• Aptamers 2016
    3rd Oxford Symposium on Aptamers
    04-05 April 2016
    St Hilda's College, Oxford, UK

    Co-hosted with our 2nd Therapeutic and Antisense Oligonucleotides Symposium, Oligo 2016 on 06 April at St Hilda's College, Oxford, UK
  • Aptamers 2016
    3rd Oxford Symposium on Aptamers
    04-05 April 2016
    St Hilda's College, Oxford, UK

    Co-hosted with our 2nd Therapeutic and Antisense Oligonucleotides Symposium, Oligo 2016 on 06 April at St Hilda's College, Oxford, UK

Posters & Guidelines

Thank you for considering to present your work as a poster at Aptamers 2016.

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:


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 Should you wish your abstract not to be published, please notify us in writing at the time of abstract submission.

Poster presenters are requested to send us their poster as PDF at least two weeks before the event. The posters will be made available via the event website or other electronic media after the event. Please also bring a printed version for presentation.

Posters will be displayed in the JdP foyer for the full duration of the event.

>>Where can I print my poster in Oxford?
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)

Development of an enzyme-linked apta-sorbent assay (ELASA) for the quality control of a birch pollen immunotherapy vaccine

Lorenz AGLAS 1, Frank STOLZ 2, Angela NEUBAUER 2, Gottfried STEGFELLNER 2, Ronald VAN REE 3, Michael WALLNER 1, Fatima FERREIRA 1

Department of Molecular Biology, University of Salzburg, Austria
Biomay AG, Vienna Competence Center, Vienna, Austria
Academic Medical Center, Amsterdam, The Netherlands

Abstract: Birch pollen allergy is the main causes for spring pollinosis in the temperate climate zone of the northern hemisphere, and over 95% of birch pollen allergic patients are sensitized to the major birch pollen allergen Bet v 1. The only causal and effective treatment targeting the underlying immune mechanism responsible for developing an allergy is allergen-specific immunotherapy (AIT). Within the EU-funded project “BM4SIT – Innovations for Allergy” a hypo-allergenic but hyper-immunogenic mutant of Bet v 1 (termed BM4) was created for therapeutic use to replace current natural allergen extracts in AIT. The main goal of the project is to make allergy treatment safer and more effective. Quality control of the BM4 substance is a major aspect of developing a safe vaccine. Therefore, we aimed at producing BM4-specific aptamers to use within an…

Novel Based Aptamer Biomarker Discovery

Edward Barnes 1, Dr David Bunka 2, Dr Arron Tolley 2

Institute for Cancer Science, University of Manchester, St Mary’s Hospital, Manchester, UK
Aptamer Group Limited, Bio Centre, Innovation Way, Heslington, York, UK

Abstract: Cell-based aptamer selection is an incredibly powerful tool in fields such as cancer research. The ability to isolate cell or tissue-specific aptamers, without the need to first identify or purify a disease associated protein is giving scientists new tools to better understand and combat these complex diseases. The selection process also allows simultaneous selection of aptamers against multiple surface biomarkers. Unfortunately, this process has several problems which must be overcome. ‘Dead-cells’ amongst the target culture can non-specifically take up aptamers, leading to enrichment of non-aptamer sequences….

DNA aptamer-based affinity chromatography system for purification of Tat49-57-tagged proteins

Filip Bartnicki, Ewa B Kowalska, Klaudia Muszynska, Malgorzata Bodaszewska-Lubas, Wojciech Strzalka

Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland

Abstract: Cell-Penetrating Peptides (CPPs), also known as protein transduction domains (PTDs) or membrane translocating sequences (MTSs), are a group of usually short peptides which can cross the cell membrane barrier. CPPs are characterized by different origin (e.g. protein-derived, chimeric or synthetic) and biochemical properties. They can transport various cargoes into a living cells e.g. peptides, proteins, siRNA, or plasmids. Among numerous different CPPs molecules a fragment of the HIV-1 Tat protein called Tat peptide is one of the most frequently used. This cationic oligopeptide is able to transport  whole proteins into both animal and plant cells. In many cases, before final application, CPP-tagged proteins must undergo a purification process…

