of versatile RNA-targeting systems.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2023)

Article Mathematical & Computational Biology

Synthetic biology open language (SBOL) version 3.1.0

Lukas Buecherl et al.

Summary: Synthetic biology applies engineering principles to design biological systems, and the Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information. SBOL 3.1.0 improves on version 3.0.0 with validation rules, an online repository for best practices, and updates based on community-approved enhancement proposals.

JOURNAL OF INTEGRATIVE BIOINFORMATICS (2023)

Review Chemistry, Multidisciplinary

Synthetic Cells: From Simple Bio-Inspired Modules to Sophisticated Integrated Systems

Camila Guindani et al.

Summary: Bottom-up synthetic biology is the scientific approach of building systems that imitate the structure and function of living cells from the ground up. Recent developments have allowed scientists to engineer synthetic cells and organelles that mimic the essential functions and behaviors of natural cells.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2022)

Review Biotechnology & Applied Microbiology

Merging automation and fundamental discovery into the design-build-test-learn cycle of nontraditional microbes

Nicolas Gurdo et al.

Summary: This article proposes a 'metabolism-centric' approach to the design-build-test-learn cycle in synthetic biology, supported by multi-omic analyses, to facilitate the deployment of microbial cell factories designed for bioproduction beyond the typical landscape of target products.

TRENDS IN BIOTECHNOLOGY (2022)

Review Biochemistry & Molecular Biology

Synthetic chromosomes, genomes, viruses, and cells

J. Craig Venter et al.

Summary: Synthetic genomics involves synthesizing complete genomes or chromosomes to create viruses, bacteria, and eukaryotic cells. This field has revolutionized viral reverse genetics, vaccine design, and bacterial resistance. Future advances in DNA synthesis will open up extraordinary opportunities in medicine, industry, agriculture, and research.
Review Biochemical Research Methods

New synthetic biology tools for metabolic control

Xueqin Lv et al.

Summary: In industrial bioprocesses, controlling microbial metabolism is crucial for enhancing product yields and advancing towards a bio-based economy. Recent developments in machine learning-based metabolic modeling, CRISPR-derived synthetic biology tools, and synthetic genetic circuits have greatly aided in manipulating metabolic pathways and gene expression in microorganisms for bioproduction. This review highlights the latest advancements and the challenges in metabolic engineering strategies.

CURRENT OPINION IN BIOTECHNOLOGY (2022)

Review Multidisciplinary Sciences

Direct and indirect impacts of synthetic biology on biodiversity conservation

Nicholas B. W. Macfarlane et al.

Summary: The potential application of synthetic biology to biodiversity conservation can have both positive and negative impacts. It is important to consider these impacts in light of the ongoing biodiversity loss. The negotiation of the post-2020 Global Biodiversity Framework by the United Nations provides an opportunity for synthetic biologists, conservationists, and policy makers to come together and discuss the application of these technologies to biodiversity conservation.

ISCIENCE (2022)

Article Biochemistry & Molecular Biology

Targeted Modification of Mammalian DNA by a Novel Type V Cas12a Endonuclease from Ruminococcus bromii

Ruslan Vasilev et al.

Summary: A novel enzyme, RbCas12a, has been discovered in this study, which can efficiently cleave DNA in a wide temperature range and be active in mammalian cells when charged by RNA. This enzyme shows potential for clinical and biotechnological applications in genome editing.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

Review Biotechnology & Applied Microbiology

Synthetic Biological Circuits within an Orthogonal Central Dogma

Alan Costello et al.

Summary: Researchers aim to control cellular behavior by reducing or eliminating unwanted interactions, in order to achieve reliable and predictable gene circuits and develop context-independent biological activities. Current focus is on biological orthogonalization, isolating researcher-specified bioactivities from host processes, with the potential to create an orthogonal central dogma and novel cellular functions.

TRENDS IN BIOTECHNOLOGY (2021)

Review Biochemical Research Methods

Multilayer Genetic Circuits for Dynamic Regulation of Metabolic Pathways

Shixiu Cui et al.

Summary: Dynamic regulation of metabolic pathways involves complex genetic circuits to process various signals and control metabolic flux for optimal synthesis of target molecules.

ACS SYNTHETIC BIOLOGY (2021)

Article Microbiology

Simultaneous Multiplex Genome Engineering via Accelerated Natural Transformation in Bacillus subtilis

Aihua Deng et al.

