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J Venom Res
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Aptamers
Open-access
Aptamers 2019
03-04 April 2019, Oxford
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Welcome to Aptamers 2017, 11-12 April, Oxford

Dear Colleagues:

View Agenda

Download Symposium Documents – please email us if you haven’t received your password yet.

Twitter: @AptamerSociety; @JAptamers; #AptaOx17

We are delighted to announce our forth Oxford symposium on aptamers, Aptamers 2017, 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 oral and poster abstracts. We particularly encourage final year doctoral students and early/mid career postdoctoral researchers/junior group leaders to submit oral abstracts, as we believe this event will provide their research an excellent exposure, critical analysis by attending senior researchers and new career opportunities. Please contact us on AptamersOxford@gmail.com, should you require any further information.

Aptamers 2017 will be co-hosted with our 3rd symposium on antisense and therapeutic oligonucleotides, Oligo 2017, on 10th April.

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

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


Symposium Chair

Professor Dr Ulrich Hahn
University of Hamburg
Department Chemistry
Institute for Biochemistry and Molecular Biology
Hamburg
Germany

HozBox500x3

DAY 1 – 11th April

0800: Registration

0830: Housekeeping

0840: Welcome by the Symposium Chair

0850: Welcome by the INSOAP President


Session 1 – Chemical Modifications

Chair: Professor Philip Johnson, York University, Canada


0900:

Professor Jesper Wengel
Professor and Center Director
, BioNEC – A VKR Center of Excellence, FKF – University of Southern Denmark, Odense, Denmark

Title: Novel aptamers based on LNA and UNA


0930:

Dr Xianbin Yang
Director of R&D
, AM Biotechnologies, Houston, TX, USA

Title: X-Aptamers – Chemically modified aptamers that can be used for biomarker discovery


0950:

Dr Daniel Schneider
Senior Director
, Technology Development, Boulder, CO, SomaLogic, USA

Title: Next Generation Aptamers:  Enhancing Chemical Diversity with Multiple Pyrimidine Modifications


Session 2 – Disease

Chair: Professor Dr Beatrix Suess, Technical University of Darmstadt, Germany


1010:

Dr Gregory Penner
President & Founder
, NeoNeuro SAS, 38 Rue de Berri, Paris, France

Title: Development of aptamers for the treatment and diagnosis of Alzheimer’s disease


1030: Refreshments, exhibition, posters


1110:

Professor Dr Ulrich Hahn (Symposium Chair)
University of Hamburg, Department Chemistry, Institute for Biochemistry and Molecular Biology, Hamburg, Germany

Title: Selectin and Integrin Aptamers


1140:

Professor Yoshikazu Nakamura
CEO & President, Ribomic Inc, Japan

Title: Anti-FGF2 aptamer restores bone growth affected in Achondroplasia transgenic mice


1210:

Professor Fernando Pastor Rodriguez
Principal Investigator
, Foundation for Applied Medical Research, Pamplona, Spain

Title: Targeting Co-Stimulation with Bi-Specific Aptamers to Melanoma Cancer Stem Cells


 1230:

Dr Sarah Shigdar
Senior Lecturer in Medicine, Schoool of Medicine, Deakin University, Waurn Ponds, Australia

Title: Treating brain metastases with a bifunctional aptamer


1300: Group Photo, Lunch, exhibition, posters


Session 3 – Analysis/Diagnostics

Chair: Professor Yoshikazu Nakamura, Ribomic Inc, Japan


1400:

Professor Anthony Cass
Professor of Chemical Biology
, Department of Chemistry, Institute of Biomedical Engineering, Imperial College London, UK

Title: Aptamers in Bioanalysis: from Lateral Flow to Nanopore Sensing


1430:

Dr Julian Tanner
Associate Professor & Coordinator
of Education Division of Biochemistry, University of Hong Kong, PR China

Title: Aptamers for Malaria Diagnosis


1500:

Professor Victoria Calzada
Principal Investigator,
Área de Radiofarmacia, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo-Uruguay

Title: Aptamers as molecular probes: multimodal imaging


1520: Refreshments, exhibition, posters


Session 4 – Tools/selection/design (Part I)

Chair: Professor Marit Nilsen-Hamilton, Iowa State University, USA


1600:

Dr David Bunka
Chief Technical Officer,
 Aptamer group, Bio Centre, Innovation Way, Heslington, York, UK

Title: Aptabind; Enabling Protein Purification


1630:

Dr Duncan Borthwick
Staff Scientist,
Dynamic Biosensors GmbH, Lochhamer Str 15, Planegg, Germany

Title: A Regenerating Biochip, Modelling the Kinetics of Aptamer Interactions using switchSENSE® Technology


1650:

Dr Sean Dembowski
Department of Chemistry, University of Minnesota–Twin Cities, 207 Pleasant St. SE, Minneapolis, MN, USA

Title: Isolating aptamers for membrane proteins using capillary electophoresis-SELEX


1710:

Mr John Goertz
Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA

Title: A novel photocatalyzed colorimetric reaction for real-time biosensing with catalytic aptamers