Hydrogen exchange rates of imino protons in the cocaine binding aptamer: An NMR study

Zachary R Churcher, Howard N Hunter, Miguel AD Neves, and Philip E Johnson

Depart of Chemistry, York University, Toronto, ON, M3J 1P3

Abstract: The hydrogen exchange rates of the imino protons in the cocaine binding aptamer were studied using magnetization transfer NMR experiments. This was done for two variants of the cocaine binding aptamer. The structure of the cocaine binding aptamer is three stems centred around a three-way junction, with a two base protrusion just before stem three. The two variants studied differ in their stem one length with MN4 having a stem one length of six base pairs, and MN19 having a stem one length of three base pairs. This short stem one variant under goes a structure switching binding mechanism, while the long stem one molecule is structure in its free and bound forms. The cocaine binding aptamer is unusual as it is able to binding to quinine approximately 50 times tighter than its intended ligand…

Selection of Antimalarial Drug Binding Aptamers for Point-of-Care Drug Detection in Fingerstick Blood Samples

Erin Coonahan,1,2,3 Maarten De Vos,2 Joel Tarning,3 Rick Fairhurst 1

Laboratory of Malaria and Vector Research, NIAD, National Institutes of Health, Bethesda, MD 20814, USA

2 Institute of Biomedical Engineering, Department of Engineering Science, Old Road Campus Research Building, University of Oxford, Headington, Oxford OX3 7DQ, UK

3 Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400 Thailand

Abstract: Malaria parasites in Cambodia have begun to develop resistance to several first-line antimalarial drug therapies – artemisinin-based combination therapies (ACTs). Preventing the spread of drug resistant parasites through Southeast Asia and to Africa is a top priority for global malaria elimination campaigns. The ability to detect these small molecule drugs in malaria patient samples at the point-of-care would allow healthcare workers to identify previous treatment failures and adjust future treatment to improve efficacy and reduce the spread of resistant parasites. Additionally, a simple assay to detect these drugs would allow for real-time reporting of drug use for mapping and compliance studies…

Development of DNA aptamers specific for lung cancer stem-cells

Mateja Delač1,2, Helena Motaln1, Nika Janež5, Matjaž Peterka5, Henning Ulrich3 & Tamara Lah Turnšek1,3,4

1 Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Ljubljana, Slovenia
Nanosciences and Nanotechnologies Programme, Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
3 Department of Biochemistry, Institute of Chemistry, Sao Paolo University, Sao Paolo, Brasil
Department of Biochemistry, Faculty of Chemistry and Chemical Engineering, University of Ljubljana, Slovenia
Center of Excellence for Biosensors, Instrumentation and Process Control, Center for Biotechnology, Ajdovščina, Slovenia

Abstract: Lung cancer remains the most common cause of death from cancer worldwide, according to International Agency for Research on Cancer. Increasing data over recent years have indicated the existence of cancer-initiating cells, with stem cell characteristics crucial for lung cancer development. Cancer stem cell (CSC) hypothesis is gaining recognition also in metastasis formation. It is assumed that circulating tumor cells (CTCs), a population of pre-metastatic cells found in blood and other interstitial fluids is enriched with CSCs. Due to their resistance to therapies those may be responsible for treatment failure and tumor relapse. The level of CSC/CTC in serum is emerging as a potential new prognostic factor of cancer progression…

Adaptive Dynamic Artificial Poly-ligand Targeting (ADAPT): a highly multiplexed aptamer-based biomarker discovery platform

Valeriy Domenyuk 1, Zhenyu Zhong 1, Adam Stark 1, Jie Wang 1, Sonal Tonapi 1, Heather O’Neill 1, Nianqing Xiao 1, Mark R. Miglarese 1, Günter Mayer 2, Michael Famulok 2,3, David B. Spetzler 1

