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J Venom Res
Open-access
Aptamers
Open-access
Aptamers 2019
03-04 April 2019, Oxford
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Speakers & Agenda

Day-1: 24th March 2014

9am: Professor Dr Jean-Jacques Toulmé (Inuagural Keynote Address)
ARNA Laboratory, Inserm U869, European Institute of Chemistry and Biology, University of Bordeaux, Pessac, France
Title: Aptamers: a world of structural and functional diversity
Abstract: Aptamers are oligonucleotides identified in large randomly synthesized libraries containing up to 1015 different oligomers, through in vitro selection, a process known as SELEX (Systematic Evolution of Ligands by EXponantial enrichment). Aptamers have been successfully raised against a wide range of targets: amino acids, nucleic acid bases, proteins, intact viruses and live cells. They generally display a high efficiency of binding thanks to their 3D shape resulting from intramolecular interactions. We raised aptamers against many different target molecules, such as foldamers or biomarkers of human tumors…

9.45am: Dr Axel Vater
Vice President Drug Discovery, NOXXON Pharma AG, Germany
Title: The integration of chiral principles into the SELEX process – Development of Spiegelmer therapeutics
Abstract: The SELEX process is a powerful technology to identify oligonucleotide-based aptamers to targets. In order to avoid stability issues with aptamers, we have adopted the SELEX process to first identify an aptamer against the non-natural enantiomer of a given target. The corresponding enantiomer to the aptamer, i.e. an aptamer consisting of non-natural, mirror-image nucleotides, will then consequently recognize the natural selection target. These mirror-image aptamers, also called a Spiegelmers, display very high biological stability. The mirror-image nature of Spiegelmer…

10.10: Dr Vittorio de Franciscis
Research Director CNR, Istituto per l’Endocrinologia e l’Oncologia Sperimentale del CNR “G. Salvatore”, Naples, Italy
Title: Multi-functional aptamer-miRNA conjugates for targeted cancer therapy
Abstract: An emerging class of therapeutic inhibitors is now represented by short nucleic acid aptamers.We have recently generated and characterized two 2’fluoro-pyrimidines modified RNA aptamers, named GL21.T and Gint4.T, that bind to and antagonize human Axl tyrosine kinase receptor and PDGFRβ, respectively. These molecules act as high affinity ligands with several advantages over conventional antibodies for their use in vivo, including their small size and negligible immunogenicity. These aptamers also rapidly internalized into target cells, getting about 30% of cell internalization…

11.15: Professor Said Ismail
Head, Molecular Biology Research Laboratory, Medical School, University of Jordan, and Head, Molecular Diagnostics Lab, Jordan University Hospital, Amman, Jordan
Title: Aptamers: Promising Molecules for Cancer Stem Cell Targeting
Abstract: The term Cancer Stem Cells (CSCs) has been coined to refer to a subpopulation of tumor cells that has the ability to self-renew and to generate the diverse cell pool of a given tumor. In recent years, CSCs have been receiving a great research interest due to their cancer initiating and maintaining capabilities making them the real driving force within a malignant mass that pushes towards more aggressive proliferation and more resistance against anticancer drugs. The cell surface glycoprotein CD44 is one of the most common surface markers used to identify CSCs. Our lab has been able to isolate RNA aptamers…

11.40: Dr Sarah Shigdar
Lecturer in Medical Sciences, School of Medicine, Deakin University, Australia
Title: Aptamers as effective cancer stem cell targeting modalities (co-authors: Sarah Shigdar, Dongxi Xiang, Wei Duan)
Abstract: Aptamers are becoming known for their ability to replace other agents, such as antibodies, in diagnostic and therapeutic applications. Within cancer research, aptamers can be very versatile molecules, capable of being used for in vitro diagnostic applications, therapeutics and in vivo molecular imaging. Having generated an aptamer against the cancer cell marker, EpCAM, we sought to develop this aptamer into a smart drug delivery vehicle. Using a common chemotherapeutic, doxorubicin, we intercalated this drug into the stem of the aptamer and tested its effectiveness to…

