Archive for the ‘Uncategorized’ Category

Molecular Switches from DNA

The idea of using DNA-based devices to create highly specific sensors, diagnostic tools, and therapeutics has inspired widespread research. DNA molecular switches, a basic class of DNA nanostructures, turn some process on and off depending on whether a substrate binds to the switch. They are typically coupled with some form of signal amplification process to increase sensitivity and should theoretically provide enhanced signal-to-noise. Unfortunately, current amplification procedures have a significant amount of background reactions, called leakage, that limit their current utility. One approach to design better switches is to find ways to observe single molecule dynamics. Combining transient binding of complimentary oligonucleotides with high resolution fluorescence microscopy allows for the development of highly sensitive molecular switches without leakage problems.

To do this, researchers in China developed a series of three-way junction DNA-based molecular switches. These TWJs possess a recognition domain, which interacts with the target of interest and induces a structural change in the TWJ, and a transduction domain, which then becomes accessible and binds to a fluorescent molecule (Figure 1).

Figure 1. General scheme of three-way junction molecular switch with two domains noted.

Experimentally, the TWJs were captured on the imaging surface and only fluorophores bound to a TWJ would remain in place long enough for signal to be acquired by the camera with a 500 ms integration time. The researchers found that shorter transduction domains with 5 or fewer base pairs were not stable enough to allow the fluorescent probes access in the absence of a bound target. The next generation of TWJs feature a hybridization probe to allow the switch to recognize specific DNA inputs. In the presence of inputs, the researchers observed transient binding behavior of the fluorophore, whereas they observed only nonspecific binding in the absence of inputs. The ability to differentiate between non-specific and transient binding in the single-molecule system gives a detection limit of 10 fM without concerns about leakage.

Building on this work, the researchers utilized the same general framework and substituted aptamer sequences for the hybridization probe in the recognition domain. They utilized split aptamer fragments that only draw together when bound to a target molecule. This motif was tested on ATP, a small molecule, and thrombin, a protein. These aptamer-coupled TWJs exhibited sensitivity to concentrations as low as 20 – 50 pm with high sensitivity (Figure 2). In the presence of molecular analogs to ATP or thrombin, the signal level showed no significant difference from that of a blank.

Figure 2. A) Split aptamer-based molecular switch schematic. B) Single-molecule fluorescence-time trajectory data in the presence (top) or absence (bottom) of targets. C) and D) Linear relationship between thrombin concentration and signal and specificity when compared to analogs. E) and F) Linear relationship between ATP concentration and signal and specificity when compared to analogs.

Another advantage of this system is its ability to provide information on the binding affinity of substrates, as it should impact the kinetics of the fluorescent probes. The dwell times of the fluorescence on and off states demonstrated exponential trends with changing input concentrations and could be fit to extract time constants. These time constants can then be used to derive the kinetics parameters and binding affinities of the target species. The general stability of the molecular switch framework allows for studying these types of interactions in a range of pH and salinity conditions, useful for mimicking different environments relevant to future applications. This provides a platform for studying the fundamental interactions that will allow DNA-based nanotechnology to move forward.

To find out more, please read:

Single-molecule dynamic DNA junctions for engineering robust molecular switches

Shuang Cai, Yingnan Deng, Shengnan Fu, Junjie Li, Changyuan Yu and Xin Su

Chem. Sci., 2019, 10, 9922-9927.

About the blogger:

Beth Mundy is a PhD candidate in chemistry in the Cossairt lab at the University of Washington in Seattle, Washington. Her research focuses on developing new and better ways to synthesize nanomaterials for energy applications. She is often spotted knitting in seminars or with her nose in a good book. You can find her on Twitter at @BethMundySci.

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HOT Chemical Science articles for October

We are happy to present a selection of our HOT articles for October. To see all of our HOT referee-recommended articles from 2019, please find the collection here.

As always, Chemical Science articles are free to access.

