Welcome to Aptamers 2016

View a selection of Aptamers 2016 photos on the INSOAP website.

Dear Colleagues:

We are delighted to announce our third Oxford symposium on aptamers, Aptamers 2016, which is designed to bring together academic and industrial aptamer researchers and solution providers. The symposium will address therapeutic, diagnostic, analytical as well as basic research applications of aptamers and invites proposals for podium (now closed!) and poster presentation. Please contact us on AptamersOxford@gmail.com, should you require any further information.

Aptamers 2016 will be co-hosted with our 2nd symposium on antisense and therapeutic oligonucleotides, Oligo 2016, on 6th April 2016.

We very much look forward to welcoming you at the symposium.

Professor Dr Beatrix SuessSuess
(Symposium chair)
Synthetic Genetic Circuits
Technical University of Darmstadt


Speakers and Agenda


08.00-08.50: Registration, Networking, Exhibition and welcome coffee

08.50: Welcome and housekeeping

08.55: Opening by Professor Dr Beatrix Suess

09.00: INSOAP updates by Dr Sarah Shigdar

Session 1: SELEX – New technological developments
Chair Dr David Bunka

09.10: Professor Thomas Brown, University of Oxford, United Kingdom
Synthesis of chemically modified oligonucleotides for the production of high-affinity aptamers

09.40: Dr Gregory Penner, President & CEO, NeoVentures Biotechnology Inc, Canada
FRELEX. free-free selection of aptamers

10.10: Dr Nathalie Vollmer, Horiba Scientific, France
Multiplex quantification of small molecule targets with SPRi analysis

10.30: Refreshment break, exhibition, posters and networking

11.10: Professor Chin-Yih Hong, Graduate Institute of Biomedical Engineering, National Chung Hsing University, Taiwan
Multiplex Immunoassays Using ssDNA Aptamers Generated by Magnetic-Assisted Rapid Aptamer Selection (MARAS)

11.30: Dr Bill Jackson, Base Pair Biotechnologies, USA
Applications of newly discovered aptamers in a variety of biosensors and assay formats

11.50: Professor Darryl J Bornhop, Professor of Chemistry, Vanderbilt University, TN, USA
Backscattering interferometry marries aptamer-based assays to enable quantitation of nerve agent metabolites and human cytomegalovirus in urine at clinical relevant levels

12.10: Dr Michael Blank, AptaIT GmbH, Germany
Improved Aptamer Identification and Optimization by Usage of Next Generation Sequencing

12.30: Lunch, exhibition, posters and networking

Session 2: Small molecule binding aptamer–Characterization and their application for gene control
Chair Professor Darryl Bornhop

13.40: Dr Philip Johnson, York University, Canada
Understanding Ligand Binding by the Cocaine-Binding Aptamer

14.00: Professor Dr Jörg S Hartig, Department of Chemistry, University of Konstanz, Germany
Engineering of synthetic riboswitches based on ribozyme expression platforms

14.30: Professor Dr Beatrix Suess, Technische Universität Darmstadt, Germany
Application of aptamers in the control of alternative splicing by engineered riboswitches

15.00: Professor Dr Uli Hahn, Hamburg University, Germany
Aptamers to inhibit cancer cell adhesion

15.30: Refreshment break, exhibition, posters and networking

Session 3: Aptamers as diagnostic tools
Chair Professor Said Ismail

16.00: Dr David Bunka, The Aptamer Group, United Kingdom
Novel Based Aptamer Biomarker Discovery

16.30: Processor Tony Cass, Imperial College London, United Kingdom
Engineering Aptamers for Use in Biosensors and Point of Decision Testing

17.00: Dr Julian Tanner, University of Hong Kong, China
Progress in aptamer-mediated malaria diagnosis

17.20: Dr Ana María de Lucas Cerrillo, Centro de Astrobiología (INTA/CSIC), Spain
RNA and DNA aptamers targeting HCV CORE protein and its applicability to HCV diagnosis

17.40: Dr Marimuthu Citartan, Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Malaysia
REPORA-6 RNA aptamer, an agent in the aptamer-based capture assay (AptaCapture) of Erythropoietin (EPO) in doping detection



08.50: Welcome and housekeeping

Session 4: Therapeutic aptamers
Chair Professor Beatrix Suess

9.00: Professor Yoshikazu Nakamura, RIBOMIC Inc, Japan
Dual therapeutic action of a neutralizing anti-FGF2 aptamer in bone diseases and bone cancer pain

09.30: Professor Nicola Stonehouse, University of Leeds, United Kingdom
Manipulating viral protein-protein interactions with RNA aptamers