12.05: Professor Peter Stockley
Leeds University, UK
Title: Using aptamers to unmask the multi-tasking roles of viral RNAs
Abstract: In vivo ssRNA viruses co-assembly their protein (nucleo)-capsids spontaneously around genomic RNA, at very low concentrations, and with great fidelity in terms of selectivity, speed, accuracy, yield and timing. I will describe the latest results that indicate that genomic RNAs can play significant roles in regulating these processes via a series of RNA-CP interactions. SELEX has been used to identify these putative packaging signal (PS) sites, uncovering a novel anti-viral drug target…

12.30: Dr Meltem Avci-Adali
Wendel Laboratory, Department of Thoracic, Cardiac, and Vascular Surgery, University Hospital Tuebingen, Tuebingen, Germany
Title: Use of stem cell specific aptamers for in vivo tissue engineering (Co-authors: M. Avci-Adali, N. Perle, H. Stoll, N. Wilhelm, C. Schlensak, Hans P Wendel)
Abstract: Aptamers are not only auspicious ligands for small molecules, peptides, and proteins, but also for whole living cells, such as stem cells or cancers cells. Using cell SELEX including counter selections with non-target cells, stem cell specific aptamers can be selected. Thus, a great advantage of cell SELEX is that it is not necessary to know the target on stem cells during the selections. The target can be identified after the enrichment of aptamers and thereby, new up to now unknown markers on stem cells…

14.00: Dr David Bunka (Keynote Address)
Aptamer Group, UK
Title: Aptamers coming of age and their application in biomarker discovery
Abstract: Over the last 20+ years there have been significant developments in the field of aptamer based research, largely lead by academic institutions. More recently the uptake and development of aptamer based technologies has exploded, leading to the broad application of aptamers across almost all sectors of the life sciences; including areas such as research applications and novel reagents, diagnostics & biosensors, therapeutics, drug discovery & biomarker discovery. The continued ‘push’ towards early diagnosis and disease prevention, improved stratification of patient populations, personalised medicine and drug regime monitoring…

14.45: Professor Anne Varenne
Professor at Chimie ParisTech, Unité de Technologies Chimiques et Biologiques pour la Santé, Chimie ParisTech, Université Paris Descartes, UMR CNRS 8151, INSERM U1022, France
Title: Aptamers and analytical sciences for the development of challenging diagnostics
Abstract: Aptamers, considered as a nucleic acid version of antibodies and therefore as serious rivals to them, could be widely employed as sensitive affinity probes, diagnosis agents and biomedical research tools. For this purpose, a deep cooperation occurs between aptamers and analytical sciences, going from the development of analytical methods for aptamer selection and characterization, to the use of aptamers for improving diagnostics, as we will first present. We developed electrophoretic methods for aptamer characterization in solution…

15.10: Professor Ciara O’Sullivan
Universitat Rovira i Virgili, Spain
Title: High affinity truncated aptamer against the anaphylatic toxin ß-conglutin (Lup-an-1)
Abstract: Lupin is an herbaceous plant of the leguminous family, belonging to the genus Lupinus and has recently been added to the list of allergens requiring mandatory advisory labelling on foodstuffs sold in the European Union, and since December 2008, all products containing even trace amounts of lupin must be labeled correctly as it has been reported that lupin produces a variety of different allergic responses, including anaphylaxis. Lupin globulins consist of two major globulins called α-conglutin and ß-conglutin and another additional two-globulins, γ-conglutin and δ-conglutin, with toxicity having been associated primarily with…