1725: Close of Day 1

1730: INSOAP AGM (open to all attendees)

1800: Aptamers Board meeting (Aptamers editorial board members only)

1915: Networking dinner (by prior booking or invitation only)


DAY 2 – 12th April

Session 4 – Tools/selection/design (Part II)

Chair: Professor Fernando Pastor Rodriguez, Foundation for Applied Medical Research, Spain


0840:

Dr Terry Steele
Assistant Professor, School of Materials Science & Engineering, College of Engineering, Nanyang Technological University, Singapore

Title: Exploiting aptamer adaptive binding towards reversible aptasensors


0900:

Dr Meltem Avci-Adali
University Hospital Tuebingen, Dept of Thoracic and Cardiovascular Surgery, University Hospital Tübingen, Tübingen, Germany

Title: Biofunctionalization of hydrogels with aptamers for tissue engineering applications


0920:

Professor Philip Johnson
Associate Professor
, Department of Chemistry, York University, Toronto, ON, M3J 1P3, Canada

Title: Two-Site Binding by the Cocaine-Binding Aptamer


Session 5 – Riboswitches

Chair: Professor Dr Ulrich Hahn, University of Hamburg, Germany


1000:

Professor Dr Beatrix Suess (Aptamers 2016 Chair)
Professor of Synthetic Biology, Technical University of Darmstadt, Germany

Title: Development of novel engineered riboswitches


1030: Refreshments, exhibition, posters


1100:

Dr Florian Groher
Department of Biology, Technical University Darmstadt, Schnittspahnstr 10, Darmstadt, Germany

Title: In Vivo Screening For New Synthetic Riboswitches


1120:

Dr Carlos Penedo
Principal Investigator
, Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. Andrews, St Andrews, United Kingdom

Title: Single-molecule FRET structural analysis of nascent aptamer-expression platform riboswitch sequences along their transcriptional pathway


1150:

Professor Dr Mario Mörl
Biochemistry and Molecular Biology, Institute for Biochemistry, Leipzig University, Brüderstr 34, Leipzig, Germany

Title: From Plug & Pray to Plug & Play – Aptamer-based transcriptional Riboswitches


1220: Lunch, exhibition, posters


Session 6 – Computation

Chair: Dr David Bunka, Aptamer Group, UK


1310:

Dr Muslum Ilgu
Aptalogic Inc, Molecular Biology Building, Ames, Iowa, USA

Title: Evaluation of MC-SYM structural predictions for an RNA aptamer with additional base stacking calculations and fluorescence of 2AP-substituted aptamers


1330:

Dr Gregory Penner
President & CEO, NeoVentures Biotechnology Inc, 5 York St, London, Ontario, N6A 1A1, Canada

Title: Using next generation sequence analysis to understand aptamer selection and application


1350:

Dr Maureen McKeague
Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, Zürich, Switzerland

Title: Computational approaches for improving aptamers and their application to metabolic engineering


1410: Discussion Closing remarks by Professor Dr Ulrich Hahn


1430: Close and departure


Posters

Structural basis for specific inhibition of Autotaxin by DNA aptamer and its structure-based post-SELEX modifications

Kazuteru Aoki1, Kazuki Kato2, Hisako Ikeda1, Satoshi Futakawa1, Masatoshi Fujiwara1, Junken Aoki3, Osamu Nureki2, Yoshikazu Nakamura1

1Ribomic Inc., Tokyo, Japan
2Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
3Graduate School of Pharmaceutical Sciences, Tohoku University, Miyagi, Japan

Autotaxin (ATX) is a plasma lysophospholipase D that hydrolyzes lysophosphatidylcholine (LPC) and produces lysophosphatidic acid (LPA). ATX-LPA axis is an attractive therapeutic target for the treatment of pulmonary fibrosis. We have generated anti-ATX DNA aptamers that inhibit ATX with high specificity and efficacy. We solved the crystal structure of ATX in complex with the anti-ATX aptamer RB011, at 2.0-angstrom resolution. Our structural analysis revealed that the aptamer inhibits the ATX activity in a manner distinct from those of the known small-molecule inhibitors. RB011 binds in the vicinity of the catalytic domain through base-specific interactions and also forms water-mediated interaction…


Syntheses optimizations of Sgc8-c aptamer as multimodal imaging probes for cancer

Estefanía Sicco,1,2 Jessica Báez,1,3 Jimena Margenat,1 Fernanda García,1 Manuel Ibarra,3 Pablo Cabral,1 María Moreno,2 Hugo Cerecetto,1 Victoria Calzada1

1Área de Radiofarmacia, Centro de Investigaciones Nucleares, Facultad de Ciencias
2Departamento de Desarrollo Biotecnológico-Instituto de Higiene, Facultad de Medicina
3Centro de Evaluación de Biodisponibilidad y Bioequivalencia de Medicamentos, Facultad de Química, Universidad de la República