1 Caris Life Sciences, Phoenix, AZ, USA
LIMES Program Unit Chemical Biology & Medicinal Chemistry, University of Bonn, Germany
3 Chemical Biology Max-Planck-Fellowship Group, Center of Advanced European Studies and Research, Bonn, Germany

Abstract: Biomarker discovery for next generation therapies and diagnostics based on expression of DNA, RNA and proteins is restricted and can only measure a limited number of functional components simultaneously. We developed a highly multiplexed ssDNA aptamer-based biomarker discovery platform (ADAPT) and report its potential use in breast cancer diagnostics and target identification. We enriched a ssDNA library of 1012 oligodeoxynucleotides (ODNs) for interaction with exosome-associated proteins contained in blood plasma from women with positive and negative breast cancer biopsies. Enrichment was confirmed by comparing binding profiles of the starting and the enriched ODN libraries to plasma exosomes using Next Generation Sequencing (NGS), qPCR, flow cytometry and mass spectrometry. Aptamer properties were verified by…

Cell-SELEX using a genetic alphabet expansion system, targeting breast cancer cells

Kazunobu Futami 1, Michiko Kimoto 2, 3, Ichiro Hirao 2, 3

1 TagCyx Biotechnologies, 1-6-126 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
2 RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
3 Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #04-01, Singapore

Abstract: As an improved version of DNA aptamer generation, we are providing a new SELEX method for non-natural DNA aptamers (Xenoligo* DNA aptamers), in which an unnatural hydrophobic base, 7-(2-thienyl) imidazo [4,5-b] pyridine (Ds), is introduced as a fifth base by using a genetic alphabet expansion system. In the SELEX method, DNA species that bind to a target protein are isolated from a DNA library containing A, G, C, T, and Ds in its random sequence region. Then, the selected DNA species are amplified by PCR involving an unnatural base pair…

DNA aptamers as potential antimicrobial drugs. Search for inhibitors of the methylerythritol phosphate pathway of isoprenoid biosynthesis

Andreu Saura 1, Josep Maria Cornet 1, Alba García 1,  Ariadna Payà 1, Alexandre Serra 1, Xavier Fernández-Busquets 2 and Santiago Imperial 1

1 Department of Biochemistry and Molecular Biology, School of Biology, University of Barcelona. Avda Diagonal 643, ES08028-Barcelona
2 Nanomalaria Joint Unit. Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute for Global Health (ISGlobal). Centre Esther Koplowitz, planta 1, ISGlobal Rosselló 149-153 ES08036 Barcelona

Abstract: Human malaria is devastating disease caused by five species of Plasmodium parasites and today remains one of the major infectious diseases of the world. Although considerable effort has been spent on the development of vaccines, chemotherapy continues to be the main weapon against this disease for the near future. Resistance to commonly used malaria drugs is spreading and new drugs are required urgently. Plasmodium parasites have an organelle called apicoplast, which offers numerous new targets for drug therapy because contains a range of metabolic pathways and enzymes not found in host cells. Of these pathways, the enzymes required for biosynthesis of the isoprenoid precursors, IPP and DMAPP are particularly attractive. These precursors are produced in Plasmodium from pyruvate…

Characterization of a new DNA aptamer selected against STAT5B, a protein involved in leukemia

Hassan Isber, Séverine P Lefèvre, Alain Friboulet, Bérangère B Avalle

Sorbonnes Universités, Université de Technologie de Compiègne, CNRS FRE 3580 (Enzyme and Cell Engineering), Compiègne, France

Abstract: STAT5A and B are common transcription factors that constitute a convergent point for many cellular pathways. Among their multiple biological functions, they are well known in promoting immune cell development and differentiation. When some oncogenic mutations occur, STAT5A and B are highly activated leading to uncontrolled proliferation and then to leukemia. Thus, they constitute a prime target to therapeutic intervention. This work aims to select and characterize DNA aptamer specifically against STAT5 in order to regulate its activity in leukemia disease. We performed 7 SELEX rounds resulting in a DNA sequence (Apta2) that present a potential affinity to STAT5B…