10.00: Professor Said Ismail, University of Jordan, Jordan
Targeted gene silencing in cancer cells using Anti-CD44 aptamer-functionalized liposomes

10.30: Refreshment break, exhibition, posters and networking

11.00: Dr Sarah Shigdar, Deakin University, Australia
Aptamers as theranostic agents: the companion diagnostic test

11.30: Dr Sorah Yoon, Beckman Research Institute of City of Hope, USA
ApDCs (Aptamer Drug Conjugates) for targeted therapies in pancreatic cancer; from nucleic acid to chemotherapeutics

12.00: Mr Chao Liang, Hong Kong Baptist University, Hong Kong, China
Oligopeptide aptamer-modified chalcone derivative specifically targets Smurf1 in osteoblasts and promotes bone formation

12.20: Lunch, exhibition, posters and networking

Session 5: Technologies
Chair Dr Sarah Shigdar

13.10: Miguel AD Neves, Department of Chemistry, York University, Toronto, ON, M3J 1P3, Canada
The Cocaine-Binding Aptamer: Structural and Thermodynamic Analysis of Two-Site Binding and Stem Length Variation

13.30: Rajesh Ahirwar, Academy of Scientific and Innovative Research, Delhi, India
Aptamer-mediated detection and targeting of estrogen receptor positive cells in human breast cancer

13.50: Dr Zhaofeng Luo, Core Facility Center for Life Sciences, University of Science and Technology of China (USTC), Hefei, PR China
Monitoring the aptamer selection progress by Q-PCR amplification curve



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…


Aptamers 2016 Sponsors

Gold Sponsor and Exhibitor


Aptamer Solutions Ltd is a York based Biotechnology Company specialising in the custom selection of high-affinity and highly specific nucleic acid aptamers for use in the life sciences sector. Our proprietary automated high-throughput aptamer selection processes allow us to offer a flexible and competitive pricing structure for the development of RNA and DNA aptamers. In addition, we are about to launch a new complementary technology in the area of biomarker discovery.

Our proprietary aptamer based biomarker discovery platform and proprietary combinatorial libraries contain up to and over 1018 different molecules, this diversity and bespoke library design is fundamental to the success of the screening process. This technology enables us to greatly speed up the identification of novel biomarkers as well as diagnostics and/or therapeutic candidate molecules. This technology builds on one of the most powerful uses of aptamer technology, which is the ability for aptamers to be isolated against targets without any prior knowledge of the target.

Our aptamer-based proteomic technology identifies novel biomarkers within the cell surface (such as tumours, cell lines or stem cells) or in samples of biological fluids (such as, urine, plasma and saliva). The technology is versatile and can also be applied to viruses, bacteria, fungi or any other cell based materials or extracts. The discovery process is driven by identifying differences between sample population using enormous aptamer libraries. Samples are prepared based on broad classifications such as: disease vs normal; pre-metastatic vs. post metastatic cancers; pathogenic vs non-pathogenic fungi etc. The process is fast and efficient and identifies differences between ‘healthy’ and ‘diseased’ whilst simultaneously developing the affinity reagent. This cuts out many of the steps associated with traditional biomarker discovery processes.

Gold Sponsor and Exhibitor


RIBOMIC Inc is a biopharmaceutical venture company based in Tokyo. The company is developing molecular targeted pharmaceutical drugs using RNA aptamers with its unique and advanced platform technologies called the RiboART System.

RIBOMIC has been promoting the pharmaceutical discovery program in collaboration with Otsuka Pharmaceutical Co., Ltd., Taisho Pharmaceutical Co., Ltd., The University of Tokyo, and some other academic partners. Especially in April 2014, RIBOMIC entered into a world-wide exclusive license agreement for the anti-NGF aptamer (RBM004) with Fujimoto Pharmaceutical Corporation. In September 2015, RIBOMIC Inc. was listed on The Tokyo Stock Exchange Corporation Mothers Market…read more on the company website

Bronze Sponsor and Exhibitor


HORIBA is a Japanese company divided in 5 segments, Automotive test systems, Process and Environment, Medical, Semiconductors and Scientific. The HORIBA Group mission is to provide superior technologies, unique products, and top-quality services in the analytical and measurement fields. Applying core technologies accumulated over the years, HORIBA provides products and services derived from unremitting research and development. Throughout its business activities, the HORIBA Group energetically focuses on three concerns: the environment, safety, and health. HORIBA Scientific is a worldwide leader in development and production of analytical measurement equipment for research, analysis for laboratories, and quality control. Life science is the scientific pursuit of life and its processes. This contributes to improving the Quality of Life and the progress of drug development and medical treatment, and is connected to mankind’s ultimate concern, «living life in good health». Materials and physico-chemical mechanisms play a central role in life phenomena. Thanks to our long-standing expertise in advanced materials, HORIBA Scientific has developed a full range of instruments (Fluorescence and Raman spectroscopy, Particle size analysers, ellipsometry and  Surface Plasmon Resonance Imaging) to improve our understanding of life, from the molecular to the organism level.

