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You searched for: Subject "genetic code" Remove constraint Subject: "genetic code"
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1. Creation, Optimization, and Use of Semi-Synthetic Organisms that Store and Retrieve Increased Genetic Information

Author:
Floyd E. Romesberg
Source:
Journal of molecular biology 2022 v.434 no.8 pp. 167331
ISSN:
0022-2836
Subject:
genetic code,   etc   ; RNA; anticodons; codons; molecular biology; nucleotides; therapeutics;     Show all 7 Subjects
Abstract:
... With few exceptions, natural proteins are built from only 20 canonical (proteogenic) amino acids which limits the functionality and accordingly the properties they can possess. Genetic code expansion, i.e. the creation of codons and the machinery needed to assign them to non-canonical amino acids (ncAAs), promises to enable the discovery of proteins with novel properties that are otherwise difficu ...
DOI:
10.1016/j.jmb.2021.167331

2. Mechanisms supporting aminoadenine-based viral DNA genomes

Author:
P. A. Kaminski
Source:
Cellular and molecular life sciences 2022 v.79 no.1 pp. 51
ISSN:
1420-682X
Subject:
genetic code,   etc   ; DNA; adenine; biochemical pathways; cyanophages; genome; hydrogen; synthetic biology; thymine;     Show all 9 Subjects
Abstract:
... Bacteriophage genomes are the richest source of modified nucleobases of any life form. Of these, 2,6 diaminopurine, which pairs with thymine by forming three hydrogen bonds violates Watson and Crick’s base pairing. 2,6 diaminopurine initially found in the cyanophage S-2L is more widespread than expected and has also been detected in phage infecting Gram-negative and Gram-positive bacteria. The bio ...
DOI:
10.1007/s00018-021-04055-7

3. Potentially Prebiotic Synthesis of Aminoacyl-RNA via a Bridging Phosphoramidate-Ester Intermediate

Author:
Samuel J. Roberts; Ziwei Liu; John D. Sutherland
Source:
Journal of the American Chemical Society 2022 v.144 no.9 pp. 4254-4259
ISSN:
1520-5126
Subject:
genetic code,   etc   ; acid hydrolysis; aminoacylation; anhydrides; carbon dioxide; liquids; pH; prebiotics; solubility; stereoselectivity;     Show all 10 Subjects
Abstract:
... Translation according to the genetic code is made possible by selectivity both in aminoacylation of tRNA and in anticodon/codon recognition. In extant biology, tRNAs are selectively aminoacylated by enzymes using high-energy intermediates, but how this might have been achieved prior to the advent of protein synthesis has been a largely unanswered question in prebiotic chemistry. We have now elucid ...
DOI:
10.1021/jacs.2c00772

4. Recent Advances in Genetic Code Expansion Techniques for Protein Phosphorylation Studies

Author:
Xuewen Qin; Tao Liu
Source:
Journal of molecular biology 2022 v.434 no.8 pp. 167406
ISSN:
0022-2836
Subject:
genetic code,   etc   ; Escherichia coli; humans; molecular biology; phosphotransferases (kinases); post-translational modification; protein phosphorylation;     Show all 7 Subjects
Abstract:
... Protein phosphorylation is a reversible, residue-specific posttranslational modification that plays a pivotal role in cell signaling, and the phosphorylation state of proteins is tightly regulated by kinases and phosphatases. Malfunction of this regulation is often associated with human diseases, and therefore elucidation of the function and regulation of this posttranslational modification is imp ...
DOI:
10.1016/j.jmb.2021.167406

5. Film-like organelles equip cells with multiple genetic codes

Author:
Neil C. Taylor; Ivana Nikić-Spiegel
Source:
Trends in biochemical sciences 2022 v.47 no.5 pp. 369-371
ISSN:
0968-0004
Subject:
genetic code,   etc   ; organelles; separation;     Show all 3 Subjects
Abstract:
... The simultaneous incorporation of distinct noncanonical amino acids into different proteins within eukaryotic cells remains challenging. This new study by Reinkemeierand Lemke demonstrates how 2D phase separation can be used to engineer spatially separated organelles. These film-like organelles translate proteins independently from each other and the canonical genetic code. ...
DOI:
10.1016/j.tibs.2021.11.006