Common Themes in Aptamer-Protein Complexes from Crystal Structures

Amy D. Gelinas 1, Douglas R. Davies 2 and Nebojsa Janjic 1

SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301
Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110

Abstract: Crystal structures of only sixteen aptamer-protein complexes have been reported to date.  Even from this small set, some common themes are emerging.  In contrast to aptamer-small molecule complexes in which the aptamer forms a cage around the small molecule, a substantial fraction of the aptamer surface makes contact with the protein.  Well-established nucleic acid secondary structure motifs are prevalent.  Unsurprisingly, double-helices represent the most recurring motif, which in aptamers often contain non-canonical base pairs, base mismatches or internal loops, hairpin loops of various sizes, or are found in the context of higher order assemblies such as pseudoknots and three-way helix junctions….

Selection of a ssDNA aptamer against SUMO2 from Arabidopsis as a potential tool for studying post-translational modifications of plant proteins

Ewa B Kowalska, Klaudia Muszynska, Filip Bartnicki, Malgorzata Bodaszewska-Lubas and Wojciech Strzalka

Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland

Abstract: SUMO (Small Ubiquitin-like MOdifier) is a well characterized post-translational modifier of many eucaryotic proteins. It was demonstrated that SUMO is involved in cellular signal transduction and can play a regulatory function in cellular processes. Studies on the plant model revealed that in response to stress the sumoylation pattern of Arabidopsis thaliana proteins changes. The identity between the amino acid sequences of Arabidopsis SUMO1-8 proteins is very high and therefore the possibilities of differentiation between particular members of the Arabidopsis SUMO family using antibodies are limited. The selection of ssDNA aptamers against the SUMO2 protein was performed using the SELEX…

Selection, identification of ligand binding domain, and binding optimisation of aptamers targeting small organic molecules

Shalen Kumar1,2, Shiwei Li1,2, Jeremy Jones2 and Kenneth P McNatty1

School of Biological Sciences, Victoria University of Wellington, New Zealand
Auramer Bio Limited, Wellington, New Zealand

Abstract: Synthetic single stranded oligonucleotides, also known as DNA or RNA aptamers have been developed to bind both small and large molecular weight molecules. DNA aptamers are generated using in vitro directed evolution methodology known as systemic evolution of ligands by exponential enrichment (SELEX) where, a library of randomised nucleic acid sequences are subjected to various rounds of affinity based selection and amplification processes.  The resulting aptamers with increased affinity to the target molecule are sequenced and the target binding properties then characterised before desired applications. In the present studies, a random library of 75mer single-stranded DNA (ssDNA) was…

Studying binding affinities of aptamers to diverse targets with a large molecular size range using MicroScale Thermophoresis

Clemens Entzian, Corinna Kuttenberger, Tobias Mauerer, Lukas Kniep, Estefanía Muciño and Thomas Schubert

2bind GmbH, Am Biopark 13, 93053, Regensburg, Germany 2bind GmbH

Aptamers have become important tools in research, diagnostics and therapeutics. Biophysical characterization of the binding parameters of aptamers is essential for the well functioning of these in diverse applications. MicroScale Thermophoresis (MST) is a rapid and precise method to analyze aptamer-target interactions in solution at microliter scale. The basis of this technology is a physical effect referred to as thermophoresis, which describes the directed movement of molecules through temperature gradients. The thermophoretic properties of a molecule depend besides – on its size – also on charge and hydration shell. Upon binding of a ligand at least one of these parameters is altered, which enables MST to analyze virtually…

MicroScale Thermophoresis – a versatile tool to study aptamer-target interactions beyond classical binding parameters

Clemens Entzian, Corinna Kuttenberger, Tobias Mauerer, Lukas Kniep, Estefanía Muciño  and Thomas Schubert