Bronze Sponsor and Exhibitor


Izon Science designs, manufactures and sells precision instrumentation for nano- and micro-scale particle analysis.  Using its technology, Tunable Resistive Pulse Sensing (TRPS), thousands of particles can be accurately analyzed for their size, concentration and charge.  The technology is highly flexible and directly measures a wide range of biological and synthetic particles with individual particle resolution.   Applications include the characterization of extracellular vesicles, viruses, cells and nanoparticles and microbubbles for drug delivery research.  Izon’s instruments are in use in research institutes, universities, and pharmaceutical and biotechnology companies around the world.

Bronze Sponsor and Exhibitor

ATDBioATDBio was established to provide high quality oligonucleotides to scientists around the world. ATDBio oligonucleotides are used successfully in academic and commercial research in the fields of genetics, genomics, molecular biology, biochemistry, biotechnology and nanotechnology. We supply a wide range of custom-made unmodified and chemically modified oligonucleotides for small and large scale applications. ATDBio specialises in highly modified oligonucleotides. Each oligonucleotide we make is unique, and we insist on the highest standards to maintain the best possible quality for every oligonucleotide.

Bronze Sponsor and Exhibitor


AuramerBio is an aptamer development company from Wellington New Zealand, we specialise in the translation of aptamer science into analytical tools and diagnostic assays. Our team is particularly proficient with small molecule targets, as illustrated by our growing catalogue of gold standard hormone binding aptamers. It is our vision to see aptamer science break out of niche science labs and into mainstream analytical and diagnostic use. As well as offering a number of aptamer based assays we are also developing a quantitative point of care device for measuring fertility hormones. Our team has a wide skill-base consisting of molecular biologists, synthetic chemists, physicists and surface chemistry experts positioning us perfectly to rapidly deploy aptamers into many analytical assay and device platforms.

We work with a wide range of customers from academic to commercial to develop aptamer solutions to meet their needs. Using our proprietary selection and optimisation methods we can produce industry leading DNA aptamers to bind the target of your choice. Once an aptamer has been developed we also offer a service to optimise the performance of the aptamer on a range of assay platforms.

Please contact us to discuss your aptamer development needs: jeremy.jones@auramerbio.com or chat to us at Aptamers 2016.

Lunch Sponsor


2bind GmbH, Regensburg, Germany, provides biophysical analyses of molecular interactions. We work with worldwide customers from pharma, biotech as well as universities on the characterization of molecular interactions in terms of binding affinities, stoichiometries and binding energetics. Our semi-automated platform based on the MicroScale Thermophoresis technology (MST) allows us to offer cost-efficient, precise and fast analyses of molecular interactions. The integrated quality controls of the MST system enable us to easily identify sticking and aggregation effects and to directly improve measurement conditions ensuring high quality data. In addition to immobilization-free measurements in free solution, MST offers free choice of buffer, allowing close to native measurements in sera and lysates. Besides the low sample consumption our customers benefit from the broad application range of the MST. With our strong expertise in assay development, the company established standardized assays to analyze aptamer-target interactions in semi-high throughput for the aptamer developing industry and scientists. Further MST services includes competition assays, binding site mapping assays and binding assays that simultaneously test multiple binding partners. Hence, our services based on the MST technology are perfectly suitable for the identification, characterization and optimization of aptamer-target interactions.



IBA GmbH – Your partner for custom-made Aptamers

IBA GmbH is a biotech company located in Goettingen, Germany. Since 1991 our nucleic acid division has focused on specialized nucleic acid custom services, which require particular care and highest quality. These include custom-made DNA and RNA oligonucleotides, chimers, modified and labeled nucleic acids (e.g. for real-time PCR) as well as dinucleotides and triphosphates.

Taking advantage of the new Click Chemistry we can offer new dye combination options and unsurpassed labeling densities. More than 200 fluorescent labels and more than 80 modifications are available to suit your needs.

With our expertise in high quality oligonucleotide synthesis we produce custom DNA and RNA Aptamers according to your individual specifications. You ask for it – we synthesize! Just let us know your DNA/RNA sequence and required modification.

For the generation of new DNA or RNA Aptamers we are performing a complete aptamer development process consisting of in vitro selection by SELEX, sequences analysis, aptamer characterization and optimization in collaboration with Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam.

More details can be found at www.oligo-specialist.com.