15.35: Dr Frédéric Ducongé
CEA, Institut d’imagerie biomédicale, Service Hospitalier Frédéric Joliot, INSERM U1023; université Paris Sud; 4 place du Général Leclerc, 91401, Orsay Cedex, France
Title: Identification of tumor targeting aptamers from cell-SELEX to in vivo molecular imaging
Abstract: An increasing number of aptamers have been selected against biomarkers expressed at the surface of cells. Since 2005, our group and others have been adapting the SELEX against whole living cells. Using this cell-SELEX strategy, we selected several nuclease resistant 2′-Fluoro-pyrimidines (2′-F-Py) RNA aptamers against cell surface biomarkers that can represent surrogate markers of cancer cells. Although these aptamers represent promising tools for in vitro experiments

16.30: Dr Johanna-Gabriela Walter
Gottfried-Wilhelm-Leibniz Universität Hannover, Institut für Technische Chemie, Hannover, Germany
Title: Aptamers in affinity separeation (co-authors: Johanna-Gabriela Walter, Guohong Zhu, Frank Stahl, Thomas Scheper)
Abstract: Based on their affinity and specificity aptamers can be thought of as nucleic acid-based alternatives to antibodies, which have several advantages over their amino acid-based counterparts. In the context of affinity separation, the main advantages of aptamers are their high stability, the possibility to select aptamers that are functional under desired conditions and to design suitable methods for the elution of the target during the selection process of the aptamer. To demonstrate the applicability of aptamers for the purification of proteins, we have used two different aptamers…

16.55: Dr Beate Strehlitz
Department Centre for Environmental Biotechnology, Helmholtz Centre for Environmental Research GmbH – UFZ, Germany
Title: Aptamers for environmental applications (co-authors: Regina Stoltenburg, Christine Reinemann, Beate Strehlitz)
Abstract: At present, the main focus for aptamer applications lies in medical diagnostics and treatment. However, aptamers are also very suitable for environmental analytics and technology. In this context, the aim of our work is mainly the development of DNA aptamers for the detection of emerging pollutants and microbial pathogens. Here we describe exemplarily two DNA aptamers selected for protein A and for fluoroquinolones. Protein A is known as a cell surface protein originally found in the cell wall of the bacterium Staphylococcus aureus. The aptamer was selected by…

17.20: Miss Katharina Berg
University of Hamburg, Germany
Title:
Stabilized Interleukin-6 receptor binding RNA aptamers (Co-authors: Katharina Berg, Cindy Meyer, Inken Lorenzen, Joachim Grötzinger, Stefan Rose-John & Ulrich Hahn)
Abstract: Interleukin-6 (IL-6) is a multifunctional cytokine that is involved in the progression of various inflammatory diseases, such as rheumatoid arthritis, and certain cancers, for example multiple myeloma or hepatocellular carcinoma. To interfere with IL-6 dependent diseases, targeting IL-6 receptor (IL-6R) presenting tumor cells using aptamers might be a valuable strategy to broaden established IL-6 or IL-6R directed treatment regimens. Recently, we reported on the in vitro selection of RNA aptamers binding to the human IL-6 receptor (IL-6R) with nanomolar affinity…

17.35: Miss Feriel Melaine
SPrAM, UMR 5819 (CEA-CNRS-UJF-Grenoble 1), INAC/CEA-Grenoble, 38054 Grenoble cedex 9, France
Title: Aptamer biosensor for small molecules detection using Surface Plasmon Resonance imaging(co-authors: Feriel Melaine, Yoann Roupioz and Arnaud Buhot)
Abstract: Aptamers are single-stranded DNA (ssDNA) or RNA molecules capable of binding to target molecules, including proteins, metal ions and drugs. Because of their specific binding abilities and many advantages over antibodies (higher stability, lower cost, easy chemical modification…), they provide a great opportunity to produce sensing surfaces for effective and selective detection of small molecules. Surface Plasmon Resonance imaging (SPRi) has become one of the most widely used label-free method for the study of biorecognition events on sensor surfaces. This technique…

