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HOT Chemical Science articles for December

20 Dec 2013

The conformational behaviour of free D-glucose—at last
José L. Alonso, María A. Lozoya, Isabel Peña, Juan C. López, Carlos Cabezas, Santiago Mata and Susana Blanco
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52559G, Edge Article

GA?id=C3SC52559G

Free to access until 19th January 2014

Simultaneous detection and quantification of three bacterial meningitis pathogens by SERS
Kirsten Gracie, Elon Correa, Samuel Mabbott, Jennifer A. Dougan, Duncan Graham, Royston Goodacre and Karen Faulds
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52875H, Edge Article

C3SC52875H

Free to access until 19th January 2014

Constraint-induced structural deformation of planarized triphenylboranes in the excited state
Tomokatsu Kushida, Cristopher Camacho, Ayumi Shuto, Stephan Irle, Masayasu Muramatsu, Tetsuro Katayama, Syoji Ito, Yutaka Nagasawa, Hiroshi Miyasaka, Eri Sakuda, Noboru Kitamura, Zhiguo Zhou, Atsushi Wakamiya and Shigehiro Yamaguchi
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52751D, Edge Article

C3SC52751D

Free to access until 19th January 2014

Direct observation of a lithiated oxirane: a synergistic study using spectroscopic, crystallographic, and theoretical methods on the structure and stereodynamics of lithiated ortho-trifluoromethyl styrene oxide
Antonio Salomone, Filippo M. Perna, Aurelia Falcicchio, Sten O. Nilsson Lill, Anna Moliterni, Reent Michel, Saverio Florio, Dietmar Stalke and Vito Capriati
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52099D, Edge Article

C3SC52099D

Free to access until 19th January 2014

Sugar-coated sensor chip and nanoparticle surfaces for the in vitro enzymatic synthesis of starch-like materials
Ellis C. O’Neill, Abdul M. Rashid, Clare E. M. Stevenson, Anne-Claire Hetru, A. Patrick Gunning, Martin Rejzek, Sergey A. Nepogodiev, Stephen Bornemann, David M. Lawson and Robert A. Field
Chem. Sci., 2014,5, 341-350
DOI: 10.1039/C3SC51829A, Edge Article

C3SC51829A

Free to access until 19th January 2014

Electrochemistry in a drop: a study of the electrochemical behaviour of mechanically exfoliated graphene on photoresist coated silicon substrate
Peter S. Toth, Anna T. Valota, Matěj Velický, Ian A. Kinloch, Kostya S. Novoselov, Ernie W. Hill and Robert A. W. Dryfe
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52026A, Edge Article

C3SC52026A

Free to access until 19th January 2014

Core solution: a strategy towards gold core/non-gold shell nanoparticles bearing strict DNA-valences for programmable nanoassembly
Huiqiao Wang, Yulin Li, Ming Gong and Zhaoxiang Deng
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52445K, Edge Article

C3SC52445K

Free to access until 19th January 2014

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A cut above the rest: the evolution and application of inteins

19 Dec 2013

In this new Perspective, Chemical Science Associate Editor Tom Muir of Princeton University elucidates the biological role and evolutionary origin of inteins – a fascinating class of proteins which have the ability to “process”, or sever, their own peptide backbone. Usually, this type of post-translational modification is done enzymatically by proteases, but inteins contain a module which allows the spontaneous scission of peptide bonds with no external factor or energy source required. The only things needed are certain chemical functional groups in the neighbouring peptide residues, and the correct spatial folding of the domain.