Among the applications of molecular imaging is the in vivo diagnosis of cancer with agents that recognize tumour markers, allowing an optimal image acquisition. One of the main tools used in molecular imaging is an imaging agent or probe. Probe consists on the part that recognizes specifically the target, and the part responsible for the image, which allows the external detection and evaluation of a process. In this work, the 41 nb DNA aptamer Sgc8-c was modified at the 5′-end, adding an amino-terminal group. Sgc8-c was selected by Shangguan et al against PTK7 receptor which is overexpressed in various types of cancers. Imaging-frameworks that have…


Development of sandwich aptamer-based lateral flow strip tests for Plasmodium specific malaria diagnosis

Yee-Wai Cheung and Julian A Tanner

School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong

Lateral flow strip assays are convenient and low-cost detection methods which are ideal for the rapid diagnosis of infectious diseases in remote areas.  Antibodies are the mainstay for molecular recognition in these tests, yet aptamers have potential advantages in cost, stability and manufacturing. In the diagnosis of malaria, for many endemic regions it is important to have a test which can discriminate malaria caused by Plasmodium falciparum or by Plasmodium vivax as the management and treatment is different…


In vivo selection of DNA aptamers targeting prostate cancer

Laia Civit1, Ioanna Theodorou2, Franziska Frey1, Holger Weber3, Andreas Lingnau3, Carsten Gröber4, Michael Blank4, Michael Kubbutat3, Frédéric Ducongé2, Günter Mayer1

1Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk Str. 1, 53121 Bonn, Germany
2CEA, DSV, I2BM, Molecular Imaging Research Center (MIRCen), Fontenay-aux-Roses, France
3Research Division ProQuinase, Breisacher Str. 117, 79106 Freiburg, Germany
4AptaIT GmbH, Am Klopferspitz 19a, 82152 Planegg-Martinsried, Germany

Aptamers that recognize specific cell subpopulations have emerged as promising targeting vehicles and they have shown to be suitable for in vivo imaging of tumors. The identification of aptamers is commonly accomplished through an in vitro selection process termed SELEX (Systematic Evolution of Ligands by EXponential enrichment). Binding of aptamers to their target highly depends on the biological environment. Due to the difficulty to reproduce biological conditions in vitro, traditionally selected aptamers often fails when used in vivo


Rapid Aptamer Selection by Capillary Electrophoresis

Sean K Dembowski, Michael T Bowser

Department of Chemistry, University of Minnesota–Twin Cities, 207 Pleasant St. SE, Minneapolis, MN, USA

Nucleic acid aptamers are currently seeing exponential growth in their use and development in a multitude of applications from clinical therapeutics and diagnostics to laboratory separations to environmental biosensors. Despite this rapid increase in applications, in vitro isolation (SELEX) of aptamers for novel targets is still the weak link in the development chain due to its time-consuming and labor-intensive nature. Many SELEX options are available – from bulk methods like nitrocellulose filtration and magnetic separation to highly…


APTUS Biotech: Diagnostic tools for viral pathogens

Marta García-Hernández1, Ignacio Klett2, Celia Pinto1, Miriam Barragán1, Lissette López3, Carlos Briones4, Gerónimo Fernández2, María Elena Martín1, Víctor Manuel González1,2, Ana García-Sacristán2

1Grupo de aptámeros. Departamento de Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal, 28034 Madrid, Spain
2Aptus Biotech SL, c/ Faraday, 7, Parque Científico de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
3INGENASA, Calle de los Hermanos García Noblejas, 39, 28037 Madrid, Spain
4Centro de Astrobiología, Carretera de Ajalvir Km 4. Torrejón de Ardoz, 28850 Madrid, Spain

Aptus Biotech is a Spanish biotechnology company founded in 2010 as a spin off of the aptamers group of the IRYCIS-Ramón y Cajal Hospital from a collaboration agreement with the Foundation for Biomedical Research of the Hospital Ramón y Cajal (FIBio-HRC). Our priority is to invest in research and development in aptamer technology. Our R&D activities are focused in developing and implementing specific biotechnological applications, where the aptamer technology brings an added value…


Screening of an aptamer library for novel diagnostic aptamers for potentially carcinogenic toxins

Brian Henderson, Steve Meaney, Niamh Gilmartin

School of Biological Sciences and Environmental Sustainability and Health Institute, Dublin Institute of Technology, Kevin St, Dublin 8, Ireland

The recent classification of red and processed meat as probable carcinogenic and carcinogenic respectively by the World Health Organisation is based on three groups of compounds found in meat as a result of the processing or preparation of the meat.  By cooking meat known or suspected carcinogens can be produced, including heterocyclic aromatic amines (HAA) and polycyclic aromatic hydrocarbons (PAH) and even the consumption of red and processed meat induces the formation of the carcinogenic N-nitroso-compounds (NOC)…


A novel photocatalyzed colorimetric reaction for real-time biosensing with catalytic aptamers