Development of a DUB-selective fluorogenic substrate

ChemSci., 2019, 10, 10290-10296

 

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Facile triflic acid-catalyzed α-1,2-cis-thio glycosylations: scope and application to the synthesis of S-linked oligosaccharides, glycolipids, sublancin glycopeptides, and TN/TF antigens

Sanyong Zhu, Ganesh Samala, Eric T. Sletten, Jennifer L. Stockdill and Hien M. Nguyen

ChemSci., 2019, 10, 10475 – 10480

 

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Preferential binding of unsaturated hydrocarbons in aryl-bisimidazolium·cucurbit[8]uril complexes furbishes evidence for small-molecule π–π interactions

Steven J. Barrow, Khaleel I. Assaf, Aniello Palma, Werner M. Nau and Oren A. Scherman

ChemSci., 2019, 10, 10240 – 10246

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Synthesis of bicyclo[3.1.0]hexanes by (3 + 2) annulation of cyclopropenes with aminocyclopropanes

Bastian Muriel, Alec Gagnebina and Jerome Waser

ChemSci., 2019, Advance Article

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Development of a hydrolysis-based small-molecule hydrogen selenide (H2Se) donor

Turner D. Newton and Michael D. Pluth

ChemSci.,  2019, Advance Article

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Ruthenium based antimicrobial theranostics – using nanoscopy to identify therapeutic targets and resistance mechanisms in Staphylococcus aureus

Kirsty L. Smitten, Simon D. Fairbanks, Craig C. Robertson, Jorge Bernardino de la Serna, Simon J. Foster and Jim A. Thomas

ChemSci.,  2019, Advance Article

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1st International Conference on Noncovalent Interactions

Last month, Chemical Science sponsored the 1st International Conference on Noncovalent Interactions, in Lisbon, Portugal. The talks highlighted the important role of noncovalent interactions in a range of disciplines, such as theoretical chemistry, synthesis, catalysis, crystal engineering, molecular recognition, medicinal chemistry, biology, materials science, and electrochemical immobilization.

Chemical Science, along with Dalton Transactions and RSC Advances, sponsored poster prizes at the conference. Congratulations to Anh Tuan Pham (University of Geneva, Switzerland) who received the Chemical Science poster prize, Sara R. G. Fernandes (University of Lisbon, Portugal) who received the Dalton Transactions poster prize, and Errui Li (Zhejiang University, China) who received the RSC Advances poster prize. There was a fantastic array of posters on display at the meeting, and we would like to extend a huge congratulations to all those who presented.

       

 

 

 

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10th National Conference on Inorganic Chemistry of the Chinese Chemical Society

Chemical Science was pleased to support the 10th National Conference on Inorganic Chemistry of the Chinese Chemical Society which took place at Shandong University last month. Poster prizes were given on behalf of Chemical Science as well as Inorganic Chemistry Frontiers, Materials Chemistry Frontiers, Catalysis Science & Technology, Physical Chemistry Chemical Physics, Green Chemistry, Dalton Transactions, RSC Advances, Nanoscale, Nanoscale Advances, Materials Horizons and Journal of Materials Chemistry A, B and C. Energy & Environmental Science and Sustainable Energy & Fuels also provided a joint prize. The winners are:

Poster prize winners of the 10th National Conference on Inorganic Chemistry of the Chinese Chemical Society

Yuan Xiong 熊昱安 东南大学
Southeast University
Lingling Xu 徐令令 西安交通大学
Xi’an Jiaotong University
Fan Guo 郭帆 南京大学
Nanjing University
Wenbin Wang 王文彬 华中科技大学
Huazhong University of Science and Technology
Mengfei Li 李梦菲 中国石油大学(华东)
China University Of Petroleum
Jing Dong 董婧 北京理工大学
Beijing Institute Of Technology
Bingqi Han 韩冰琪 吉林大学
Jilin University
Wenzhu Yu 于文竹 山东大学
Shandong University
Liang Zhou 周亮 北京大学
Peking University
Genfeng Feng 冯根锋 南京大学
Nanjing University
Peipei Cui 崔培培 德州学院
Dezhou University
Xiaoting Liu 刘晓婷 南开大学
Nankai University
Dong Li 李冬 厦门大学
Xiamen University
Zhi Wang 王芝 山东大学
Shandong University
Shuang Liu 刘爽 东北师范大学
Northeast Normal University

Congratulations to all the winners!