Obviously, this is a truly interesting process, as the functions and actions of a protein are determined by its amino acid sequence and structure. By breaking peptide bonds and creating new ones, inteins essentially act as an on/off switch for the protein, the potential application for which is staggering. The intein is flanked on either side by two exteins; during the “processing” reaction, the bonds between intein and exteins are broken, and a new bond between the exteins is created. Inteins share a common biochemical mechanism for this process, which is illustrated below. Crucially, all inteins must contain a cysteine or serine at their N-terminus which provides the nucleophile for the initial acyl shift. A subsequent trans(thio)esterification and an additional acyl shift forms the spliced product and the excised intein.: Mechanism of protein splicing

Muir and co-author Neel Shah investigate the evolutionary origin of inteins, which can be found in all domains of life – eukaryotes, bacteria, archaea and viruses. Although they are often found in proteins involved in genetic “housekeeping” – DNA replication, transcription, and maintenance – inteins have no obvious biological role, and do not provide any benefit to the host organism. As such, they are known as “selfish” genes. Despite the mystery of their purpose and origin, what is clear is that the future is bright for inteins.

The authors discuss a number of applications of inteins, the most exciting of which is conditional protein splicing (CPS) where inteins can be used as an on/off switch for the proteins they are splicing, even in vivo. CPS is currently achieved in a number of ways, shown below, in which the intein is kept in an inactive state – via (a) conformational distortion, (b) caging of the active site, or (c) the physical separation of a split intein – until activation is desired. Ligand binding, deprotection or dimerisation, respectively, then releases the active intein and triggers the peptide splicing. CPS is a promising tool for cell biology and should facilitate the development of “smart” protein therapeutics that are activated only at the target site. All in all, this Perspective makes for an interesting read on a class of proteins with impressive potential. I think it’s a safe bet to predict that when it comes to future smart therapeutics, inteins will definitely make the cut.: Conditional protein splicing (CPS): a) Allosteric intein activation by ligand binding; b) Intein activation via deprotection of a photo-caged active site residue; c) Activation via chemically-induced dimerisation

For more, you can read Muir and Shah’s Chemical Science Perspective here:

Inteins: nature’s gift to protein chemists

Neel H. Shah and Tom W. Muir

Chem. Sci., 2014, Advance Article

DOI: 10.1039/C3SC52951G

Professor Muir serves as one of Chemical Science‘s Associate Editors, handling submission in chemical biology – read more about him and what useful advice he wishes someone had told him as an undergraduate.

Our Associate Editors Tom Muir and Ben Davis have highlighted their recommended chemical biology papers on Chemical Science – read their Editor’s Choice selection for FREE today!

Find many more excellent articles on chemical biology here: Online collection: Chemical biology

Ruth E. Gilligan is a guest web-writer for Chemical Science. She recently completed her PhD in the group of Prof. Matthew J. Gaunt at the University of Cambridge, and is currently pursuing an internship at Science Foundation Ireland.

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Disarming bacteria to beat infection

16 Dec 2013

Researchers in Germany looking to find unprecedented ways of combating bacterial infection have demonstrated that certain small molecules can reduce the ability of Staphylococcus aureus to cause disease. ‘The classic antibiotic approach puts bacteria in a life or death situation, meaning that they need to become resistant in order to survive. We aimed to find a way of reducing the ability of bacteria to make the toxins that harm eukaryote cells during infection, without putting them under selective pressure,’ explains Stephan Sieber of the University of Technology in Munich who led the study.

α-methylene-γ-butyrolactones can inhibit virulence factors like α-haemolysin (hla) to render pathogenic bacteria harmless

Transcriptional regulators control the virulence factors in bacteria, that enable a microorganism to establish itself within a host or enhance its potential to cause disease, by directly binding to DNA promoter regions of toxin-encoding genes. In the study, the researchers identified a series of α-methylene-γ-butyrolactones that covalently modify cysteine residues on three transcriptional regulators in S. aureus, markedly decreasing the expression of α-haemolysin, one of the most prominent virulence factors.