John P Goertz and Ian M White

Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA

We present a photocatalyzed reaction which enables sub-nanomolar detection of redox-active aptamers. This system provides a simple yet sensitive signal transduction mechanism for both aptamer-mediated target detection and isothermal nucleic acid amplification. We utilize hemin-binding DNA sequences which are known to catalyze reduction-oxidation reactions in a similar manner to horseradish peroxidase. These catalytic aptamers (termed here “peroxidymes”) have been used to detect a wide range of analytes via peroxide-mediated oxidation of a substrate…


Synthetic aptamer-peptide conjugates for targeted activation of T cells

Silvana Hassel1, Verena Schütte2, Sven Burgdorf2, Günter Mayer1

1Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str. 1, Germany
2Life and Medical Sciences (LIMES), University of Bonn, Carl-Troll-Str. 31, Germany

Immunotherapies are treatments that restore or boost the immune system’s ability to fight against infections, diseases or cancer. The development of protective long-term immunity requires activation of the effectors of the adaptive immune system, in particular T cells, by cells involved in innate immunity. Dendritic cells (DCs) represent the interface between the non-specific innate immunity and the highly specific adaptive immunity. Upon recognition of antigenic structures, DCs deliver all signals necessary for adequate activation of T cells. Hence, immunization with DC-based vaccines became of utmost importance in immunotherapy…


The delivery of a common chemotherapeutic agent using a DNA chemical antibody targeting EpCAM

Justin L Henri, Wei Duan and Sarah Shigdar

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

Current therapy for cancer typically involves indiscriminate chemotherapies that can have severe off target effects on healthy tissue and are still plagued by aggressive recurrence. Recent shifts towards targeted therapies offer the possibility of circumventing the obstacles experienced by these traditional treatments. While antibodies are the pioneering agents in such targeted therapies, clinical experience has demonstrated that their antitumor efficacy is limited due to their high immunogenicity, large molecular size…


Search for new inhibitors of the methylerythritol phosphate pathway of isoprenoid biosynthesis from Plasmodium falciparum. Isolation of DNA aptamers against the enzyme DXP reductoisomerase

Laura Llinàs1, Sandra Currás1, Carlota Roca1, Elena Lantero2, Beatriz Prieto-Simón3, Ariadna Payà1, Alexandre Serra1, Andreu Saura1, Xavier Fernàndez-Busquets2, Santiago Imperial1

1Department of Biochemistry and Molecular Biomedicine, School of Biology, University of Barcelona. Avda Diagonal 643, ES08028-Barcelona, Spain
2Nanomalaria Joint Unit. Institute for Bioengineering of Catalonia (IBEC) and Barcelona Institute for Global Health (ISGlobal). Centre Esther Koplowitz, planta 1, ISGlobal, Rosselló 149-153, ES08036 Barcelona, Spain
3Future Industries Institute, University of South Australia, Adelaide, Australia

Malaria is one of the most severe public health problems worldwide because of the severity of the disease, the numbers of people affected and the complexity of the life cycle of its causative agent, the protozoan Plasmodium spp. Although nowadays relatively effective treatments exist, resistance is arising and spreading even to the most potent antimalarials. In this project, we investigate a novel approach for the treatment of malaria: the use of aptamers. By means of a Flumag-SELEX procedure, we have selected ssDNA aptamers binding the deoxy-5-phosphate reductoisomerase (DXR) enzyme from Plasmodium falciparum


Development of ssDNA aptamers capable of binding neonicotinoid family of pesticides in environmental samples

Shalen Kumar1,2, William Odey1, Shiwei Li1,2, Jeremy Jones2, Valérie Guieu3, Janet L Pitman1 and Kenneth P McNatty1

1School of Biological Sciences, Victoria University of Wellington, New Zealand
2Auramer Bio Limited, Wellington, New Zealand
3Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, Grenoble France

The neonicotionoid family of pesticides (i.e. clothianidin, imidacloprid, and thiacloprid) are used extensively in the horticultural industry. Neonicotionoids are known to penetrate all parts of the plant including sap, nectar, and pollen of flowers. Despite being considered non-toxic to humans, a ban on their use was put in place by the EU due to concerns they contribute to the declining populations of pollinator bees. Nucleic acid species (aptamers) may be utilised as target capture agents in biosensors to detect compounds of environmental and medical significance. The objective…


The Challenge of Using the Intraerythrocytic Parasite Plasmodium falciparum as Aptamer-Selecting Target

Elena Lantero1,2,3, Ernest Moles1,2,3, Alexandros Belavilas1,2,3, Miriam Ramírez2, Beatriz Prieto4, Santiago Imperial5 and Xavier Fernàndez-Busquets1,2,3

1Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona, Spain
2Nanomalaria Group, Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
3Nanoscience and Nanotechnology Institute (IN2UB, Universitat de Barcelona), Barcelona, Spain
4Future Industries Institute, University of South Australia, Adelaide, Australia
5Department of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain

Knowledge of the malaria parasite’s physiology and of Plasmodium-infected red blood cell (pRBC) biochemistry and the development of specific antibodies against their antigens are currently essential pillars for identifying molecular targets to be used in future antimalarial therapies and prophylaxis. Because these are lengthy and expensive procedures, new fast and cost-effective strategies are of utmost importance for vaccine development and targeted-delivery treatments. The identification of short single-stranded DNA (ssDNA) sequences termed aptamers featuring binding specificities and affinities comparable to those …


An aptamer-based screening assay for potential drug candidates against osteoporosis

Mon-Juan Lee1 and Yuan-Pin Huang2

1Department of Bioscience Technology, Chang Jung Christian University, Tainan, Taiwan
2Department of Cosmetics and Fashion Styling, Cheng Shiu University, Kaohsiung, Taiwan

Osteoporosis is considered a major and global public health concern, especially in the elderly population. Currently, only a limited selection of therapeutics is capable of stimulating bone formation, with potential health risks such as the induction of osteosarcoma. Sclerostin, a secreted glycoprotein expressed predominantly in osteocytes that inhibits bone formation by antagonizing the Wnt/β-catenin signaling pathway, is considered a new target for the treatment of osteoporosis. Strategies for targeting sclerostin are focused on the development of anti-sclerostin antibodies, but the safety and side effects of long-term treatment…


Heading for light-switchable riboswitches

Thea S Lotz1, Florian Groher1, Thomas Halbritter2, Alexander Heckel2, Beatrix Süß1                                                      

1Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
2Goethe Universität Frankfurt, Department of Chemisty, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany

Engineered riboswitches are of high interest in synthetic biology. We are adapting standard SELEX procedures to enrich RNA libraries against small, light-switchable ligands, thus developing novel tools for spatiotemporal control of gene expression. For an azobenzene based light-switchable ligand, a SELEX light elution protocol has been established to compliment standard affinity SELEX. After successfully enriching aptamers against the ligand, motif analysis was carried out, leading to the design of a new, motif-doped pool. SELEX using this pool lead to an extremely fast exponential enrichment…


Targeted delivery of RNA aptamers into the skin as a therapeutic approach for chronic inflammatory skin conditions

Tom Macleod1, Ozlem Cesur1, Rosie Doble1, Miriam Wittmann2, Nicola Stonehouse1

1School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
2Leeds Institute of Rheumatic and Musculoskeletal Medicine (LIRMM), University of Leeds, Leeds, UK

We have seen little innovation in topical treatments over the last decades.  While considerable progress has been made to treat patients severely affected by inflammatory skin diseases with systemic biologics, this is very costly and therefore not available to patients with mild-moderate skin conditions.  However, these mild-moderate conditions can significantly impair the patients’ quality of life e.g. due to severe itchiness and sleep loss.  A majority of the 2-3% and   ̴15% of the population respectively, who suffer from psoriasis and eczema (and many sufferers of other localised skin diseases) fall into the mild to moderate disease category…


The Application of Bioinformatics to Aptamer Discovery

Alex S Martin, Helen B Lavender

AptamerDiscovery, Centauri Therapeutics Ltd, Discovery Park, Sandwich, Kent, CT13 9ND, UK

SELEX (systematic evolution of ligands by exponential enrichment) is an established methodology for the discovery of high affinity aptamers. The SELEX process incorporates multiple cycles of enzymatic amplification; with the consequent liability that highly enriched sequences represent those most amenable to PCR recovery, rather than the highest affinity binders to the target substrate. Next Generation Sequencing (NGS) enables the detection of oligonucleotide families present at very low percentages of a SELEX pool.  NGS technologies combined with rigorous bioinformatic analysis can be employed to facilitate the identification of sequence families…


An aptamer-based biosensor for doxorubicin using impedance spectroscopy

Nicole Bahner2, Katharina Schieke2, Doreen Lisicki2, Peggy Reich2, Daniel Martin2, Anja Klevesath1, Dieter Beckmann2, Marcus Menger1 and Dieter Frense2

1Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses(IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
2Institute for Bioprozessing und Analytical Measurement Technique e.V., Rosenhof, D-37308 Heilbad Heiligenstadt, Germany

The contamination of municipal waste water with drug residues is an increasingly serious environmental problem. In sewage treatment plants these substances cannot be completely disintegrated, thus reach ground and drinking water and contaminate the environment. Therefore, there is a need for devices to monitor the effluent of sewage treatment. Aptamers are single-stranded nucleic acids that bind target molecules highly specific and highly affine with their three-dimensional structure. Because of their similar affinity, but higher stability, they represent a potential alternative for antibodies…


Conditional control of splicing by RNA device

Adam Mol, Florian Groher, Beatrix Suess

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

Alternative splicing of pre-mRNA in mammals is one of the important cellular processes and it is responsible for protein diversity. 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 tool to control splicing events. We established a TetR-aptamer…


Investigations of the Interactions of Fluorinated Super-ligands with the Broccoli and Spinach2 Aptamers

Sharif Anisuzzaman1 , Ivan Geraskin2 , Muslum Ilgu3 , Lee Bendickson1 , George A Kraus2Marit Nilsen‐Hamilton1,3 

1Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University,  Ames, IA 50011, USA
2Department of Chemistry, Iowa State University, Ames, IA 50011, 3 Aptalogic Inc.,  Ames, IA 50014, USA

The ability of aptamers to undergo structural changes upon ligand binding is of great advantage for devising sensors and has also been exploited in nature for the evolution of riboswitches. The ligand-bound aptamer structure may be induced by its interaction with ligand or selected by ligand amongst many alternative structures that can be adopted by the apo-aptamer. The two possibilities are difficult to distinguish when aptamer-ligand interactions occur at close to diffusion limited time scales with each binding event being the result of a single collision…


Mutagenesis of RNA Aptamers Against HPV-16 L1 Virus-Like Particles

Giovanni Palomino-Vizcaíno, Diana G Valencia-Reséndiz, Luis Marat Alvarez-Salas

Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México

Sc5-c3 and its shortened version Sc5-c3Δ18 are RNA aptamers that recognize virus-like particles of the human papillomavirus type 16 (VLPs-HPV16) with high affinity and specificity. VLPs-HPV16 are immunologically indistinguishable from the natural virions. Our goal is to modify the RNA content/structure to increase the aptamers resistance to nucleases. Initially, Sc5-c3 was synthesized as an oligodeoxynucleotide and used in binding assays with VLPs-HPV16 and GFP and BSA as negative controls. This DNA version of Sc5-c3 did not show binding even though it retained the same predicted secondary structure, suggesting that some RNA features like the 2’-OH or specific U positions may participate in VLPs-HPV16 recognition…


Click-SELEX enables the identification of tetrahydrocannabinol-recognizing clickmers

Malte Rosenthal, Franziska Pfeiffer, Fabian Tolle, Patrick Günther and Günter Mayer

Life and Medical Sciences-Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany

THC (tetrahydrocannabinol) is the most widely used illicit drug in the world. Its consumption poses a problem with regard to driving, as 0.3 – 7.4% of drivers tested positive for THC and the odds ratio for motor vehicle collisions is increased to 1.92 under the influence of THC. The detection of THC on the roadside is mostly limited to urine testing, but the correlation between drug detection and impairment is poor. Oral fluid tests for THC have emerged as an alternative in recent years, but fail to reach the necessary specificity. Aptamers are short, single-stranded RNA- or DNA-oligonucleotides that fold into defined 3-dimensional structures and specifically bind to a target molecule…


Isolation of aptamers against non-modified small molecule targets for simplified assay development

Christine Reinemann, Edward T Barnes, Andrew S Brentnall, David H J Bunka, Arron C Tolley

Aptamer Group, Suite 2.80 – 2.91, Bio Centre, Innovation Way, Heslington, York, YO10 5NY, UK

There is an increasing need to reliably detect and monitor levels of small molecules in all areas of the life sciences. This need ranges from monitoring food or environmental contaminants, to pathogen or individual patient drug level monitoring. In every case, more favourable outcomes are achieved when tests are performed ‘on-site’ or at ‘point-of-care’ as immediate action can be taken. Monitoring small molecules often relies on expensive laboratory based methods such as chromatography and mass spectrometry. Simple field based diagnostic devices, such as lateral flow devices, are widely employed as a first pass assay to determine if more thorough analysis is required. These tests often utilise…


A split aptamer can facilitate protein recognition in DNA nanotweezers

Simon Chi-Chin Shiu, Yee-Wai Cheung, Roderick M. Dirkzwager, Shaolin Liang, Andrew B. Kinghorn, Lewis A. Fraser, Marco S. L. Tang and Julian A. Tanner

School of Biomedical Sciences, The University of Hong Kong, Laboratory Block, 21 Sassoon Road, Hong Kong SAR, China

DNA can be used to fabricate nanostructures including DNA tweezers, nanomachines and other DNA mechanisms with a variety of designs. Most responsive mechanisms have previously been triggered by presence of complementary nucleic acids. DNA nanomachines triggered by proteins would be a significant step forward to integrate DNA nanotechnology with protein molecular recognition. Single-stranded aptamers can be split and incorporated into DNA nanostructures…


Generation of Pseudomonas aeruginosa specific DNA aptamers for therapeutic applications

Jennifer P Soundy and Darren J Day

Centre for Biodiscovery, School of Biological Sciences, Victoria University of Wellington, Kelburn, Wellington, New Zealand

Abstract withheld on request of authors


A Highly Multiplexed Protein Sensing Platform in Nanopores

Jasmine Y Y Sze1, Tony Cass1,2, Joshua B Edel1

1Department of Chemistry, Imperial College London, UK SW7 2AZ
2Institute of Biomedical Engineering and Chemical Biology Centre, Imperial College London, UK SW7 2AZ

Biosensors play an important role in diagnostics, defense, food safety control and various detection strategies. Successful biosensors should be highly specific, label free, able to perform multiplex detection, and have low cost, portability and ideally to be usable by semi-skilled operators. Electrochemical biosensors are particularly promising towards these goals due to several combined advantages such as low-cost, operational convenience and miniaturize devices. Nanopore sensors1 are single-molecule electrochemical devices…


