Biotechnology articles within Nature Chemistry

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  • Review Article |

    Nanopore label-free sequencing of DNA and RNA at the single-molecule level offers rapid readout, high accuracy, low cost and portability. This Review surveys technologies underpinning commercial and academic nanopore sequencing, and examines how underlying biochemical advances can fuel future developments in nanopore-based protein sequencing.

    • Adam Dorey
    •  & Stefan Howorka

  • Article |

    The lack of effective methods for mirror-image (d-) protein sequencing hampers the development of mirror-image biology systems and related applications. Now, total chemical synthesis of mirror-image trypsin enables the sequencing of long d-peptides and d-proteins, which may facilitate applications of d-peptides and d-proteins as potential therapeutic and informational tools.

    • Guanwei Zhang
    •  & Ting F. Zhu

  • Article |

    Now a reactivity-based RNA profiling strategy can measure the global off-target transcriptome interactions of small-molecule drugs at single-nucleotide resolution. Using this approach, three FDA-approved drugs were evaluated, uncovering pervasive drug–RNA interactions and interactions that perturb RNA functions in cells.

    • Linglan Fang
    • , Willem A. Velema
    •  & Eric T. Kool

  • Article |

    Celastrol is a potent anti-obesity agent found in the root of Tripterygium wilfordii, but its medicinal application is compromised by limited availability. Now, by combining plant biochemistry with metabolic engineering and chemistry, the biosynthetic pathway of celastrol has been elucidated and has afforded its scalable production in yeast.

    • Yong Zhao
    • , Nikolaj L. Hansen
    •  & Sotirios C. Kampranis

  • Article |

    Mutually orthogonal aminoacyl transfer RNA synthetase/transfer RNA pairs are required for genetically encoding non-canonical amino acids into proteins, as well as for the encoded cellular synthesis of polymers and macrocycles; however, the scalable discovery of such pairs is challenging. A quintuply orthogonal set of pyrrolysyl-tRNA synthetase/pyrrolysyl-tRNA pairs has now been generated through tRNA screening, engineering and directed evolution.

    • Adam T. Beattie
    • , Daniel L. Dunkelmann
    •  & Jason W. Chin

  • News & Views |

    Complexity is a hallmark of biological systems, but scientific experiments are typically conducted in simplified conditions. Now, diverse polymers that mimic the local environments of complex biological mixtures have been shown to improve protein folding, stability and function.

    • Alana P. Gudinas
    •  & Danielle J. Mai

  • News & Views |

    From humans designing machines, to machines designing biology, deep learning is turning the tables for assisted exploration of biologically active and diverse protein designs. Now, a deep-learning-based strategy has been used to design artificial enzymes that catalyse a light-emitting reaction.

    • Christian Dallago
    •  & Kevin K. Yang

  • Research Briefing |

    Nanomachines are central to life and are becoming an important part of self-regulated nanotechnologies. Inspired by natural self-assembled nanosystems, it has been shown that artificial nanosystems can evolve and adopt regulatory functions upon fragmentation of their structures into multiple components that reassemble to form the same nanostructure.

  • Article |

    Stereochemistry can affect the reactivity and transport properties of small molecules; however, it is unclear whether the stereochemistry of components in a lipid nanoparticle influences its activity in vivo. Now, it has been shown that lipid nanoparticles made with a stereopure component can increase delivery of mRNA. A biological mechanism driving the effect is also proposed.

    • Marine Z. C. Hatit
    • , Curtis N. Dobrowolski
    •  & James E. Dahlman

  • Article |

    A nanopore framework has been developed to reveal the crosstalk effect on the renin–angiotensin system. By reading the single-amino-acid differences in angiotensin peptides with high accuracy and high efficiency, the selective inhibition of angiotensin-converting enzyme by angiotensin-converting enzyme 2 was revealed. This activity was shown to be suppressed by the spike protein of SARS-CoV-2.

    • Jie Jiang
    • , Meng-Yin Li
    •  & Yi-Tao Long

  • Article |

    The complementarity of the two strands in the DNA double helix provides a mechanism for the storage and processing of genetic information. Now, an alternative ‘strand commutation’ mechanism of data processing with DNA/RNA has been revealed based on the reversible low-affinity interactions of essentially non-complementary nucleic acids.

    • Maxim P. Nikitin

  • Article |

    Identifying and quantifying the biodistribution of synthetic polymeric nanoparticles in biological milieu is crucial for biomedical applications. Now, it has been shown that encoded polymeric amphiphiles with discrete molar masses undergo sequence- and length-dependent self-assembly into precise digital micelles that can be used in direct sequence reading and ex vivo label-free quantification assays.