6. Characterization of the mitogenome of Gongronella sp. w5 reveals substantial variation in Mucoromycota

Author:
Shu Zhang; Shuang Wang; Zemin Fang; B. Franz Lang; Yong-Jie Zhang
Source:
Applied microbiology and biotechnology 2022 v.106 no.7 pp. 2587-2601
ISSN:
0175-7598
Subject:
genetic code,   etc   ; Absidia; Cunninghamellaceae; biotechnology; fungi; gene order; horizontal gene transfer; introns; mitochondria; mitochondrial genome; phylogeny; ribonucleases; soil;     Show all 13 Subjects
Abstract:
... Gongronella is a genus of fungi in Mucorales (Mucoromycota). Some of its members have important biotechnological applications, but until now, not a single mitogenome has been characterized in Gongronella. Here, we present the complete mitogenome assembly of Gongronella sp. w5, a soil isolate known to interact with plants and several fungi. Its 36,593-bp circular mitogenome encodes the large and sm ...
DOI:
10.1007/s00253-022-11880-8

7. Formation of the Codon Degeneracy during Interdependent Development between Metabolism and Replication

Author:
Dirson Jian Li
Source:
Genes 2021 v.12 no.12 pp. -
ISSN:
2073-4425
Subject:
genetic code,   etc   ; codons; coevolution; metabolism; prebiotics;     Show all 5 Subjects
Abstract:
... Nirenberg’s genetic code chart shows a profound correspondence between codons and amino acids. The aim of this article is to try to explain the primordial formation of the codon degeneracy. It remains a puzzle how informative molecules arose from the supposed prebiotic random sequences. If introducing an initial driving force based on the relative stabilities of triplex base pairs, the prebiotic s ...
DOI:
10.3390/genes12122023

8. Manipulating Cation-π Interactions with Genetically Encoded Tryptophan Derivatives

Author:
Hongxia Zhao; Chao Liu; Wenlong Ding; Ling Tang; Yu Fang; Yulin Chen; Linzhen Hu; Ying Yuan; Dong Fang; Shixian Lin
Source:
Journal of the American Chemical Society 2022 v.144 no.15 pp. 6742-6748
ISSN:
1520-5126
Subject:
genetic code,   etc   ; chemistry; energy; histones; tryptophan;     Show all 5 Subjects
Abstract:
... Cation-π interactions are the major noncovalent interactions for molecular recognition and play a central role in a broad area of chemistry and biology. Despite tremendous success in understanding the origin and biological importance of cation-π interactions, the design and synthesis of stronger cation-π interactions remain elusive. Here, we report an approach that greatly increases the binding en ...
DOI:
10.1021/jacs.1c12944

9. Generation of Premature Termination Codon (PTC)-Harboring Pseudorabies Virus (PRV) via Genetic Code Expansion Technology

Author:
Tong-Yun Wang; Guo-Ju Sang; Qian Wang; Chao-Liang Leng; Zhi-Jun Tian; Jin-Mei Peng; Shu-Jie Wang; Ming-Xia Sun; Fan-Dan Meng; Hao Zheng; Xue-Hui Cai; Yan-Dong Tang
Source:
Viruses 2022 v.14 no.3 pp. -
ISSN:
1999-4915
Subject:
genetic code,   etc   ; Suid alphaherpesvirus 1; cell lines; genetically modified organisms; live vaccines; models; stop codon; swine; virus replication; viruses;     Show all 10 Subjects
Abstract:
... Despite many efforts and diverse approaches, developing an effective herpesvirus vaccine remains a great challenge. Traditional inactivated and live-attenuated vaccines always raise efficacy or safety concerns. This study used Pseudorabies virus (PRV), a swine herpes virus, as a model. We attempted to develop a live but replication-incompetent PRV by genetic code expansion (GCE) technology. Premat ...
DOI:
10.3390/v14030572

10. Recent Technologies for Genetic Code Expansion and their Implications on Synthetic Biology Applications

Author:
Hongting Tang; Pan Zhang; Xiaozhou Luo
Source:
Journal of molecular biology 2022 v.434 no.8 pp. 167382
ISSN:
0022-2836
Subject:
genetic code,   etc   ; biosynthesis; molecular biology; synthetic biology;     Show all 4 Subjects
Abstract:
... Genetic code expansion (GCE) enables the site-specific incorporation of non-canonical amino acids as novel building blocks for the investigation and manipulation of proteins. The advancement of genetic code expansion has been benefited from the development of synthetic biology, while genetic code expansion also helps to create more synthetic biology tools. In this review, we summarize recent advan ...
DOI:
10.1016/j.jmb.2021.167382