Inhibition of human papillomavirus type 16 pseudoinfection using an RNA aptamer

Diana G Valencia-Reséndiz, Juana V Tapia-Vieyra, Ana G Leija-Montoya, Giovanni Palomino-Vizcaíno, Luis M Alvarez-Salas

Laboratorio de Terapia Génica. Departamento de Genética y Biología Molecular. Centro de Investigación y de Estudios Avanzados del IPN. Ciudad de México, México

Human papillomaviruses (HPV) are small non-enveloped DNA viruses causally associated with cervical cancer. Particularly, HPV type 16 (HPV-16) DNA has been found in approximately 50% of cervical tumours. HPV infection starts with the binding of the virus capsid to heparan sulphate (HS) receptors exposed on the surface of epithelial basal layer keratinocytes. Several HS union sites located on the HPV capsid surface have been characterised using HPV pseudoviruses (PsV) with a pseudogenome containing the green fluorescent protein (GFP) reporter…


An innovative gain-loss cell-SELEX strategy for development of a nucleic acid aptamer against PD-L1 for immunotherapy of triple negative breast cancer

Yuanyuan Yu, Yongshu Li, Xiaoqiu Wu, Fangfei Li, Aiping Lu, Ge Zhang

Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China

Triple-negative breast cancer (TNBC) shows unsatisfactory response to first-line chemotherapy. Programmed cell death ligand 1 (PD-L1) interacts with PD-1 to suppress T-cell antitumor activity. Anti-PD-L1 monoclonal antibody could remarkably enhance the antitumor efficacy of chemotherapy in metastatic TNBC patients but with high immunogenicity. Aptamers possess similar affinity and specificity to targets as antibodies, but have advantages in no immunogenicity. Therefore, an aptamer against PD-L1 could be a promising alternative for TNBC therapy…


Screening of single-stranded DNA aptamers against the monoclonal antibody Rituximab

Sabrina Wildner1, Christian Huber1,2, Gabriele Gadermaier1,3

1Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, Austria
2University of Salzburg, Department of Molecular Biology, Division of Chemistry and Bioanalytics, Austria
3University of Salzburg, Department of Molecular Biology, Division of Allergy and Immunology, Austria

Subtle conformational differences are often undetectable by bioanalytical methods but they can impact the safety, efficacy and stability of biopharmaceuticals. Aptamers, which are single-stranded DNA or RNA oligonucleotides, can help to detect subtle changes in the tertiary structure of proteins. As they present defined secondary structures with high affinity to a target they can be used as surrogate antibodies. This study aims to generate a panel of aptamers reactive to the therapeutic anti-CD20 antibody Rituximab. The Magnetic bead-based Systematic Evolution of Ligands…


Aptamers 2017 Sponsors

Gold Sponsor and Exhibitor

Ribomic2

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


Gold Sponsor and Exhibitor

Aptamer-Group2

Aptamer Solutions Ltd: Continued success and growth has enabled Aptamer Group to restructure its Scientific Operations team. Increasing interest in the development of aptamers against small molecule targets has led to the formation of a dedicated scientific team. This is in addition to the existing team focused on aptamer generation against larger targets (proteins, viruses, cells etc).

Aptamer Group has developed a unique displacement method to overcome issues with the traditional bound target approach to select aptamers against small molecules. In a reversal, the aptamer library is bead immobilised and, after removal of non-specific aptamers, the small molecule target is presented in solution. Small molecule target specific aptamers are eluted, amplified and quantified before preparing a refined library for the subsequent round of selection. Counter selection steps can be included to drive specificity. We have had success selecting aptamers to a range of small molecules, including; anti-cancer therapeutics, a food contaminating neurotoxin, ATP and phospholipids.

An application of interest for many of our customers is protein purification. We are using our AptaBind selection process to develop aptamers for use in Aptamer-Mediated Affinity Chromatography (AMAC). The AptaBind process isolates only those that both bind and release the target protein under the customer specified purification conditions. These AptaBind aptamers are then immobilised onto an appropriate resin for use in aptamer-mediated column purification.

Aptamer selection is achieved using an automated high-throughput robotic selection platform. This enables rapid delivery of aptamers with the required specificity and binding characteristics.


Gold Sponsor and Exhibitor

SCIEX helps to improve the world we live in by enabling scientists and laboratory analysts to find answers to the complex analytical challenges they face. The company’s global leadership and world-class service and support in the capillary electrophoresis and liquid chromatography-mass spectrometry industry have made it a trusted partner to thousands of the scientists and lab analysts worldwide who are focused on basic research, drug discovery and development, food and environmental testing, forensics and clinical research.

With over 40 years of proven innovation, SCIEX excels by listening to and understanding the ever-evolving needs of its customers to develop reliable, sensitive and intuitive solutions that continue to redefine what is achievable in routine and complex analysis. For more information, please visit sciex.com.

SCIEX social: Twitter: @SCIEXnews, LinkedIn and Facebook.