    • Qiangqiang Shi
    • , Hao Yin
    •  & Shiyong Liu

  • Article |

    Synthetic chemical networks with far-from-equilibrium dynamics akin to genetic regulatory networks in living cells could precisely regulate the kinetics of chemical synthesis or self-assembly. Now standardized excitable chemical regulatory elements, termed genelets, that enable predictive bottom-up construction of in vitro networks with designed temporal and multistable behaviour have been developed.

    • Samuel W. Schaffter
    • , Kuan-Lin Chen
    •  & Rebecca Schulman

  • News & Views |

    Antibody-mediated delivery of therapeutics has been primarily limited to agents containing amine, alcohol or thiol functional groups. Now, an approach has been developed to create stable and bio-reversible prodrugs that mask ortho-quinones. Drug release requires both protease activation followed by acid-assisted elimination.

    • Thomas Pillow

  • Q&A |

    In 2017 Professor Frances S. Ligler was inducted into the National Inventors Hall of Fame for her inventions in portable optical biosensors. Professor Ligler now talks to Nature Chemistry about the challenge of developing new sensor designs into reliable products, and some of the pitfalls to avoid in the development process.

    • Russell Johnson

  • Article |

    Soft bioelectronic devices have exciting potential applications in robotics, computing and medicine, but they are typically restricted by the requirement for tethers or stiff electrodes. Now, a synthetic nerve has been developed that is bioinspired, wireless and powered by light. By patterning functionalized lipid membrane compartments, information was directionally conveyed using electrochemical signals.

    • Charlotte E. G. Hoskin
    • , Vanessa Restrepo Schild
    •  & Hagan Bayley

  • News & Views |

    Peptides are a class of versatile biomolecules that function as hormones, signalling messengers and drugs. Now, two papers report alternative approaches to tailor their chemical properties, which enables the transport of biomacromolecules into cells. These approaches could find use in a wide range of biomedical applications.

    • Yuan Ping

  • Article |

    Reliable intracellular delivery of antibodies is one of the grand challenges in biomedical research, with the potential to address unmet clinical needs or to enable basic research. Now, it has been shown that tricyclic peptide complexes can transport functional antibodies into the cytoplasm and nucleus of cells to specifically target intracellular proteins.

    • Ole Tietz
    • , Fernando Cortezon-Tamarit
    •  & Katherine A. Vallis

  • Article |

    Coacervate microdroplets formed from pH- and redox-responsive peptides and self-assembled by liquid–liquid phase separation have been shown to quickly recruit macromolecular therapeutics—such as peptides, large proteins and mRNAs—and directly enter the cytosol of cells via a non-endocytic pathway. The subsequent release of therapeutic cargo is mediated by endogenic glutathione.

    • Yue Sun
    • , Sze Yi Lau
    •  & Ali Miserez

  • News & Views |

    A protein–nanopore machine that can unfold, thread and degrade a protein has now been developed. Fabricated in a bottom-up fashion, the nanopore machine is assembled from three proteins and provides an important step towards deciphering the sequence of single proteins via nanopores.

    • Yi-Lun Ying

  • News & Views |

    Medium-chain linear α-olefins are commodity chemicals; however, manufacturing α-olefins from biomass is challenging due to inefficient removal of the last oxygen atoms. Now, a two-step biological–chemical catalysis strategy to produce medium-chain linear α-olefins provides a route to sustainable polymers.

    • Shaafique Chowdhury
    •  & Pamela Peralta-Yahya

  • Article |

    An integrated multiprotein nanopore has been fabricated using components from all three domains of life. This molecular machine opens the door to two approaches in single-molecule protein analysis, in which selected substrate proteins are unfolded, fed to into the proteasomal chamber and then processed either as fragmented peptides or intact polypeptides.

    • Shengli Zhang
    • , Gang Huang
    •  & Giovanni Maglia

  • Article |

    Non-canonical amino acids can be incorporated into proteins through translation of orthogonal mRNAs. Now, automating the design of orthogonal mRNAs—which are more selectively and efficiently translated—in combination with compact orthogonal aminoacyl-tRNA synthetase/tRNA expression systems, enables the incorporation of four distinct non-canonical monomers via a 68-codon genetic code.

    • Daniel L. Dunkelmann
    • , Sebastian B. Oehm
    •  & Jason W. Chin

  • News & Views |

    DNA-encoded libraries are a powerful tool to identify hit compounds for drug discovery. Now, two papers have reported new advances in this technology. One paper reports a method to screen for binders inside a living cell, and the other investigates the effects of stereo- and regiochemistry on ligand discovery.

    • Minsoo Song
    •  & Gil Tae Hwang

  • Article |

    RNA origami can be used for the modular design of RNA nanoscaffolds but can be challenging to design. Newly developed computer-aided design software has now been shown to improve the folding yield of kilobase-sized RNA origami. These structures fold from a single strand during transcription by an RNA polymerase, and are able to position small molecules and protein components with nanoscale precision.