11. Redox Biochemistry of the Genetic Code

Author:
Bernd Moosmann
Source:
Trends in biochemical sciences 2021 v.46 no.2 pp. 83-86
ISSN:
0968-0004
Subject:
genetic code,   etc   ; amino acids; evolution; metals; protein folding;     Show all 5 Subjects
Abstract:
... New findings on the chemistry of the amino acids, their role in protein folding, and their sequential primordial introduction have uncovered concealed causalities in genetic code evolution. The genetically encoded amino acids successively provided (i) membrane anchors, (ii) halophilic protein folds, (iii) mesophilic protein folds, (iv) metal ligation, and (v) antioxidation. ...
DOI:
10.1016/j.tibs.2020.10.008

12. Recent Advances in Fluorescence Imaging by Genetically Encoded Non-canonical Amino Acids

Author:
Sanghee Lee; Jonghoon Kim; Minseob Koh
Source:
Journal of molecular biology 2022 v.434 no.8 pp. 167248
ISSN:
0022-2836
Subject:
genetic code,   etc   ; bioimaging; fluorescence; fluorescent dyes; molecular biology;     Show all 5 Subjects
Abstract:
... Technical innovations in protein labeling with a fluorophore at the specific residue have played a significant role in studying protein dynamics. The genetic code expansion (GCE) strategy enabled the precise installation of fluorophores at the tailored site of proteins in live cells with minimal perturbation of native functions. Considerable advances have been achieved over the past decades in flu ...
DOI:
10.1016/j.jmb.2021.167248

13. Site-Specific Dinitrophenylation of Single-Chain Antibody Fragments for Redirecting a Universal CAR-T Cell against Cancer Antigens

Author:
Liang Rong; Rebecca M. Lim; Xiaosuo Yin; Liyao Tan; Jae H. Yang; Jianming Xie
Source:
Journal of molecular biology 2022 v.434 no.8 pp. 167513
ISSN:
0022-2836
Subject:
genetic code,   etc   ; antibodies; antigens; derivatization; molecular biology; neoplasms; peptides;     Show all 7 Subjects
Abstract:
... We have previously developed a universal chimeric antigen receptor (CAR), which recognizes dinitrophenyl (DNP) and can redirect T and NK cells to target cancer and HIV antigens using DNP-conjugated antibodies as adaptor molecules. However, the DNP-antibody conjugates are generated by random modification, which may not be optimal for this modular system. Here, we report the development of enhanced ...
DOI:
10.1016/j.jmb.2022.167513

14. Optoproteomics elucidates the interactome of L-type amino acid transporter 3 (LAT3)

Author:
Liquan Wang; Xiwen Sun; Linjie Lu; Arul Marie; Damien Carrel; Shu Zhao; Clemence Mille; Qiong Song; Yan Zhang; Shixin Ye
Source:
Chemical communications 2021 v.57 no.38 pp. 4734-4737
ISSN:
1364-548X
Subject:
genetic code,   etc   ; amino acid transporters; humans; protein-protein interactions;     Show all 4 Subjects
Abstract:
... Membrane protein interactions are crucial for diverse biological processes. We report the application of genetic code expansion in combination with photo-crosslinking chemistry, as we termed “optoproteomics”, to identify proteins interacting with the human L-type membrane amino acid transporter 3 (LAT3, also known as SLC43A1). The site-specifically incorporated photo-cross-linker p-azido-L-phenyla ...
DOI:
10.1039/d0cc08423a

15. Rebirth of the translational machinery: The importance of recycling ribosomes

Author:
David J. Young; Nicholas R. Guydosh
Source:
BioEssays 2022 v.44 no.4 pp. e2100269
ISSN:
0265-9247
Subject:
genetic code,   etc   ; gene expression regulation; peptides; ribosomes; stop codon;     Show all 5 Subjects
Abstract:
... Translation of the genetic code occurs in a cycle where ribosomes engage mRNAs, synthesize protein, and then disengage in order to repeat the process again. The final part of this process—ribosome recycling, where ribosomes dissociate from mRNAs—involves a complex molecular choreography of specific protein factors to remove the large and small subunits of the ribosome in a coordinated fashion. Err ...
DOI:
10.1002/bies.202100269

