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Aptamers
Open-access
Aptamers 2018
11-12 April 2018, Oxford
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Posters & Guidelines

Thank you for considering to present your work as a poster at Aptamers 2018.

Please prepare your poster in A1 portrait format (59cm wide x 84cm long). Please do not laminate your poster or use heavy printing material. Further information about poster sizes can be found on the following link:

http://tinyurl.com/y7bf

Posters larger than A1 will only be displayed subject to the availability of space.

Maximum capacity 30 A1 posters

Please ensure you have appropriate permissions for the publication of your abstract from the original copyright holders. Should you wish your abstract not to be published, please notify us in writing at the time of abstract submission.

>>Where can I print my poster in Oxford?

Invitation to submit an article to the journal Aptamers

We invite you to submit your research to the journal Aptamers (ISSN: 2514-3247), which is a new official open-access journal of the International Society on Aptamers, dedicated to publishing peer-reviewed research and reviews on all aspects of aptamer research.

We are happy to waive basic open access publication fee until 30th April 2018, as long as the manuscripts are prepared according to the guidelines for authors.


Best Poster Prize

We are delighted to announce that MDPI Pharmaceuticals will fund the best poster award this year.  Poster presenters are requested to send us their poster as PDF at least two weeks before the event in order to enter the poster prize competition. The posters will also be made available via the event website or other electronic media after the event. Please also bring along a printed version for presentation. Posters will be displayed in the JdP foyer for the full duration of the event.


Accepted Posters

If your abstract has been accepted for presentation but it does not appear in the list below, please let us know as soon as possible by email on aptamersoxford@gmail.com.

(Presenter in bold)


Ligand-dependent base pair stability in the cocaine-binding aptamer

Zachary R Churcher, Philip E Johnson

Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario, Canada, M3J 1P3

Using NMR spectroscopy, the effect of temperature on the base pair stability of of the cocaine-binding aptamer has been investigated by studying the imino proton exchange rates of the base pairs in their free and ligand bound states.  MN4 is a variant of the cocaine-binding aptamer that binds to cocaine tighter than the originally selected sequence. It consists of a three stems centered on a three-way junction with a dinucleotide bulge and 2 A-G mismatches. What make this aptamer exciting however is that it binds to quinine tighter than the ligand it was selected for. Off target ligand binding is not uncommon with aptamers, but off target binding that is tighter the intended ligand is rarely seen. The MN4 aptamer was studied using magnetization transfer NMR. This is done by selectively magnetizing the potion of the NMR spectrum where the imino resonances are found, and then seeing how long it take for the peaks…


Selection of high-affinity fully modified 1,5-anhydrohexitol aptamers against rat vascular endothelial growth factor 164

Elena Eremeeva1, Lia Margamuljana1, Mikhail Abramov1, Elisabetta Groaz1, Piotr Leonczak1, Sam Noppen2, Peter Carmeliet3, and Piet Herdewijn1

Medicinal Chemistry, Rega Institute for Medicinal Research, KU Leuven, Herestraat 49, 1041, 3000 Leuven, Belgium

Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medicinal Research, KU Leuven, Herestraat 49, 1043, 3000 Leuven, Belgium

Laboratory of Angiogenesis and Vascular Metabolism, VIB Vesalius Research Centre, VIB, Herestraat 49, 912, Leuven 3000, Belgium

Aptamers are unique nucleic acid molecules that hold a promising potential for various applications in therapy and biotechnology. Fully modified 1,5-anhydrohexitol (HNA)–2’-OMe-RNA hybrid aptamers targeting the rat vascular endothelial growth factor 164 (rVEGF164) have been selected using an in vitro evolution procedure. Three sequences were found to interact with the target protein with affinities in the low-nanomolar to picomolar range. The evolution of such chemically altered aptamers was accomplished starting from a completely sugar-modified library containing a 20 2’-OMe-ribonucleotide sequence at the 5’-end followed by distinct 47 mer HNA regions. The resulting aptamers exhibited a remarkable resistance to nuclease degradation even after 24 h of incubation with DNase I. The high affinity of the selected aptamers was…


Riboswitching with ciprofloxacin – development and characterization of a novel RNA regulator

Florian Groher1, Cristina Bofill-Bosch1, Christopher Schneider1, Johannes Braun1, Sven Jager2, Katharina Geißler1, Kay Hamacher2,3 and Beatrix Suess1