2bind GmbH, Am Biopark 13, 93053, Regensburg, Germany 2bind GmbH

Aptamers are potent binding molecules recognizing various classes of target molecules. Thereby, aptamers are used in a great variety of different complex approaches in therapeutics and diagnostics. Establishment of these complex assays often needs more information than just the classical binding parameters such as affinity, stoichiometry and thermodynamics. Detailed information on aptamer binding site, aptamer performance in complex liquids or with multiple binding partners may be necessary. In therapeutics, information on the potency of an aptamer to inhibit an important target interaction may be of great interest. The versatile technique of MicroScale Thermophoresis offers a great variety of different highly informative assays…

Tumor cell-targeted delivery of CRISPR/Cas9 by aptamer-functionalized lipid nanoparticles for therapeutic genome editing of miR-214 in osteosarcoma

Fangfei Li, Chao Liang, Luyao Wang, Chao Wang, Bing He, Hailong Zhu, Aiping Lu, Ge Zhang

Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China

Abstract: Osteosarcoma (OS) is a malignant primary bone sarcoma mostly occurring in children and adolescence, which is the third common pediatric cancer with the highest mortality rate. The conventional treatment for osteosarcoma is surgery in combination with chemotherapy and radiotherapy. However, the prognosis is still poor due to chemo-resistance and metastasis. microRNAs (miRNAs) are important regulators of diverse physiological processes and the altered expression of particular miRNAs contributes to tumor disease. The over-expression of miR-214 was shown to be related to osteosarcoma malignancy, metastasis and poor prognosis. However, the antagomir-214 could only temporarily deactivate the miR-214 in the cytoplasm….

Rapid Prototyping Aptamer-Enabled Malaria Diagnostics Using Three-Dimensional Printing

Shaolin Liang, Roderick M Dirkzwager and Julian A Tanner

School of Biomedical Science, Faculty of Medicine, University of Hong Kong, 21 Sassoon Road, Hong Kong SAR, P.R.China

Abstract: The integration of three-dimensional (3D) printing into diagnostic development gives the creative power for rapid prototyping diagnostic devices by adapting basic molecular technologies.  Thanks to the quick printing time and low printing cost, customized parts can be generated to fit different assay formats and optimized via the process of “design – test – redesign”. In this study, we present the development of 3D printed aptamer-enabled diagnostic devices based on our previously reported aptamer-tethered enzyme capture (APTEC) assay for malaria diagnosis. A paper-based syringe test and a magnetic bead-based well test were developed using 3D printed parts. Both were found to successfully detect…

A Homogenous, Universal Enzymatic Assay for Histone Methyltransferases Based on a Microbial Riboswitch

Meera Kumar1, Ronald R. Breaker2 and Robert G. Lowery1

1 BellBrook Labs, 5500 Nobel Drive, Suite 230, Madison, WI USA 53711
2 Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA

Abstract: Epigenetic regulation affects diverse diseases, and high throughput screening for histone methyltransferase (HMT) inhibitors is an area of intense activity.  HMTs produce many different methylated products, and assay methods that detect S-adenosylhomocysteine (SAH) – the invariant product of S-adenosylmethionine (SAM)-dependent methylation reactions – are therefore advantageous over methods that detect specific methylation events.  However, direct detection of SAH requires a reagent capable of discriminating between SAH and SAM, which differ by a single methyl group.  There is a significant sensitivity challenge as well because HMTs are slow enzymes and use low levels of SAM.  Currently there are no SAH assays with sufficient selectivity…

Conditional control of splicing by synthetic riboswitches

Adam Mol, Florian Groher, Beatrix Suess

Technical University of Darmstadt, Department of Biology, Schnittspahnstr. 10, 64287 Darmstadt, Germany