Read the full article in Chemistry World»

Read the original journal article in Chemical Science:
α-Methylene-γ-butyrolactones attenuate Staphylococcus aureus virulence by inhibition of transcriptional regulation
Martin H Kunzmann, Nina C. Bach, Bianca Bauer and Stephan Axel Sieber
Chem. Sci., 2013, Accepted Manuscript, DOI: 10.1039/C3SC52228H

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Compressing/decompressing data with DNAzymes

16 Dec 2013

When most people read a book they don’t remember every word. They compress the story down to the main points and remember those. The reverse is also true – given a few facts most people can embellish a story to a suitably lengthy tale of adventure and mystery.

These data compression/decompression processes are called logic operations and are a central theme in information theory. They are also replicated in biological systems where scaffolding proteins within the regulatory cellular networks carry out the operations. However, there has been no synthetic DNA-based system that can carry out this data compression/decompression process, until now.

Logic circuit showing how 4 inputs (I) can be compressed to one output (S)

Itamar Willner from the Hebrew University of Jerusalem and colleagues have developed such a system based on Mg²⁺-dependent DNAzyme subunits. Unlike previous approaches where the demonstration is done using two inputs and one output the team have investigated enhanced multiplexing in the compression process with four inputs producing one output.

Additionally they have also demonstrated the expansion of a single input to produce two outputs. Having such systems based on nucleic acids also raises the possibility of resetting the computational module. This means you could reconfigure and change its operation in situ by the addition of suitable complementary nucleic acid strands.

This article details important advances in DNA based logic networking and raises the potential to compress information held within genes into a single output. It also raises challenges for the future that must be overcome before these synthetic biomolecular computational systems can control natural intracellular processes.

For more, read the Chemical Science Edge article in full:

DNAzyme-Based 2:1 and 4:1 Multiplexers and 1:2 Demultiplexer
Ron Orbach, Francoise Remacle, R. D. Levine and Itamar Willner*
Chem. Sci., 2013, Accepted Article
DOI: 10.1039/C3SC52752B

Iain Larmour is a guest web writer for Chemical Science. He has researched a wide variety of topics during his years in the lab including nanostructured surfaces for water repellency and developing nanoparticle systems for bioanalysis by surface enhanced optical spectroscopies. He currently works in science management with a focus on responses to climate change. In his spare time he enjoys reading, photography, art and inventing.

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A cytochrome from scratch

29 Nov 2013

Artificial proteins could be closer to participating in natural biochemical pathways after UK and US researchers show that bacteria will process amino acid sequences entirely unrelated to any natural protein to produce a fully functioning cytochrome.

Scientists trick E. coli into producing their artificial proteins © Shutterstock

The burgeoning field of synthetic biology demands that functional artificial proteins and enzymes seamlessly integrate with natural proteins and substrates. ‘We’re trying to build artificial proteins that exhibit some of the properties and chemistries of natural proteins,’ explains team member Ross Anderson from the University of Bristol.

Anderson and colleagues have used a relatively new methodology called the maquette approach that lets them escape some of the complexities of natural systems to construct their artificial cytochrome. They begin with a generic protein sequence designed only to fold into a 4-helix bundle. Engineered elements are added onto the stripped-down protein chassis; the role of every residue in the amino acid sequence is defined and adjusted by altering critical residues.

Read the full article in Chemistry World»

Read the original journal article online:
Constructing a man-made c-type cytochrome maquette in vivo: electron transfer, oxygen transport and conversion to a photoactive light harvesting maquette
J. L. Ross Anderson, Craig T. Armstrong, Goutham Kodali, Bruce R. Lichtenstein, Daniel W. Watkins, Joshua A. Mancini, Aimee L. Boyle, Tammer A. Farid, Matthew P Crump, Christopher C. Moser and P. Leslie Dutton
Chem. Sci., 2014, Advance Article, DOI: 10.1039/C3SC52019F

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HOT Chemical Science articles for November