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Chemical biology symposium 2019

The Chemical biology symposium 2019 was recently held at Burlington House in London, UK on 20th May. Chemical Science and Organic & Biomolecular Chemistry were proud to support the meeting, and Chemical Science Senior Editor James Moore attended to meet with delegates and represent the Royal Society of Chemistry.

The symposium showcased the state of the art in chemical biology, bringing together the wider community with leading national and international experts in the field. The programme explored all aspects of chemical biology and highlighted the wider scope and impact of the field.

Chemical Science were proud to present Tiffany Chan from Imperial College London with the poster prize for her poster on ‘Targeted delivery of metal complexes across the blood-brain barrier for the treatment of Alzheimer’s disease’.

Organic & Biomolecular Chemistry were proud to present Sophie Newgas from King’s College London with the runner up poster prize for her poster on ‘Understanding the role of nitric oxide synthase in biosynthetic nitration’.

Congratulations to them both!

Tiffany Chan

Sophie Newgas

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17th Symposium on Host-Guest and Supramolecular Chemistry

The 17th Symposium on Host-Guest and Supramolecular Chemistry was held in Kanazawa, Japan, on 18th and 19th of May, chaired by Professor Shigehisa Akine of Kanazawa University. Professor Tatsuya Nabeshima of the University of Tsukuba and president of the Association of Research for Host-Guest and Supramolecular Chemistry was also in attendance, as was Hiromitsu Urakami on behalf of the Royal Society of Chemistry.

The Chemical Science poster prize was awarded to Mr. Akihiro Kanamori of Kanazawa University for his poster on the ‘Synthesis of Salicylideneimine-Based Cryptophane Derivatives through Chiral Self-sorting and Their Guest Recognition Behavior’.

The Chemical Communications poster prize was awarded to Mr. Lingyun Hu of the University of Tokyo for his poster on the ‘Construction of Metal-responsive DNAzymes by Incorporating CuII-mediated Imidazole-4-carboxylate Base Pairing’.

The Organic & Biomolecular Chemistry poster prize was awarded to Mr. Sota Yonemura of the University of Tsukuba for his poster on the ‘Formation of Chiral Single Isomer by Metal Complexation of a β-Cyclodextrin Derivatives introduced Seven Bipyridyl Groups and Origomer Complex of the Isomer’.

Congratulations to Akihiro, Lingyun & Sota!

(From left) Hiromitsu Urakami, Tatsuya Nabeshima, Akihiro Kanamori (ChemSci poster winner), Shigehisa Akine

Organic & Biomolecular Chemistry poster winner Sota Yonemura

(From left) Hiro Urakami, Tatsuya Nabeshima, Lingyun Hu (ChemComm poster winner), Shigehisa Akine

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Bioorthogonal & Bioresponsive Symposium 2019

The second Bioorthogonal & Bioresponsive symposium will be held at the Institute of Genetics & Molecular Medicine in Edinburgh on the 6th and 7th of June 2019. Chemical Science is proud to sponsor the symposium and our new Assistant Editor Amelia Newman will be attending.

The symposium aims to bring together chemists and biologists interested in the latest advances in bioorthogonal and bioresponsive strategies. Talks will highlight state-of-the-art work from leading UK and international experts, and speakers include Jason Chin, Ben Davis, Karen Faulds, Sarah Heilshorn, Ludovic Jullien and Vincent Rotello.

It’s not too late to join us at this exciting meeting – registration is still open at the RSC Events webpage. The registration deadline is 31st May 2019.

If you cannot attend the symposium next month, you can follow @BBSymposium1 on Twitter to stay updated.

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CPE Annual Symposium 2019

The Centre for Plastic Electronics is hosting its prestigious annual symposium on 10 and 11 June 2019. It will take place at Imperial College London and and will include talks from several high-profile speakers to discuss their latest advances in the science and technology of organic conducting materials and of organic/flexible electronics and photonics. The program includes a day of short talks and poster presentations by students and early career scientists giving them a platform to highlight their recent work.

More information and details of how to register is available at: http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/centres/plasticelectronics/eventssummary/event_20-2-2019-14-14-7. Abstracts submissions for poster presentations are open until the 31 May.