For Research Use Only. Not for use in diagnostic procedures. RUO-MKT-12-5101-A

AB Sciex is operating as SCIEX.
©2017 AB Sciex. The trademarks mentioned herein are the property of the AB Sciex Pte. Ltd. or their respective owners. AB Sciex™ is being used under license.


Silver Sponsor and Exhibitor

SomaLogic is transforming healthcare by applying our proprietary protein-measurement technology to enable the precise monitoring of each individual’s health and wellness status in real time. We work with many different partners across research, health management, pharmaceutical development, and other health-related fields to build applications on our “SOMAscan Platform,” a single cost-effective and reliable testing platform that provides actionable and timely information to patients and healthcare providers across a wide range of diseases and conditions. Our SOMAmer® and SOMAscan® technologies also have multiple applications across the biomedical and life sciences, and are currently available to the entire scientific community for their own research needs. For more information, visit www.somalogic.com.


Bronze Sponsor and Exhibitor

ChemGenes is offering nucleic acid expertise since 1981. ChemGenes Corporation, a biotechnology company, recently relocated to a state-of-the-art facility in Wilmington, Massachusetts. We have consistently been a strong partner to researchers engaged in the field of DNA/RNA synthesis for 36 years. By starting out as a supplier of ‘Ultra Pure Products’ and then by becoming an active Contract Researcher, ChemGenes Corporation has achieved unparalled expertise in the field of DNA/RNA synthesis. Thus, all of us at ChemGenes have the opportunity and great pleasure to serve a vast number of scientists in the US and all over the world. ChemGenes’ product lines include phosphoramidites for RNA and DNA synthesis, Antisense phosphoramidites, modified bases for DNA, as well as RNA modification. In addition, we produce a variety of modified phosphoramidites for the introduction of chromophores and ligands. The availability of prepacked disposable columns of various pore sizes, loadings, low volume columns, ancillary reagents in configurations suitable for each synthesizer, and DNA purification cartridges is another way ChemGenes meets its customers’ needs. A large variety of Reagents for the synthesis of DNA/RNA are also available, which include many natural and modified nucleoside bases, tetrazole, 5-thioethyltetrazole, DMT-chloride, DMT protected deoxy and ribo nucleosides, 2’-O-methyl and 2’-O-propargyl nucleosides, silyl protected ribonucleosides, several types of phosphorylating reagents, and many more. As the market for oligonucleotides continues to grow, ChemGenes will stay committed to introducing novel products, while maintaining its existing product mix. We also have the capacity to custom-synthesize products on request. Our highly-trained technical staff is always available and happy to help you with your special needs and demands in this area. For information regarding the full range of products and their applications, please call us at 800-762-9323.


Exhibitor

Biophysical Analysis of Molecular Interactions with switchSENSE®

switchSENSE® is an automated biosensor chip technology that employs electrically actuated DNA nanolevers for the real-time measurement of binding kinetics (kON, kOFF) and affinities (KD). Interactions between proteins, DNA/RNA, and small molecules can be detected with femto-molar sensitivity. At the same time, protein diameters (DH) are analyzed with Angstrom accuracy and conformational changes as well as melting transitions (TM) can be measured using minimal amounts of sample.

The principles and applicability of three complementary measurement modalities provided by switchSENSE® will be introduced in this talk: Fluorescence Proximity Sensing, Molecular Ruler Measurements, and Switching Dynamics Measurements. In addition to standard workflows we’ll discuss unique possibilities for the functionalization of the sensor surface, i.e. the electrical adjustment of ligand densities and the precise assembly of different ligands on bifunctional nanolevers.

Application examples from drug development, quality control, and fundamental research will be discussed, including:

  • – Analysis of complex binders: high-affinity antibodies and bispecific antibody formats
  • – Small molecule induced conformational changes in proteins including dimers and aggregates
  • – RNA/DNA binding proteins including riboswitches and aptamers
  • – ‘large’ object binding including liposomes and virus-like particles
  • – nucleic acid : nucleic acid methodologies for genotyping, antisense and SNP detection
  • – Enzymatic activity of polymerases and CRISPR/Cas9

An introductory movie is presented here https://www.youtube.com/watch?v=amGw7txpGzM&autoplay=1


Exhibitor

2bind GmbH is a globally acting provider for biophysical, analytical services. Our mission is to help our customers and collaboration partners to drive their science.

Since 5 years, we are deepening our knowledge in the characterization of aptamer-target interactions by intense collaborations with experts in the field. We optimized our MicroScale Thermophoresis (MST) platform in terms of speed, accuracy, sample consumption and cost-efficiency, to be able to offer high quality binding data (affinity, stoichiometry and thermodynamics) of aptamer-target interactions of any kind. The in-solution method MST offers free choice of buffers and works independent of the size of the aptamer ligand.

Our service portfolio comprises of high throughput screening assays, binding assays, competition assays, assays in bioliquids and assays with multiple binding partners.

If you need to determine basic binding parameters of your favorite interaction, be smart and work with the MST experts at 2bind.