    • Cody Geary
    • , Guido Grossi
    •  & Ebbe S. Andersen

  • Article |

    Robust delivery of proteins into cells is challenging, but it has now been shown that by conjugating arginine-rich cell-penetrating peptides to the surface of cells, proteins containing a cell-penetrating peptide can be delivered efficiently into them. Using a thiol-reactive cell-penetrating peptide enables thiol-containing proteins to be delivered by simple co-incubation.

    • Anselm F. L. Schneider
    • , Marina Kithil
    •  & Christian P. R. Hackenberger

  • Article |

    RNA-cleaving DNA enzymes (DNAzymes) have the potential to function as therapeutic agents by silencing the expression of disease-associated proteins. Xeno-nucleic acids were used to improve the catalytic activity and biological stability of a highly evolved DNAzyme known as 10–23. The enzyme exhibits a robust multiple-turnover activity in cultured mammalian cells.

    • Yajun Wang
    • , Kim Nguyen
    •  & John C. Chaput

  • Article |

    The self-assembly of haemoglobin-containing erythrocyte membrane fragments onto the surface of preformed coacervates has been used to make hybrid synthetic cells that can initiate nitric-oxide-induced vasodilation. These synthetic cells encapsulate enzymes that generate a flux of nitric oxide, as well as exhibiting high haemocompatibility and increased blood circulation times.

    • Songyang Liu
    • , Yanwen Zhang
    •  & Stephen Mann

  • Article |

    A chemoenzymatic method to site-specifically conjugate peptide and protein thioesters to folded proteins at lysine residues has been developed. The method uses a genetically encoded four-residue tag that is recognized by the E2 SUMO-conjugating enzyme Ubc9. This approach enables isopeptide formation with just Ubc9 in a programmable manner and obviates the need for E1 and E3 enzymes.

    • Raphael Hofmann
    • , Gaku Akimoto
    •  & Jeffrey W. Bode

  • Article |

    Cyclic β-amino acids can add useful properties to peptides, such as inducing turn structures or providing resistance to proteases. To harness these properties up to ten consecutive cyclic β-amino acids have now been ribosomally incorporated via genetic code reprogramming into a foldamer peptide library that has been screened for potent binders against a protein target, human factor XIIa.

    • Takayuki Katoh
    • , Toru Sengoku
    •  & Hiroaki Suga

  • Article |

    Engineering reverse transcriptases for modified or unnatural nucleic acids is challenging, but now a versatile method has been developed that enables the discovery of efficient reverse transcriptases. The method works with a wide range of template structures, including xeno-nucleic acids and can also be used to produce high-fidelity reverse transcriptases for RNA.

    • Gillian Houlihan
    • , Sebastian Arangundy-Franklin
    •  & Philipp Holliger

  • News & Views |

    Three versatile and mutually orthogonal tRNA/aminoacyl-tRNA synthetase pairs have been developed. Collectively, these pairs enable the site-specific incorporation of three different non-canonical amino acids into a protein that can still be terminated faithfully by a natural stop codon.

    • Christopher D. Reinkemeier
    •  & Edward A. Lemke

  • Article |

    Non-canonical amino acids (ncAAs) can be incorporated into proteins in cells using orthogonal aminaocyl–tRNA synthetase/tRNA pairs; the most widely adopted system is based on a pyrrolysyl–tRNA synthetase (PylRS)/tRNA pair. Now, three new PylRS/tRNA pairs have been developed that are mutually orthogonal and can be used together to site-specifically incorporate three distinct ncAAs into a single protein.

    • Daniel L. Dunkelmann
    • , Julian C. W. Willis
    •  & Jason W. Chin

  • Article |

    Oxygen is a potent inhibitor of radical polymerization reactions, but the facultative bacterium Shewanella oneidensis has now been shown to facilitate aerobic radical polymerizations by first consuming dissolved oxygen and then directing extracellular electron flux to a metal catalyst. Aerobic polymerization activity is dependent on the S. oneidensis genotype and can be initiated using lyophilized or spent cells.

    • Gang Fan
    • , Austin J. Graham
    •  & Benjamin K. Keitz

  • News & Views |

    Monoclonal antibodies have shown tremendous success in cancer treatment; however, humanization for clinical applications is expensive and not straightforward. Now, molecularly imprinted polymer nanogels have been developed that can block cell-surface proteins and disrupt tumour spheroids.

    • Alessandra Maria Bossi

  • Article |

    DNA is capable of self-assembling into a wide range of user-defined structures and so can be used as a scaffold to arrange binding motifs with nanometre precision. Now, DNA has been used to accurately display aptamers that fit the repeated epitope pattern of a dengue viral antigen to produce a nanostructure that can be a potent viral inhibitor or a fluorescent sensor.

