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Flash-talks: Poster presenters will have the optional opportunity to introduce their poster in a short, 90 second flash presentation using PowerPoint slides during their allocated break. If you are planning to give a flash-talk, please submit PowerPoint slides, appropriately named to match your digital poster file e. The session chair will share your slides on your behalf during your presentation. Please check the website for your poster presentation schedule. Practice beforehand so that you can finish your presentation within your allocated time slot. The poster PDF files, whether the presenter is attending virtually or in-person, will be made available via the secure conference documents page to the conference participants before the meeting. Hardcopy posters: If attending in-person, you may bring along a printed copy of your maximum A1 size, portrait , to be displayed during the conference. Only A1-sized posters will be displayed. Your poster may be displayed on Day 1 or Day 2 only due to space constraints. Before uploading your poster and flash-talk slides, you must make sure that you follow ALL of the instructions above! If your abstract has been accepted for presentation but it does not appear in the list below, please let us know as soon as possible by emailing AptamersOxford gmail. Aptameric biosensors for amoxicillin detection. Antibiotic resistance has increased rapidly in recent years becoming a major issue worldwide. Antibiotics can easily enter the environment reaching our food and water sources leading to health problems. A sensitive and rapid screening method for antibiotics has become essential in order to protect the sensitive consumers from life-threatening reactions. The current detection methods for antibiotics are mostly based on immunoassays which are costly and time consuming. Among the selected aptamers, Amx3 aptamer sequence has shown high specificity and affinity to Amoxicillin with a dissociation constant K d of The aptamer was then integrated in a voltametric biosensor utilizing gold-modified screen-printed electrodes. The method has a high sensitivity, with a detection limit as low as 5. Our biosensor did not show any significant cross-reactivity with other similar antibiotics such as Ciproflex and Azithromycin, indicating that the sensor had high specificity to Amoxicillin. Role of the Calcium Ion in the Ochratoxin A-binding aptamer. OTA-1 is a monomolecular anti-parallel G-Quadruplex centred around a two-tetrad core, while ochratoxin A is a mycotoxin produced by certain types of Penicillium and Aspergillus fungi. Found in grain, pork and several other sources, ochratoxin A is one of the most abundant food contaminating mycotoxins. Ochratoxin A is a strong neurotoxin thought to deplete dopamine levels in the brain and cause oxidative damage to DNA. We have used our multifaceted approach to study the OTA-1 aptamer using calcium as the ion to help facilitate binding between ochratoxin A and the aptamer. Our results show tight binding between the OTA-1 aptamer and ochratoxin A in the presence of calcium. We also find that the aptamer structure is highly stable in the presence of calcium and ochratoxin A. We investigated the role the calcium ion plays in the formation of the aptamer structure as well as how it helps facilitate the interaction between OTA-1 and ochratoxin A. A calcium or magnesium ion is needed for binding between the aptamer and ochratoxin A. Of those two, calcium allows for the strongest interaction between the OTA-1 aptamer and ochratoxin A. Not only is this cation needed for binding, but it also helps to structure the OTA-1 aptamer when ochratoxin A is not present. Overall, our results show the complexity of aptamer-ligand systems and how choices such as salt selection in buffers can impact the structure and function of an aptamer system. Structure-affinity relationship of the dopamine-binding aptamer with dopamine derivatives. Hoi Pui Chao 1 , Yunus K. Kaiyum 1 , Cameron Mackereth 2 and Philip E. Johnson 1. The dopamine binding aptamer, DA-Mut3 has been utilized to investigate the binding relationship of aptamer-dopamine ligand interactions because of its high specificity and selectivity. Dopamine is a neurotransmitter that controls emotion and movements in brains and deficiency of dopamine has been linked to Parkinson disease. It is a small ligand with one amine group attached via an ethyl chain and a catechol structure which is a benzene ring with two hydroxyl side groups. A series of ITC binding studies were performed to identify the changes in binding affinity with respect to modifications made to dopamine. The data suggests that the terminal primary amine group was a key factor in the recognition of the ligand for DA-Mut3, as modifications made to this site caused loss of binding. Additionally, the two phenolic groups as well as the aliphatic chain length appear to play a role in the interaction between DA-Mut3 and dopamine. The modifications that do not result in a loss of binding are limited indicating a high specificity of this aptamer for dopamine. Previous research done has shown that this aptamer exhibits structure switching characteristic with binding which along with its specificity for dopamine. The goal of this research aims to gain insight into how dopamine aptamer interacts with its ligand and this could help better designing biosensors. The development of aptamers against human red blood cells for forensic detection. Blood is one of the most commonly found biological fluids at crime scenes, with the detection and identification of blood holding a high degree of evidential value. It can provide not only information about the nature of the crime but can also lead to identification via DNA profiling. Presumptive tests for blood are usually sensitive, but not specific, so small amounts of the substrate can be detected but false-positive results are often encountered which can be misleading. Novel methods for the detection of red blood cells based on aptamer-target interactions may be able to overcome these issues. Aptamers are single stranded DNA or RNA sequences capable of undergoing selective antigen association due to three-dimensional structure formation. The incorporation of a target specific sensing moiety into an optical biosensor means that limited cross reactivity can be achieved, which is a hinderance to current testing methods. Within this study, a modified Systematic Evolution of Ligands by Exponential Enrichment SELEX process is used to generate aptamers against whole red blood cells via the cyclical target-incubation and enrichment of randomized