16. Prokaryotic life finds a way: insights from evolutionary experimentation in bacteria

Author:
James P. R. Connolly; Andrew J. Roe; Nicky O’Boyle
Source:
Critical reviews in microbiology 2021 v.47 no.1 pp. 126-140
ISSN:
1549-7828
Subject:
genetic code,   etc   ; bioinformatics; biotechnology; evolutionary adaptation; genomics; microbial physiology; plasticity;     Show all 7 Subjects
Abstract:
... While evolution proceeds through the generation of random variant alleles, the application of selective pressures can select for subsets of mutations that confer fitness-improving physiological benefits. This, in essence, defines the process of adaptive evolution. The rapid replication rate of bacteria has allowed for the design of experiments to study these processes over a reasonable timeframe w ...
DOI:
10.1080/1040841X.2020.1854172

17. A review on quality control agents of protein translation – The role of Trans-editing proteins

Author:
Jaykumar Jani; Anju Pappachan
Source:
International journal of biological macromolecules 2022 v.199 pp. 252-263
ISSN:
0141-8130
Subject:
genetic code,   etc   ; amino acids; homeostasis; hydrolysis; protein synthesis; quality control; ribosomes;     Show all 7 Subjects
Abstract:
... Translation of RNA to protein is a key feature of cellular life. The fidelity of this process mainly depends on the availability of correctly charged tRNAs. Different domains of tRNA synthetase (aaRS) maintain translation quality by ensuring the proper attachment of particular amino acid with respective tRNA, thus it establishes the rule of genetic code. However occasional errors by aaRS generate ...
DOI:
10.1016/j.ijbiomac.2021.12.176

18. Ribosome-mediated incorporation of fluorescent amino acids into peptides in vitro

Author:
Joongoo Lee; Kevin J. Schwarz; Hao Yu; Antje Krüger; Eric V. Anslyn; Andrew D. Ellington; Jeffrey S. Moore; Michael C. Jewett
Source:
Chemical communications 2021 v.57 no.21 pp. 2661-2664
ISSN:
1364-548X
Subject:
genetic code,   etc   ; acylation; coumarin; fluorescein; fluorescence; peptides; ribosomes; synthesis; transfer RNA;     Show all 9 Subjects
Abstract:
... We report the design, chemical synthesis, and flexizyme-catalyzed transfer RNA (tRNA) acylation of a variety of fluorescent amino acids (FAAs). The fluorescent groups include pyrene, coumarin, nitrobenzoxadiazole, and fluorescein variants. We further demonstrate site-specific incorporation of the FAAs into peptides by the ribosome in vitro through genetic code reprogramming. ...
DOI:
10.1039/d0cc07740b

19. Design and Ribosomal Incorporation of Noncanonical Disulfide-Directing Motifs for the Development of Multicyclic Peptide Libraries

Author:
Huilei Dong; Jinjing Li; Hongtan Liu; Shuaimin Lu; Junjie Wu; Youming Zhang; Yizhen Yin; Yibing Zhao; Chuanliu Wu
Source:
Journal of the American Chemical Society 2022 v.144 no.11 pp. 5116-5125
ISSN:
1520-5126
Subject:
genetic code,   etc   ; disulfides; drugs; ligands; penicillamine; peptide libraries; ribosomes; therapeutics; thiols;     Show all 9 Subjects
Abstract:
... The engineering of naturally occurring disulfide-rich peptides (DRPs) has been significantly hampered by the difficulty of manipulating disulfide pairing. New DRPs that take advantage of fold-directing motifs and noncanonical thiol-bearing amino acids are easy-to-fold with expected disulfide connectivities, representing a new class of scaffolds for the development of peptide ligands and therapeuti ...
DOI:
10.1021/jacs.2c00216

20. Genetic Code Expansion Through Quadruplet Codon Decoding

Author:
Jiantao Guo; Wei Niu
Source:
Journal of molecular biology 2022 v.434 no.8 pp. 167346
ISSN:
0022-2836
Subject:
genetic code,   etc   ; amino acids; molecular biology; mutagenesis; protein structure; stop codon;     Show all 6 Subjects
Abstract:
... Noncanonical amino acid mutagenesis has emerged as a powerful tool for the study of protein structure and function. While triplet nonsense codons, especially the amber codon, have been widely employed, quadruplet codons have attracted attention for the potential of creating additional blank codons for noncanonical amino acids mutagenesis. In this review, we discuss methodologies and applications o ...
DOI:
10.1016/j.jmb.2021.167346