1 Synthetic Genetic Circuits, Dept. of Biology, TU Darmstadt, Darmstadt, Germany

2 Computational Biology and Simulation, Dept. of Biology, TU Darmstadt, Darmstadt, Germany

3 Dept. of Physics, Dept. of Computer Science, TU Darmstadt, Darmstadt, Germany

RNA molecules play important and diverse regulatory roles in the cell. Inspired by this natural versatility, RNA devices are increasingly important for many synthetic biology applications, e.g. optimizing engineered metabolic pathways, gene therapeutics or building up complex logical units. A major advantage of RNA is the possibility of de novo design of RNA-based sensing domains via an in vitro selection process (SELEX). Here, we describe development of a novel ciprofloxacin-responsive riboswitch by in vitro selection and next-generation sequencing- guided cellular screening. The riboswitch recognizes the small molecule drug ciprofloxacin with a KD in the low nanomolar range and adopts a pseudoknot fold stabilized by ligand binding. It efficiently interferes with gene expression both in lower and higher eukaryotes. By controlling an auxotrophy marker and a resistance gene, respectively…


The delivery of doxorubicin to cancer cells using a DNA aptamer targeting EpCAM

Justin L Henri, Wei Duan & Sarah Shigdar

School of Medicine, Deakin University, Waurn Ponds, Geelong, Victoria, Australia

Current therapy for cancer typically involves indiscriminate chemotherapies that can have severe off target effects on healthy tissue and are still plagued by aggressive recurrence. Recent shifts towards targeted therapies offer the possibility of circumventing the obstacles experienced by these traditional treatments. While antibodies are the pioneering agents in such targeted therapies, clinical experience has demonstrated that their antitumor efficacy is limited due to their high immunogenicity, large molecular size, and costly and laborious in vivo production. In contrast, nucleic based chemical antibodies, also known as aptamers, are ideal for this application given their small size, lack of immunogenicity and in vitro production. This study sought to explore the efficacy of a DNA aptamer, designed to target a well-established cancer biomarker, EpCAM, to deliver a chemotherapeutic drug. By truncating a large DNA EpCAM aptamer…


A fluoroquinolone-binding aptamer as a biosensor

Jeannine Jaeger, Florian Groher, Cristina Bofill-Bosch, Johannes Braun, Beatrix Suess

Department of biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany

The massive use of antibiotics in the medical sector and animal fattening has led to a continuous increase in multidrug resistant bacteria (MDROs). In order to control and possibly contain the spread of antibiotics in food, it is necessary to detect them quickly, efficiently and cost-effectively. While today’s detection methods are based either on antibody-rapid-tests or require a great deal of technical effort, aptamer-based biosensors represent a fast and efficient analytical method. Nucleic acid-based aptamers (aptamers) consist of either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) and can be characterized by their complex three-dimensional structure. This structure makes it possible to recognize any target molecule, like antibiotics, with high affinity and specificity. The aptamer-mutant R10K6_V11, which is able to bind ciprofloxacin (CFX) and other fluoroquinolones as a ligand, was used for an aptamer-based biosensor-design…


Modular platform for chemically modified aptamers

Przemysław M Jurek, Aleksandra Adamowicz, Agnieszka J Sok, Maciej P Mazurek

Pure Biologics Inc., Research & Development Department, Wrocław, Poland

In comparison with widely used antibodies, non-modified aptamers display only a limited range of chemical groups involved in the binding to the cognate targets. The narrow diversity of natural nucleobases is no match for the multifarious properties of the 20 proteinogenic aminoacids. In spite of that, many aptamers with  excellent properties have been selected during the past 28 years that can rival antibodies in many aspects, and even outcompete them. This makes us believe that the true power of aptamers lies in the possibility of introducing new non-canonical (either natural or unnatural) modifications to the nucleobases that will allow even better binding properties, thanks to a significantly broadened chemical space coverage. To challenge this view, we have recently developed a modular platform termed PureApta™ for introduction of new chemical groups into oligonucleotides structure and its integration into the SELEX procedure…


Fluorescent-imaging assay for dissociation constant determination of triclosan specific aptamers

Shiwei Li1,2, Shalen Kumar1,2, Jeremy Jones2, Mark Clarkson3, Janet Pitman1, Kenneth McNatty1

School of Biological Sciences, Victoria University of Wellington, New Zealand

AuramerBio Limited, Callaghan Innovation Quarter, 69 Gracefield Road, Lower Hutt, New Zealand