    • Paul S. Kwon
    • , Shaokang Ren
    •  & Xing Wang

  • News & Views |

    The in situ, nanoscale positioning of a single molecule below the diffraction limit remains a challenge for chemists. Now, two approaches show how this can be accomplished through a combination of super-resolution microscopy and photo-inducible crosslinking chemistry.

    • Limin Xiang
    •  & Ke Xu

  • Article |

    Enacyloxin IIa is an antibiotic, assembled by a modular polyketide synthase, with promising activity against the Gram-negative bacterium Acinetobacter baumannii. Now, it has been shown that the enacyloxin IIa polyketide chain is released via transfer to a separately encoded carrier protein by a non-elongating ketosynthase domain, followed by condensation with 3,4-dihydroxycyclohexane carboxylic acid by a non-ribosomal peptide synthetase condensation domain.

    • Joleen Masschelein
    • , Paulina K. Sydor
    •  & Gregory L. Challis

  • Article |

    Polytheonamides are potently cytotoxic hypermodified ribosomal peptides that are produced by an uncultivated bacterium. Now, a bioinformatic mining strategy has enabled the development of a bacterial production host that can be cultivated in a laboratory. The host generates polytheonamide-like compounds within 2 days, and can efficiently introduce multiple d-amino acids, asparagine N-methylations and C-methyl groups into various peptides.

    • Agneya Bhushan
    • , Peter J. Egli
    •  & Jörn Piel

  • News & Views |

    In biological systems, order typically emerges from out-of-equilibrium molecular processes that control both static patterns and dynamic changes. Now, the self-regulating assembly and disassembly of a synthetic system has been achieved on the micrometre scale, by coupling the growth of a DNA nanotube to a biochemical oscillator.

    • Tim Liedl

  • Article |

    Nucleic acid nanotechnology offers a promising route towards the design and synthesis of reconfigurable biomolecular materials. Now, the combination of dynamic and structural DNA nanotechnology has enabled the dynamic control of the assembly and disassembly of DNA nanotubes. The process involves minimal synthetic gene systems, including an autonomous molecular oscillator.

    • Leopold N. Green
    • , Hari K. K. Subramanian
    •  & Elisa Franco

  • Article |

    Symmetrical protein oligomers perform key structural and catalytic functions in nature, but engineering such oligomers synthetically is challenging. Now, oppositely supercharged synthetic variants of normally monomeric proteins have been shown to assemble via specific, introduced electrostatic contacts into symmetrical, highly well-defined oligomers.

    • Anna J. Simon
    • , Yi Zhou
    •  & Andrew D. Ellington

  • Article |

    The preparation of conjugates between proteins and small molecules is often challenging and requires several synthetic steps to functionalize each component for conjugation. Now, a conjugation methodology that leverages an electrophilic Se–S bond of selenocysteine to create bioconjugates between polypeptides and complex small molecules has been described.

    • Daniel T. Cohen
    • , Chi Zhang
    •  & Bradley L. Pentelute

  • News & Views |

    A new pyrrolysyl-tRNA synthetase/PyltRNA (PylRS/PyltRNA) pair that is mutually orthogonal to existing PylRS/PyltRNA pairs has now been discovered and optimized. This system could enable the site-specific incorporation of a greater number of distinct non-canonical amino acids into a protein.

    • William S. C. Ngai
    •  & Peng R. Chen

  • Review Article |

    Phytochemicals exhibit great pharmaceutical importance despite their low abundance in nature. The microbial biosynthesis of complex phytochemicals offers one route to increase their availability and production. This Review discusses recent strategies to reconstruct plant biosynthetic pathways that have not been fully elucidated; enhance plant enzyme activity; and enhance overall reaction efficiency of multi-enzyme pathways.

    • Sijin Li
    • , Yanran Li
    •  & Christina D. Smolke

  • Article |

    The construction of dynamic protein–DNA nano-assemblies suitable for modulating protein proximities and activities has now been demonstrated. This approach uses DNA strand displacement and can enable control of enzyme activity to be programmed using logic gates. As a demonstration, a split enzyme capable of activating a prodrug is triggered is by cancer-specific miRNAs.

    • Rebecca P. Chen
    • , Daniel Blackstock
    •  & Wilfred Chen

  • Article |

    Proteins have the potential to serve as powerful scaffolds that control the catalytic activity and selectivity of organometallic centres; however, new methods are needed to optimize artificial metalloenzymes. Now, an efficient approach for evolving the activity and selectivity of artificial metalloenzymes has been demonstrated using dirhodium cyclopropanases. This approach does not require structural or mechanistic data to guide mutagenesis.

    • Hao Yang
    • , Alan M. Swartz
    •  & Jared C. Lewis

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