Abstract: Splicing of pre-mRNA occurs within a multicomponent complex termed the spliceosome. The accuracy of the splicing process involves the recognition of short sequences within the pre-mRNA that delimit the exon-intron boundaries. Nearly 90% of the human genes are subjected to alternative splicing and disruption of the splicing machinery lead to genetic diseases and cancer. Reprogramming of aberrant splicing could provide novel approaches to the development of molecular therapy. For this purpose, we want to use aptamers as a promising tools to control splicing events. Previous work in our group has established TetR aptamer-controlled constitutive splicing…

Tandem GGA repeat G-quadruplex as an anti-prion protein aptamer and a K+-responsive structural/functional switching device

Takashi Nagata 1,2, Tsukasa Mashima 1,2, Yudai Yamaoki 2, Fumiko Nishikawa 3, Yuji O. Kamatari 4, Satoshi Nishikawa 3, Kazuo Kuwata 5, Masato Katahira 1,2

Institute of Advanced Energy and Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
4 Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan

Abstract: Prion diseases, such as bovine spongiform encephalopathy, are caused by Prion proteins (PrPs). We carried out SELEX and obtained an anti-PrP RNA aptamer, which tightly binds to and stabilizes PrP of a normal cellular form (PrPc). This interaction is expected to inhibit the conversion of PrPc into abnormal scrapie form (PrPSc). Our aptamer comprises tandem GGA repeat, r(GGA)4. We conducted nuclear magnetic resonance (NMR) analysis and revealed that r(GGA)4 folds into a unique G-quadruplex structure and forms a dimer. Two short segments comprising twelve amino acid residues…

Binding properties of RNA aptamer against AML1 Runt domain

Ryo Amano 1, Kenta Takada 1, Takashi Nagata 2,3,Yusuke Nomura 1, Junichi Fukunaga 4, Yoichiro Tanaka 4,  Masato Katahira 2,3,  Yoshikazu Nakamura 5,6, Tomoko Kozu 4, Taiichi Sakamoto 1

Dept. of Life and Env Sci, Chiba Inst Tech, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
2 Inst of Adv Energ, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
3 Graduate School of Energ Sci, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
4 Res Inst Clin Oncol, Saitama Cancer Center, Ina, Saitama 362-0806, Japan
5 Inst Med Sci, University of Tokyo, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
Ribomic Inc. 3-16-13 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan

Abstract: AML1 is a transcription factor which is involved in the development of normal hematopoiesis, and contains a DNA-binding domain, known as Runt domain (RD), which specifically recognizes consensus DNA sequence PyGPyGGTPy (Py = pyrimidine). In the previous study, we obtained RNA aptamer that binds to RD by SELEX and revealed that the aptamer exhibits higher affinity than the target DNA. The aptamer possessed the motif containing an AC mismatch and a single bulge which are important for mimicking the structure of target DNA….

The Cocaine-Binding Aptamer: Salt-Controlled Two-Site Binding and Structure–Affinity Relationship with Quinine Derivatives

Sladjana Slavkovic, Miguel AD Neves, Oren Reinstein and Philip E Johnson

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

Abstract: Aptamers have generated great interest as biosensors as their selection process allows them to bind a wide variety of ligands, often with high affinity and specificity. However, little is known about how aptamers interact with their targets. The cocaine-binding aptamer is widely used as a model system in the development of a variety of biosensor applications and our research is focused on understanding how this aptamer functions. A unique feature of the cocaine-binding aptamer is its ligand-binding promiscuity. Despite being selected for cocaine, the cocaine-binding aptamer has 50-fold higher affinity for quinine than cocaine. This off-target affinity…

Identification of tubulin-binding aptamers with small, but significant inhibitory effects on tubulin assembly

Elsa Sotiriadis

Centre for Synthetic Biology and Innovation, Department of Molecular Biosciences, Imperial College London, London, UK, and School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong

Abstract: Despite the pressing need for novel tubulin inhibitors and great therapeutic promise of aptamers, only two tubulin-binders T1 (Kd 45µM) and T2 (Kd 19.4µM) have been obtained so far from in vitro selection. I evaluate, for the first time, the inhibitory potential of these aptamers and a previously uncharacterized population by performing in vitro polymerization assays with >99% pure tubulin. A first observation was that oligonucleotides seem to reversibly interfere with the reaction in the first 15 minutes to a small extent. Therefore, I included representative oligo controls (R1,2) to quantify non-specific effects…

The aptamer clock: a rapid prototyping template for post-selection optimization of tubulin-binding aptamers

Elsa Sotiriadis

Centre for Synthetic Biology and Innovation, Department of Molecular Biosciences, Imperial College London, London, UK, and School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong

Abstract: Post-selection optimization is widely used to improve binding affinity and activity of aptamers and to reveal secondary structure features involved in binding interactions. I aim at improving tubulin inhibitors through rational truncations from a parental aptamer with small, yet significant inhibitory effects identified in a previous study. I employ its clock-like central stem-loop as a plug-and-play prototyping platform by adding and subtracting secondary structure motifs at precise positions ‘around the clock’. I evaluate 14 mutants bearing novel (predicted) features with in vitro tubulin polymerization assays. Five mutants achieved two-fold improved phase I inhibition (nucleation) over the parental sequence…

Structural analysis of RNA aptamers targeting hIL-6R

Kristina Szameit 1, Sven Kruspe 2, Marcel Kwiatkowski 3, Hartmut Schlüter 3, Uli Hahn 1

University of Hamburg, Department of Chemistry, Institute for Biochemistry and Molecular Biology, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
2 University of Iowa, Carver College for Biomedical Research, 375 Newton Road, Iowa City, IA 52242, USA
University Medical Center Hamburg-Eppendorf, Department of Clinical Chemistry, Martinistrasse 52, 20246 Hamburg, Germany.

Abstract: Interleukin-6 and its receptor hIL-6R are involved in the genesis and progression of several inflammatory and autoimmune diseases, as well as in the development of cancer. RNA-aptamer AIR-3 and its minimal binding motif AIR‑3A which target hIL-6R also bind to cellular presented receptor and are internalized by endocytosis. They also proved to be effective tools for in vitro drug deliveries. However, concerning their structure, former studies gave only little insight. As such, it was known that AIR‑3A forms an all‑parallel G‑quadruplex and that almost all nucleotides in the binding motif are essential to maintain affinity towards hIL-6R. G-quadruplexes have recently moved into focus of DNA and RNA research, thereby evolving in significance from structural…

Development of an efficient Cell-SELEX using engineered isogenic cell lines to generate RNA aptamers against a cell surface protein of interest

Masaki Takahashi 1, Yoshifumi Hashimoto 1, Eri Sakota 1, Yoshikazu Nakamura 1,2

The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
RIBOMIC Inc., Minato-ku, Tokyo 108-0071, Japan

Abstract: Aptamers are short single-stranded nucleic acid molecules that are selected in vitro from a large random sequence library based on their high and specific affinity to a target molecule by a process known as SELEX. Modified Cell-SELEX that employs whole living cells overexpressing the defined cell surface proteins (for selection) and corresponding mock cells (for counter-selection) has been widely used as a valid and feasible method for generating aptamers against specific cell surface proteins. However, the endogenous expression of target cell surface proteins in mock cells often impeded the isolation of aptamers against target proteins. To solve this problem, we manipulated ‘negative’ cells, whose…

Preclinical trials of novel anticoagulant — DNA aptamer Trombiveb®

Askar D. Turashev 1, Nadezhda S. Samoylenkova 1,2, Elena G. Zavyalova 1,3, Alexander V. Revishchin 2, Andrey V. Golovin 1,4, Galina V. Pavlova 1,2, Alexey M. Kopylov 1,3