Callaghan Innovation, 69 Gracefield Road, Lower Hutt, New Zealand

Aptamers are nucleic acid-based receptors that bind target molecules by adopting specific three-dimensional structures. The binding affinity and specificity of an aptamer and the dissociation constant (Kd) are important characteristics when assessing it’s utility for specific applications. However, there are no universally accepted methods or recommended guidelines for the measurement of aptamer Kd. Therefore, there is a need for new and effective techniques to determine the binding characteristics of aptamers. Herein, we report a novel fluorescent-imaging assay (FIA) for determining the binding characteristics of aptamers selected against the antibacterial agent, triclosan (TCS). FIA utilises fluorescently-labelled aptamers and, in this instance, TCS that had previously been conjugated to sepharose beads. Upon binding of the TCS-selected aptamer to the TCS-bead conjugate, the complex can be visualised and the image captured…


Improving Aptamer Specificity with Stringent Counterselection Methods

Jonah C Rosch, Ethan S Lippmann

Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA

Aptamers are single-stranded oligonucleotides that have become powerful reagents for diagnostic and therapeutic applications. The utility of these reagents depends on a balance between two design parameters: affinity and specificity. While aptamers with high affinity are relatively easy to obtain from a selection process, a high degree of specificity is much more difficult to engineer due to limitations by low throughput and a lack of stringency. Methods to impart a high degree of specificity usually require complex and expensive techniques during negative counter-selection steps.  Imparting a high degree of specificity is especially important when targeting proteins that are part of large families that share sequence and structural homology, and many diseases are caused by mutations in proteins whereby the mutant protein maintains substantial similarity to its wild-type counterpart.  In these cases, aptamers selected by conventional methods can exhibit off-target recognition…


Utilizing the intrinsic fluorescence of cocaine-binding aptamer ligands: insights into the binding mechanism and development of a thermal shift assay

Aron A Shoara, Logan W Donaldson, Philip E Johnson

Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, ON M3J 1P3, CANADA

We used fluorescence spectroscopy to measure the binding affinity and provide new insights into the binding mechanism of cocaine and quinine with the cocaine-binding DNA aptamer. Using the intrinsic fluorescence of quinine and cocaine, we have observed quenching of ligand fluorescence upon binding of the aptamer. Quantification of this quenching provides an easy method to measure the binding constant using small amounts of sample. The observed quenching coupled with a red shift of the Stokes shift in the emission spectrum indicates that quinine and cocaine interact with the aptamer through stacking interactions.We then used the inherent fluorescence properties of the ligands in a thermal shift assay in two different projects. In the first, we developed a new cocaine-binding aptamer variant with a higher melting temperature when bound to a ligand than the currently used sequences without decreasing…


Insights into Ligand Binding by the Cocaine-Binding Aptamer and ATP Aptamer – an ITC Study

Sladjana Slavkovic, Zachary Churcher, Yanrui Zhu and Philip E Johnson

Department of Chemistry, York University, Toronto, ON, M3J 1P3, Canada

Both the cocaine-binding aptamer and the ATP aptamer are widely used as model systems in the development of a variety of biosensor applications. We have utilized isothermal titration calorimetry (ITC) methods to analyse the thermodynamics of how these aptamers interact with their ligands. Two unique features of the cocaine-binding aptamer are its ligand-binding promiscuity and salt-controlled two-site binding mechanism. Despite being selected for cocaine, the cocaine-binding aptamer binds quinine with higher affinity than cocaine. To further study the ability of this aptamer to bind different ligands, we looked at binding of quinine-based (amodiaquine, chloroquine, primaquine and mefloquine) and non-quinine based (pyrimethamine and dapsone) anti-malarial drugs to the cocaine-binding aptamer and compared results to both quinine and cocaine. Surprisingly, the quinine based anti-malarial drugs…


Selection of NT-proBNP specific aptamers

Zoltán Tolnai, Éva Nagyné Scholz, Zsuzsanna Szeitner, Ákos Harkai, Tamás Mészáros

Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary

Brain natriuretic peptide (BNP) are expressed and stored in myocardial tissue and plays role in regulating fluid and blood pressure. By heart failure patients the elevated serum level of BNP and of the inactive aminoterminal fragment of the BNP prohormone (NT-proBNP) are useful biomarkers in diagnosis of left-ventricular systolic dysfunction. Currently the measurements of serum BNP level are based on Immunoassay technics. Aptamers for the N terminal end of the NT-proBNP protein were selected previously in our laboratory. We aimed to select aptamers for another epitope of the NT-proBNP protein to aid the development of a proBNP specific sandwich assay. To obtain the suitable aptamers, peptides molecules from the C terminal end of proBNP and in vitro translated proBNP protein were alternately…


 

Important Dates

Early Registration: 05 Jan 2018
Register 3-for-2: 05 Jan 2018
Oral Abstracts: 22 Jan 2018
Poster Abstracts: 28 Feb 2018
Register 4-for-3: Any time

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