17.50: Miss Katharina Urmann
Department of Biotechnology and Food Engineering – Technion Haifa, Israel
Title: Porous silicon-based aptasensors (co-authors: Katharina Urmann, Ester Segal, Johanna Walter, Thomas Scheper)
Abstract: A label-free and reagentless optical biosensing platform based on nanostructured porous silicon and two different model aptamers is presented in this work. Nucleic-acid aptamers have attracted intense interest due to their many advantages as recognition elements in biosensing when compared to traditional antibodies. Herein, aptamers directed against the Fc-fragment of human Immunoglobulin G as well as an aptamer against his-tag are successfully used as recognition elements in a simple optical biosensor…

16.05: Dr Shashi Gupta
SomaLogic Inc, Wilderness Place, Boulder, CO, USA
Title: SOMAmers inhibit IL-6 signaling by blocking its interaction with IL-6 Ra and gp130 receptors
Abstract: We recently described a new class of aptamers called SOMAmers (Slow Off-rate Modified Aptamers) containing modified nucleotides with functional groups absent in natural DNA. These modifications mediate hydrophobic interactions between SOMAmers and their targets, leading to significant improvements in binding affinity and slower off-rates. Here, we describe the discovery and characterization of…

Day-2: 25th March 2014

8.30: Dr Mark Behlke
Chief Scientific Officer, Integrated DNA Technologies, USA
Title: Use of hybridization “stick” methods to attach aptamer and cargo: design considerations
Abstract: Aptamers can be employed as a targeting ligand to deliver therapeutic cargoes to specific cell types. Nucleic acid cargoes can be directly built into the aptamer at the time of synthesis or, alternatively, can be attached after synthesis using reactive chemistries or by hybridization to a dangling “stick” domain. The “stick” approach permits attachment of a variety of cargoes to the aptamer in a reversible fashion. However, addition of the complementary “anti-stick” sequence to the cargo can have unintended consequences, including reduced potency of both siRNAs or ASOs. Design considerations will be discussed.

8.55: Dr Michael Blank
CSO, AptaIT GmbH, Munich, Germany
Title: Bringing light into the black box of SELEX experiments
Abstract: We demonstrate a software-driven procedure harnessing the statistical power given by giant Next Generation Sequencing (NGS) data sets obtained from in vitro selection experiments. The combination of in vitro selection experiments with NGS and in silico analysis enables improved analysis of enriched libraries in terms of (i) identification in very early selection cycles as well (ii) identification of rare aptamer ligands (which are not accessible by the conventional approach), (iii) identification of ligands with the desired binding properties, as well as (iv) identification of aptamers in…

9.20: Dr. Thomas Schubert
CEO, 2bind GmbH, Regensburg, Germany
Title: Fast and quantitative analysis of aptamer-target interactions using microscale thermophoresis
Abstract: Microscale thermophoresis (MST) is a powerful, novel technique to determine binding affinities of molecular interactions. Furthermore, the specificity, selectivity and additional biophysical parameters of molecular interactions can be evaluated. The technology is perfectly suited to study aptamer-target interactions. The binding of candidate aptamers to any target from small molecule to multi-protein complex can be analyzed in solution, with low sample consumption, at high sensitivity and accuracy. The free choice of buffers (from SELEX binding buffer to serum), in combination with a large dynamic range of detection…

9.45: Professor Dr Günter Mayer
University of Bonn, Life and Medical Sciences Institute, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
Title: Aptamer modules and assemblies for exogenous control of biomolecule function
Abstract: Aptamers are single chained nucleic acids that specifically recognize target molecules with high affinities. They can be truncated into short but correctly folded and functional structures. Inspired by nature these properties predestine them to be employed for the assembly of multivalent architectures built on individual functional units. These architectures reveal superior biological functions in respect of target recognition and inhibition and qualifies aptamers as very interesting tools for synthetic biology and biomedical applications. Since the activity of aptamers can be exogenously controlled by light they also provide means for the spatiotemporal control of biological processes.