Apto-Pharm LLC, Kolomensky passage 13a, Moscow, 115446, Russian Federation
Institute of Gene Biology of Russian Academy of Sciences, Vavilova Str., 34/5, Moscow, 119334, Russian Federation
3 Chemistry Department of Lomonosov Moscow State University, GSP-1, 1-3 Leninskiye Gory, Moscow, 119991, Russian Federation
4 Department of Bioengineering and Bioinformatics of Lomonosov Moscow State University, GSP-1, 1-73 Leninskiye Gory, Moscow, 119991, Russian Federation

Abstract: Drug targeting depends on ability to create molecule which could tightly and highly specifically interacts (recognize) with target, in other words — molecular recognition elements (MoRE). Balancing on bilateral paradigm of low molecular weight substances vs high molecular weight substances could favor oligomers, like peptides or oligonucleotides. One of the example of therapeutic nucleic acids is aptamer — oligonucleotide which could recognize target due to specific 3D structure. Attractive academic potential of aptamers over antibodies has to be proved by extensive preclinical trials. We have explored pharmacological properties of original bipartite DNA aptamer to human thrombin…

Molecular selection, modification and development of therapeutic oligonucleotide aptamers

Yuanyuan Yu 1, Chao Liang 1, Quanxia Lv 1, Defang Li 1, Xuegong Xu2, Baoqin Liu2,*, Aiping Lu 1*, Ge Zhang 1

1 Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
2 Zhengzhou Hospital of TCM, Zhengzhou, China

Abstract: Monoclonal antibodies are dominating agents in inhibition of biological target molecules for disease therapeutics so far but with concerns of immunogenicity, production, cost and stability. Oligonucleotide aptamers have comparable affinity and specificity to targets with monoclonal antibodies whilst have minimal immunogenicity, high production, low cost and high stability, thus are promising inhibitors to rival antibodies for diseases therapy…

Aptamer library SELEX performance analysis algorithm based on percent GC nucleotide families

Zhenyu Zhong, Adam Stark, Valeriy Domenyuk, Mark Miglarese and David Spetzler

Caris Life Science, Phoenix, AZ, USA

Abstract: Next Generation Sequencing (NGS) has advanced the efficiency of the analysis of the Systematic Evolution of Ligands by Exponential Enrichment (SELEX). However, lack of appropriate algorithms to monitor the SELEX progress in massive NGS data sets has restricted the chances for successful selection of aptamers with desired function. This is especially critical for SELEX on multiple targets, where over-maturation of the library can lead to the loss of the most desired aptamers, namely those specific to targets that might be low abundance but most  informative. Here we present an algorithm, using the percentage of GC (%GC) in the aptamer sequence as a category factor to partition aptamers sequences. The algorithm is based on assumption that PCR efficiency of the aptamers with similar %GC (%GC family) are similar, so that any performance deviation from particular %GC family confident range would be highly likely driven by the SELEX selection pressure….

Development of an aptamer-based magnetic bead assay to remove 17β-estradiol from water supplies

Marlen Zschätzsch 1, Alexander Eisold2, Maria Ruhnow 1, Carolin Pohl 1, Thomas Bley1 , Dirk Labudde2, Elke Boschke 1

Institute of Food Technology and Bioprocess Engineering, Technische Universität Dresden
Department of Applied Computer and Biosciences, University of Applied Sciences, Hochschule Mittweida

Abstract: Endocrine-disrupting compounds (EDCs) are substances interfering with the hormone system in mammals and pose harmful effects on diverse species. There is a broad spectrum of EDCs. However, the most potent EDCs are endogenous steroid hormones such as 17β-estradiol (E2) and the synthetic steroid hormone 17α-ethinylestradiol (EE2). Anthropogenic EDCs accumulate in the environment via effluents from pharmaceutical and chemical industries as well as excretions from humans and animals. E2 and EE2 have been recently added to a first EU-wide watch list due to their harmful effects specifically on aquatic species. Substances that are part of the watch list are mandatorily required to be monitored thoroughly in all European countries, to be able to complete the risk assessment of these compounds and to set appropriate environmental quality standards…