Imperial College London are delighted to host Prof Erwin Reisner of the University of Cambridge who will be giving his RSC Corday-Morgan Prize talk for his work on the development of solar-driven catalysis with molecularly engineered semiconductors and semi-artificial photosynthesis.

The symposium will cover all areas related to organic/plastic electronics and photonics, including chemistry, physics, materials science and device engineering. Confirmed speakers include:

  • Christine Luscombe, University of Washington
  • Andy Cooper, University of Liverpool
  • Iain McCulloch, KAUST and Imperial College London
  • Erwin Reisner, University of Cambridge
  • Kwanghee Lee, GIST, South Korea
  • Henry Yan, Hong Kong University of Science and Technology
  • Ji-Seon Kim, Imperial College London
  • Artem Bakulin, Imperial College London
  • Maria Ibáñez, Institute of Science and Technology, Austria
  • Rachel Evans, University of Cambridge
  • Oliver Dumele, Humboldt University of Berlin, Germany
  • Hyejeong Seong, Imperial College London
  • Rowena Brugge, Imperial College London
  • Ludmilla Steier, Imperial College London
  • Jess Wade, Imperial College London
  • Alex Clark, Imperial College London

With more speakers being confirmed in the coming weeks, this will be an event not to miss!

If you cannot attend the Symposium next month, you can follow the hashtag #CPESymp19 on Twitter.

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ChemSci Pick of the Week video abstracts

We’ve produced video abstracts for our latest two ChemSci Pick of the Week articles! Check them out below – we hope you enjoy watching them!

 

Catalytic asymmetric allylation of aldehydes with alkenes through allylic C(sp3)–H functionalization mediated by organophotoredox and chiral chromium hybrid catalysis

Harunobu Mitsunuma, Shun Tanabe, Hiromu Fuse, Kei Ohkubo and Motomu Kanai

DOI:10.1039/C8SC05677C

 

An Al-doped SrTiO3 photocatalyst maintaining sunlight-driven overall water splitting activity for over 1000 h of constant illumination

Hao Lyu, Takashi Hisatomi, Yosuke Goto, Masaaki Yoshida, Tomohiro Higashi, Masao Katayama, Tsuyoshi Takata, Tsutomu Minegishi, Hiroshi Nishiyama, Taro Yamada, Yoshihisa Sakata, Kiyotaka Asakura and Kazunari Domen

DOI:10.1039/C8SC05757E

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Chemical Science prize winner at IPEROP19

Chemical ScienceSustainable Energy & Fuels, and Energy & Environmental Science were delighted to recently support the Perovskite, Organic Photovoltaics and Optoelectronics  (IPEROP19) conference that took place in Kyoto, Japan from 28-29th January 2019. On behalf of the Royal Society of Chemistry, we would like to congratulate the following prize winners who won a £200 book voucher each. A particular mention to the Chemical Science winner, Chieh-Ting Lin of Professor James Durrant’s group at Imperial College London:

Chemical Science winner: Lin, Chieh-Ting (Imperial College London)
“Probing the Enhanced Stability Against Oxygen Induced Photodegradation by Selection of Transport Layer and Defect Passivation”

Energy & Environmental Science winner: Yamaguchi, Mayu (Waseda University)
“Perovskite Precursor Solution Tuned with Polymer Addition for Effective Formation of the Photovoltaic Layer”

James Durrant (Sustainable Energy & Fuels Editor-in-Chief), Mayu Yamaguchi, Juan Bisquert (Energy & Environmental Science and Sustainable Energy & Fuels Advisory Board member)

Sustainable Energy & Fuels winner Mantulnikovs, Konstantins (EPFL)
“Differential Response of the Photoluminescence and Photocurrent of Polycrystalline CH3NH3PbI3 and CH3NH3PbBr3 to the Exposure to Oxygen and Nitrogen”

Juan Bisquert (Energy & Environmental Science and Sustainable Energy & Fuels Advisory Board member), James Durrant (Sustainable Energy & Fuels Editor-in-Chief), Konstantins Mantulnikovs, Hideo Ohkita and Atsushi Wakamiya

 

Awards presented by James Durrant, Editor-in-Chief of Sustainable Energy & Fuels

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