Review
Biochemistry & Molecular Biology
Yun Hu, Jennifer M. Schomaker
Summary: In the past decade, various metal-free bioorthogonal reactions have been developed to achieve simultaneous double-click labeling with minimal competing cross-reactivities, referred to as "mutually orthogonal". Recently, successful triple ligation strategies have also been described. This mini-review discusses the progress in developing orthogonal bioorthogonal reactions and strategies for achieving simultaneous, mutually orthogonal click reactions in one pot.
Article
Biochemistry & Molecular Biology
Agnes Szatmari, Gergely B. Cserep, Tibor A. Molnar, Bianka Soveges, Adrienn Biro, Gyorgy Varady, Edit Szabo, Krisztina Nemeth, Peter Kele
Summary: Bioorthogonal click-reactions are ideal for selectively labeling biomolecules with small synthetic dyes, and genetic code expansion facilitates the specific installation of bioorthogonal handles on proteins of interest. The introduction of bioorthogonalized non-canonical amino acids is a minimally perturbing approach to studying proteins in their native environment. Developing orthogonal bioorthogonal reactions for simultaneous modification of biomolecules has become a focus, with recent advancements allowing for efficient genetic incorporation of a new non-canonical amino acid for protein labeling in live and fixed mammalian cells.
Article
Chemistry, Multidisciplinary
Christopher D. Reinkemeier, Christine Koehler, Paul F. Sauter, Nataliia V. Shymanska, Cecile Echalier, Anna Rutkowska, David W. Will, Carsten Schultz, Edward A. Lemke
Summary: This study presents the synthesis of four new SPIEDAC reactive ncAAs that do not undergo beta-elimination and a fluorescence flow cytometry based FRET-assay to measure reaction kinetics inside living cells. The results capture specific experimental conditions that are not taken into account in other assays, demonstrating conflicting findings with some previous studies.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Zichao Luo, Dehong Hu, Duyang Gao, Zhigao Yi, Hairong Zheng, Zonghai Sheng, Xiaogang Liu
Summary: This study introduces the use of bioorthogonal nanoprobes with high tumor-targeting specificity for in vivo NIR-IIb luminescence imaging and MRI, improving imaging quality and reducing toxicity.
ADVANCED MATERIALS
(2021)
Article
Chemistry, Multidisciplinary
Wen -Fang Song, Wei-Qin Yao, Qi-Wen Chen, Diwei Zheng, Zi-Yi Han, Xian-Zheng Zhang
Summary: This study developed a bioorthogonal-mediated bacterial delivery strategy to enhance the colonization of probiotics by modulating bacterial adhesion between probiotics and gut inhabitants, thereby improving the clinical treatment efficacy of oral bacterial therapy.
ACS CENTRAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Christopher D. Reinkemeier, Edward A. Lemke
Summary: Engineering new functionality into living eukaryotic systems by enzyme evolution or de novo protein design is a formidable challenge. By developing film-like synthetic organelles that support protein translation on the surfaces of various cellular membranes, we are able to equip eukaryotic cells with dual orthogonal expanded genetic codes that enable specific reprogramming of translational machineries with single-residue precision. The ability to spatially tune the output of translation within tens of nanometers not only has implications for understanding the function of membrane-associated protein condensation in cells, but is also important for synthetic biology.
Article
Chemistry, Organic
Hongling Zhou, Yuanyuan Li, Sheng Wang, Li Wang, Rui Wang
Summary: We report the efficient synthesis and application of 2'-azidomethyl modified uridine nucleoside (2'-AmU) in labeling the nascent deoxynucleic acid of interest. This new DNA labeling tool using uridine variant (2'-AmU) has significant application potential due to its advantages, including availability, minimal size perturbation, reversible regulation, and easy click reaction.
TETRAHEDRON LETTERS
(2022)
Article
Biochemical Research Methods
Jessica T. Stieglitz, Kelly A. Potts, James A. Van Deventer
Summary: The study introduces single plasmid systems (SPSs) for genetic code expansion in yeast and compares their noncanonical amino acid (ncAA) incorporation capabilities with previously described dual plasmid systems (DPSs). Results show that SPSs perform equally well as DPSs in terms of ncAA incorporation efficiency, making them a convenient alternative. This suggests that SPSs can be used for high-throughput investigations on genetic or genomic changes affecting ncAA incorporation efficiency and the eukaryotic translation apparatus.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Hang-Qin Zhu, Xiao-Ling Tang, Ren-Chao Zheng, Yu-Guo Zheng
Summary: By specifically incorporating UAAs into proteins through genetic code expansion, more structural and functional features can be endowed to proteins, which have been widely utilized in enzyme engineering. This method provides opportunities for tuning and expanding the functional properties of enzymes.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Juan Tang, Chenfei Yu, Axel Loredo, Yuda Chen, Han Xiao
Summary: Photoactivatable fluorophores are limited in their applications due to their size and the need for ultraviolet light activation. Research has focused on more efficient protein labeling technologies, including single-step labeling processes. By using genetic code expansion and replacing oxygen with sulfur within existing fluorescent amino acids, the photoactivatable fluorescent amino acid thioacridonylalanine (SAcd) has been successfully incorporated into proteins in a single step.