21 Nov 2013

Targeting the endoplasmic reticulum with a membrane-interactive luminescent ruthenium(II) polypyridyl complex
Martin R. Gill, Denis Cecchin, Michael G. Walker, Raminder S. Mulla, Giuseppe Battaglia, Carl Smythe and Jim A. Thomas
Chem. Sci., 2013,4, 4512-4519
DOI: 10.1039/C3SC51725J, Edge Article

Free to access until 15th December 2013

Benz[c]indeno[2,1-a]fluorene: a 2,3-naphthoquinodimethane incorporated into an indenofluorene frame
Hirokazu Miyoshi, Shunpei Nobusue, Akihiro Shimizu, Ichiro Hisaki, Mikiji Miyata and Yoshito Tobe
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52622D, Edge Article

Free to access until 15th December 2013

Sodium hydroxide-assisted growth of uniform Pd nanoparticles on nanoporous carbon MSC-30 for efficient and complete dehydrogenation of formic acid under ambient conditions
Qi-Long Zhu, Nobuko Tsumori and Qiang Xu
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52448E, Edge Article

Free to access until 15th December 2013

Direct Observation of a Lithiated Oxirane: A Synergistic Study Using Spectroscopic, Crystallographic, and Theoretical Methods on the Structure and Stereodynamics of Lithiated ortho-Trifluoromethyl Styrene Oxide
Vito Capriati, Antonio Salomone, Filippo Maria Perna, Saverio Florio, Aurelia Falcicchio, Anna Moliterni, Sten O. Nilsson Lill, Dietmar Stalke and Reent G. Michel
Chem. Sci., 2013, Accepted Manuscript
DOI: 10.1039/C3SC52099D, Edge Article

Free to access until 15th December 2013

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Exotic interactions uncovered in actinide systems

15 Nov 2013

The six orbital phase changes around the internuclear axis are unique to phi interactions

Theory had predicted the presence of Φ interactions in actinide systems but it had never been observed experimentally, until now. Scientists in the US using high-energy x-ray spectroscopy to study the involvement of the f-orbitals in actinide sandwich complexes have experimental evidence for this unusual interaction in thorocene.

At its most basic level, bonding in actinide molecules is typically comprised of a small amount of covalent orbital mixing in the presence of overwhelming ionic attractions. However, in many cases it is proposed that these small changes in f-element covalency are responsible for profound changes in chemical reactivity and actinide properties.

Covalency is a fundamental concept used to describe how elements share electrons in chemical bonds. For the d-block transition metal series, 3d, 4d, and 5d orbitals extend well into the periphery of the atom and can interact with valence orbitals of ligand atoms to form covalent chemical bonds. In contrast, the 4f orbitals of lanthanides are very core-like and their interactions with ligands are – in general – assumed to be of comparatively little chemical consequence. The actinide elements lie between these two extremes, and the extent to which valence f and d orbitals participate in chemical bonding is a subject of debate in the community.

You can also read this article in Chemistry World

Read the original journal article in Chemical Science:

New evidence for 5f covalency in actinocenes determined from carbon K-edge XAS and electronic structure theory
Stefan G. Minasian, Jason M. Keith, Enrique R. Batista, Kevin S. Boland, David L. Clark, Stosh A. Kozimor, Richard L. Martin, David K. Shuh and Tolek Tyliszczak
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52030G, Edge Article

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Hole hopping in solar cells

13 Nov 2013

The technique estimates the energetic cost of a dye molecule changing conformation

Researchers in the UK, Spain and Switzerland say a method they have developed for probing electron transfer reactions could help them design more efficient solar cells.

Monitoring the behaviour of charges in photovoltaic devices is important for improving charge collection, especially in dye sensitised solar cells (DSSCs) that convert sunlight to electricity. Creating efficient solar cells is pivotal for meeting increasing energy demands especially as the world looks to move away from fossil fuels. DSSCs have many attractive features being simple to make, flexible and transparent, but they still have a way to go in terms of efficiency.