10.50: Professor Beatrix Suess
Professor, TU Darmstadt, Department of Synthetic Biology, Darmstadt, Germany
Title: Mechanistic Insights into Engineered Riboswitches
Abstract: One of the most interesting areas of Synthetic Biology is the control of cellular behaviour using engineered genetic circuits. Genes with selected features are combined in a building-block manner and transfered to organisms of interest to achieve the desired biological functions. However, the expression level of the corresponding genes must be regulated and fine-tuned to avoid unbalanced gene expression and the accumulation of toxic intermediates. In order to achieve this, a versatile set of RNA-based control devices, so called engineered riboswitches, have been developed combining the…

11.15: Dr Mark Platt
Lecturer in Analytical Chemistry, Department of Chemistry, Centre for Analytical Science, Loughborough University, Loughborough, Leicestershire, UK
Title: Monitoring Aptamer-Protein Interactions using Tunable Resistive Pulse Sensing(co-authors: Emily R. Billinge, Murray Broom and Mark Platt)
Abstract: Aptamers are short single-stranded pieces of DNA or RNA capable of binding to analytes with specificity and high affinity. Due to their comparable selectivity, stability and cost, over the last two decades aptamers have started to challenge antibodies in their use on many technology platforms. The binding event often leads to changes in the aptamers secondary and tertiary structure; monitoring such changes has led to the creation of many new analytical sensors. Here we demonstrate the use of a tunable resistive pulse sensing (TRPS) technology to monitor the interaction between several DNA aptamers…

11.40: Mr Martin Michael Rudolph
Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, Darmstadt, Germany
Title: In vitro Selection of RNA Aptamers against Photoswitchable Molecules (Co authors: Martin Michael Rudolph, Thomas Halbritter, Alexander Heckel and Beatrix Suess)
Abstract: Aptamers are nucleic acids that are capable of binding a great variety of ligands with high affinity and specificity. Naturally occurring RNA aptamers reside in a number of bacterial 5’-UTRs where they represent recognition elements of riboswitches. Here, a binding event results in a conformational change that in turn is converted into a biological signal. About a decade before aptamers were discovered in living organisms, an in vitro selection process was invented to generate aptamers by directed evolution (SELEX – Systematic Evolution of Ligands by Exponential Enrichment). Since then many efforts…

11.55: Mr Shashank Sharma
Glycoscience Group, National Centre for Biomedical Engineering and Science (NCBES), National University of Ireland Galway, Ireland
Title: Aptamer selection for specific recognition of non-human sialic acid: n-glycolyl neuraminic acid (Neu5Gc) (Co-authors: Shashank Sharma, Hsien-Yu Tsai, Satbir Kaur Gill, Marian Kane, Lokesh Joshi)
Abstract: Aptamers are nucleic acids that are capable of binding a great variety of ligands with high affinity and specificity. Naturally occurring RNA aptamers reside in a number of bacterial
5’-UTRs where they represent recognition elements of riboswitches. Here, a binding event results in a conformational change that in turn is converted into a biological signal. About a decade before aptamers were discovered in living organisms, an in vitro selection process was invented to generate aptamers by directed evolution (SELEX – Systematic Evolution of Ligands by Exponential Enrichment). Since then many efforts have been made to select RNA aptamers against synthetic molecules and to implement those sequences into functional genetic switches…

Agenda:

Day-1: 24th March 2014, St Edmund’s Hall

8.00-9.00: Registration

9.00-13.00: Presentations (including a coffee break)

13.00-14.00: Lunch break

14.00-18.00: Presentations (including a coffee break)

19.15-20.30: Networking dinner at St Hilda’s College (by prior booking or invitation only)

Day-2: 25th March 2014, St Hilda’s College

8.30-12.30: Presentation (including a coffee break)

12.30-13.15: Lunch and close

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