Summary: SMGE is a rapid and efficient method for simultaneous multiplex genome engineering in Bacillus subtilis through one-step natural transformation. By adjusting the transformed DNA, competence factors and recombinases, co-editing frequencies are improved by over 27-fold, successfully generating single to octuplet variants with genetic diversity.

FRONTIERS IN MICROBIOLOGY (2021)

Review Biotechnology & Applied Microbiology

Large-Scale de novo Oligonucleotide Synthesis for Whole-Genome Synthesis and Data Storage: Challenges and Opportunities

Li-Fu Song et al.

Summary: Significant progress has been made in large-scale de novo oligonucleotide synthesis based on phosphoramidite chemistry in recent decades, with a focus on applications such as de novo genome synthesis and DNA data storage. However, challenges remain in improving synthesis length, speed, cost, and throughput, which can be addressed by utilizing enzymatic methods. This review summarizes the current status of large-scale oligonucleotide synthesis technologies and discusses opportunities and challenges in de novo genome synthesis and DNA data storage.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2021)

Review Materials Science, Biomaterials

Development of Host-Orthogonal Genetic Systems for Synthetic Biology

Yang Zhang et al.

Summary: The importance of constructing host-orthogonal genetic systems, their potential applications in synthetic biology, and future challenges are discussed in this review.

ADVANCED BIOLOGY (2021)

Article Plant Sciences

On the road to C4 rice: advances and perspectives

Maria Ermakova et al.

PLANT JOURNAL (2020)

Article Biotechnology & Applied Microbiology

Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology

Lucia Marucci et al.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2020)

Article Multidisciplinary Sciences

The second decade of synthetic biology: 2010-2020

Fankang Meng et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

Total synthesis of Escherichia coli with a recoded genome

Julius Fredens et al.

NATURE (2019)

Article Cell Biology

RNA Switches for Synthetic Biology

Calvin M. Schmidt et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2019)

Review Biotechnology & Applied Microbiology

Yeast 2.0-connecting the dots in the construction of the world's first functional synthetic eukaryotic genome

I. S. Pretorius et al.

FEMS YEAST RESEARCH (2018)

Article Biotechnology & Applied Microbiology

Digital-to-biological converter for on-demand production of biologics

Kent S. Boles et al.

NATURE BIOTECHNOLOGY (2017)

Article Biotechnology & Applied Microbiology

Synthetic Promoters and Transcription Factors for Heterologous Protein Expression in Saccharomyces cerevisiae

Fabian Machens et al.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2017)

Review Genetics & Heredity

Cheating evolution: engineering gene drives to manipulate the fate of wild populations

Jackson Champer et al.

NATURE REVIEWS GENETICS (2016)

Review Biotechnology & Applied Microbiology

Synthetic biology approaches to improve biocatalyst identification in metagenomic library screening

Maria-Eugenia Guazzaroni et al.

MICROBIAL BIOTECHNOLOGY (2015)

Article Biochemical Research Methods

Rapid editing and evolution of bacterial genomes using libraries of synthetic DNA

Ryan R. Gallagher et al.

NATURE PROTOCOLS (2014)

Review Microbiology

A brief history of synthetic biology

D. Ewen Cameron et al.

NATURE REVIEWS MICROBIOLOGY (2014)

Article Biochemical Research Methods

Quantitative estimation of activity and quality for collections of functional genetic elements

Vivek K. Mutalik et al.

NATURE METHODS (2013)

Article Multidisciplinary Sciences

Genomically Recoded Organisms Expand Biological Functions

Marc J. Lajoie et al.

SCIENCE (2013)

Article Biotechnology & Applied Microbiology

Cell-free synthetic biology: Thinking outside the cell

C. Eric Hodgman et al.

METABOLIC ENGINEERING (2012)

Article Multidisciplinary Sciences

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

Daniel G. Gibson et al.

SCIENCE (2010)

Article Multidisciplinary Sciences

Programming cells by multiplex genome engineering and accelerated evolution

Harris H. Wang et al.

NATURE (2009)

Article Multidisciplinary Sciences

Synthetic recombinant bat SARS-like coronavirus is infectious in cultured cells and in mice

Michelle M. Becker et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Review Multidisciplinary Sciences

Foundations for engineering biology

D Endy

NATURE (2005)

Article Multidisciplinary Sciences

Efficient initiation of HCV RNA replication in cell culture

KJ Blight et al.

SCIENCE (2000)