A research team led by Piers Barnes of Imperial College London has pioneered a technique that measures the diffusion coefficient of a less well reported phenomenon known as hole hopping, which occurs between sensitised dye molecules anchored to surfaces (in this case TiO₂).

You can also read this article in Chemistry World

Read the original journal article in Chemical Science:

The reorganization energy of intermolecular hole hopping between dyes anchored to surfaces
Davide Moia, Valérie Vaissier, Ismael López-Duarte, Tomás Torres, Mohammad K. Nazeeruddin, Brian C. O’Regan, Jenny Nelson and Piers R. F. Barnes
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52359D

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Moving the goalposts for MRI

11 Nov 2013

A new class of MRI (magnetic resonance imaging) contrast agents developed by scientists in the UK is promising to deliver clearer images in less time. ‘In any NMR experiment you are chasing sensitivity. We have enhanced the intrinsic ability to observe an MRI probe signal by a factor of 20,’ explains David Parker of Durham University who led the study.

MRI is used in clinical settings to image the inside of the body. It uses strong magnetic fields and radio waves to probe the behaviour of nuclei that possess nuclear spin. Chemical shifts from proton NMR normally fall between 0–12ppm but water and fat resonate at 4.7 and 1.3ppm, respectively, and can overlap with MRI probe signals. Parker’s new probes shunt the spectral window of MRI scans well away from these interfering signals, a concept he describes as ‘moving the goalposts’. The probes consist of lanthanide complexes with a t-butyl group and the distance between the lanthanide and t-butyl group was fixed to optimise the rate of decay of the t-butyl signal as well as move its chemical shift. Data acquisition was possible just a few minutes after administering the probe and the signal from the lanthanide induced relaxation of the nine protons in the t-butyl groups has been shifted by up to 80ppm.

Proton NMR spectra showing the shifted t-butyl resonances in some of the new dysprosium and thulium complexes

Read the full article in Chemistry World»

Read the original journal article in Chemical Science:
Moving the goal posts: enhancing the sensitivity of PARASHIFT proton magnetic resonance imaging and spectroscopy
Peter Harvey, Andrew M. Blamire, J. Ian Wilson, Katie-Louise N. A. Finney, Alexander M. Funk, P. Kanthi Senanayake and David Parker
Chem. Sci., 2013,4, 4251-4258, DOI: 10.1039/C3SC51526E

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Light harvesting with many man-made leaves

07 Nov 2013

Scientists from Japan have harvested light energy using an exceptionally large number of light absorbers to relay photons via antennas into one final energy acceptor. This two-step sequence closely mimics natural photosynthesis, resulting in greater and more efficient energy transfer.

Previously, researchers had only used one-step light harvesting systems, greatly limiting the number of absorbers able to feed light into a single reaction centre. Now, by imitating photosynthetic systems, Osamu Ishitani at the Tokyo Institute of Technology, Shinji Inagaki at the Toyota Central R&D labs and their co-workers have efficiently harvested light using the highest number of artificial leaves to date.

Read the full article in Chemistry World»

Read the original journal article in Chemical Science:
Efficient Light Harvesting via Sequential Two-Step Energy Accumulation Using a Ru–Re5 Multinuclear Complex Incorporated into Periodic Mesoporous Organosilica
Yohei Yamamoto, Hiroyuki Takeda, Tatsuto Yui, Kotaro Ueda, Kazuhide Koike, Shinji Inagaki and Osamu Ishitani
Chem. Sci., 2013, Accepted Manuscript, DOI: 10.1039/C3SC51959G

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Chemical Science Blog

Archive for the ‘Hot Articles’ Category

HOT Chemical Science articles for December

A cut above the rest: the evolution and application of inteins

Disarming bacteria to beat infection

Compressing/decompressing data with DNAzymes

A cytochrome from scratch

HOT Chemical Science articles for November

Exotic interactions uncovered in actinide systems

Hole hopping in solar cells

Moving the goalposts for MRI

Light harvesting with many man-made leaves

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