Article
Chemistry, Multidisciplinary
Marcel Janis Beha, Joo-Chan Kim, San Hae Im, Yunsu Kim, Seungju Yang, Juhee Lee, Yu Ri Nam, Haeshin Lee, Hee-Sung Park, Hyun Jung Chung
Summary: Bioconjugation of proteins offers great potential in biopharmaceutical development, but the application of gene editing machinery is still limited. In this study, a self-delivered nanomedicine platform based on bioorthogonal CRISPR/Cas9 conjugates is introduced, which can be armed with a chemotherapeutic drug to achieve combinatorial therapy. The results show that multi-functionalized Cas9 can form self-condensed nanocomplexes with a drug and polymer, leading to significant gene editing without the need for conventional carrier formulations. The platform is demonstrated to be applicable for combinatorial therapy by incorporating the anti-cancer drug olaparib and targeting the RAD52 gene, resulting in significant anti-tumor effects in BRCA-mutant cancer. This development provides a versatile nanomedicine platform for combination treatment of human diseases such as cancer.
Article
Chemistry, Multidisciplinary
Jordan M. Mattheisen, Chris Limberakis, Roger B. Ruggeri, Matthew S. Dowling, Christopher W. am Ende, Emilie Ceraudo, Thomas Huber, Christopher L. McClendon, Thomas P. Sakmar
Summary: We developed a strategy to covalently tether drug fragments adjacent to allosteric sites in GPCRs to enhance their potency and enable fragment-based drug screening in cell-based systems.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Takayuki Katoh, Hiroaki Suga
Summary: The study demonstrates the feasibility of multiple and consecutive incorporations of alpha-aminoxy/alpha-hydrazino acids with different configurations into peptides during ribosomal translation, including macrocyclic peptide scaffolds.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Joongoo Lee, Kevin J. Schwarz, Hao Yu, Antje Kruger, Eric Anslyn, Andrew D. Ellington, Jeffrey S. Moore, Michael C. Jewett
Summary: This study reports a method for fluorescent labeling of amino acids catalyzed by flexizyme, and demonstrates the site-specific incorporation of these fluorescent amino acids into peptides by the ribosome in vitro through genetic code reprogramming.
CHEMICAL COMMUNICATIONS
(2021)
Article
Environmental Sciences
Hamed Kashi, Sebastian Loeppmann, Jennifer Herschbach, Carina Schink, Wolfgang Imhof, Reza Mohsenian Kouchaksaraee, Michaela A. Dippold, Sandra Spielvogel
Summary: The transformation and turnover time of medium- to long-chain dicarboxylic acids (DCA) in soil is regulated by microbial uptake and mineralization. The chain length of n-alkyl lipids has a remarkable influence on microbial utilization and mineralization of DCA, as well as the formation of stable soil organic carbon. The mineralization and microbial incorporation of DCA decrease with increasing chain length, and the mineralization rate is highest during the first days of incubation. The half-life time of DCA carbon in soil increases with chain length, but decreases again for longer chain lengths.
Article
Chemistry, Medicinal
Vimee Raturi, Kumar Abhishek, Subhashis Jana, Subhendu Sekhar Bag, Vishal Trivedi
LETTERS IN DRUG DESIGN & DISCOVERY
(2019)
Editorial Material
Biochemistry & Molecular Biology
Elise M. Van Fossen, Riley M. Bednar, Ryan A. Mehl
Article
Nanoscience & Nanotechnology
Riley M. Bednar, Thaddeus W. Golbek, Kelsey M. Kean, Wesley J. Brown, Subhashis Jana, Joe E. Baio, P. Andrew Karplus, Ryan A. Mehl
ACS APPLIED MATERIALS & INTERFACES
(2019)
Article
Medicine, Legal
Rachel N. Franklin, Noreen Karim, Zachary C. Goecker, Blythe P. Durbin-Johnson, Robert H. Rice, Glendon J. Parker
FORENSIC SCIENCE INTERNATIONAL
(2020)
Article
Chemistry, Physical
Subhendu Sekhar Bag, Hiranya Gogoi, Subhashis Jana
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY
(2020)
Article
Chemistry, Multidisciplinary
Hyo Sang Jang, Subhashis Jana, Robert J. Blizzard, Joseph C. Meeuwsen, Ryan A. Mehl
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2020)
Article
Biochemical Research Methods
Byungseop Yang, Kiyoon Kwon, Subhashis Jana, Seoungkyun Kim, Savanna Avila-Crump, Giyoong Tae, Ryan A. Mehl, Inchan Kwon
BIOCONJUGATE CHEMISTRY
(2020)
Article
Chemistry, Multidisciplinary
Andres F. Chaparro Sosa, Riley M. Bednar, Ryan A. Mehl, Daniel K. Schwartz, Joel L. Kaar
Summary: The efficiency of ligation reactions plays a crucial role in maintaining the activity and structure of enzymes on solid surfaces. Limiting enzyme exploration of surfaces may overcome the challenge of enzyme inactivation during integration. Increasing the rate constant of surface ligation reactions can enhance the probability of immobilization with reactive surface sites.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
Elise M. Van Fossen, Riley M. Bednar, Subhashis Jana, Rachel Franklin, Joseph Beckman, P. Andrew Karplus, Ryan A. Mehl
Summary: Assembling nanobodies into polyvalent multimers is an effective strategy for improving the efficacy of antibody drugs and biotechnological tools. By site-specifically inserting reactive tetrazine groups on the nanobody surface, assembly can be achieved at any desired point, resulting in improved properties compared to conventional methods.