oligonucleotide libraries. Obtained aptamer pools from Round 6, 8 and 10 were analysed via Massively Parallel Sequencing to identify viable sequences that demonstrate a high affinity for red blood cells. Through the use of bioinformatics platforms such as AptaSuite and Galaxy, 5 aptamer candidates were identified through their enrichment profiles. The replacement of all four nucleotides with analogues has been challenging, limiting the structure space explored during SELEX and, for clinical applications, necessitates further engineering of resulting functional sequences by trial-and-error medicinal chemistry to reduce their degradation by serum nucleases, which can reduce or abrogate activity. We find that libraries can be prepared and replicated via cDNA with yields of synthesis and reverse transcription comparable to RNA systems. By deep sequencing N40 as well as defined sequences following complete cycles of replication and amplification, we find no measurable loss of diversity and aggregate error rates within suitable ranges for SELEX, including a pure LNA system 7. Development of a label-free electrochemical cortisol aptasensor and automated plug-and-play sensor preparation strategy based on consumer-grade materials and processes. Cortisol is a steroid hormone that has gathered significant attention in the biosensing world due to its myriad physiological roles in health and disease. Because of its circadian rhythmicity and fast responsiveness to common sampling procedures e. However, state-of-the art cortisol quantification techniques such as mass spectroscopy are expensive and time consuming posing a roadblock to performing large-scale, long-term cortisol investigations with sufficiently high temporal resolution in a cost-effective manner. This work presents a proof-of-concept label-free low-cost electrochemical aptasensor based on a duplex dissociation principle, using an aptamer first reported by Yang et al. Although these sensors hold great promise for reducing the costs of biomarker investigations, sensor preparation is often performed manually which increases the risk of sensor variability and lowers reliability. To address this issue, a low-cost fluidic cell was developed using laser-cut acrylic sheets and off-the-shelf stick-and-play tape to allow for precise delivery of reagents to the sensor surface. Laser cutting allows hundreds of flow cells to be made within a short time frame, offering the possibility to upscale production. The fluidic design could also potentially be used for screening newly discovered aptamer sequences to rapidly assess their feasibility for biosensing applications. High-throughput selection and characterisation of aptamers on optical sequencers. For this, it utilizes the capability of optical sequencers to perform fluorescence-based assays on the immobilized DNA-clusters subsequent to sequencing. Only minor hardware modifications, i. Compared to the conventional selection of aptamers by Systematic Evolution of Ligands by Exponential Enrichment SELEX , the required effort was significantly reduced while the information content about the binding interactions was drastically increased, providing potential data for machine learning approaches. Hengxin Feng 1 , Chun Kit Kwok 1,2. G-quadruplexes G4s are special nucleic acid structures playing important roles in gene expression and becoming potential therapeutic targets. However, targeting on specific G4 remains challenging. Unveilling novel triple negative breast cancer-associated biomarkers using an aptamer-based proteomic pipeline. Breast cancer is a major public health problem worldwide. These factors, allied with the typical heterogeneity of breast cancer, make the search for new therapies essential. Therefore, the exploitation of novel and specific ligands, as aptamers, for use in TNBC-targeted therapies is of utmost importance. After 8 rounds of evolved enrichment, the aptamer pool was sequenced. Two aptamer candidates, Apt1 and Apt2, were characterized considering their binding affinity to the target cells, with kd values at the nanomolar range. The potential translation to clinical applications was proven for Apt2 by immunofluorescence staining of tissue sections. To provide a proof-of-concept for the use of Apt2, this aptamer was conjugated with carboxylate-modified nanoparticles NPs , creating NP-Apt2 conjugates. It was observed through fluorescence and flow cytometry that the NP-Apt2 conjugates led to an incredibly high fluorescence intensity compared to unconjugated NPs. Specifically, Apt2 seemed to be associated with cell membrane epitopes only present in the target cells. Aptamer-mediated pull-down coupled with proteomics gave us some hints about the possible biomarker to which this Apt2 binds to. After generating the 3D structures for Apt2, Apt2-biomarker docking studies were performed. Molecular dynamic simulations of the docked complexes and free binding energy calculations by molecular mechanics-generalized born surface area MM-GBSA allowed the identification of the potential biomarker to which Apt2 binds to. Ultimately, this novel ligand could be a truly helpful tool for targeted delivery in TNBC tumours. The therapeutic potential of a novel aptamer-drug conjugate against Glioblastoma. The limited success of current treatment options for glioblastoma, an aggressive brain cancer with poor survivability can be attributed to the blood-brain barrier BBB. This barrier is known to prevent entry of most chemotherapeutic drugs to treat brain cancer thus, a novel targeted therapeutic capable of crossing the BBB to deliver drugs is essential. Aptamers, or chemical antibodies, are small single-stranded nucleotide sequences that can bind specifically and selectively to desired targets on the cell surface. Most importantly, aptamers can be modified as a drug delivery vehicle for therapeutic purposes. In this instance, we previously generated a bifunctional aptamer by combining a transferrin receptor and epithelial cell adhesion molecule EpCAM aptamer together and intercalated the chemotherapeutic doxorubicin DOX for treatment of brain metastases. We were able to demonstrate that the bifunctional aptamer-drug conjugate, termed TEPP-DOX, was successfully able to deliver drug payloads across the BBB to EpCAM positive brain metastases both in vitro and in vivo , and reduce metastases spread and tumourigenicity. In this study, for the first time, this bifunctional aptamer-drug conjugate is being tested for treating the primary brain cancer, glioblastoma. To examine the potential of treating glioblastoma, the binding affinity of two bifunctional aptamers to glioblastoma was determined by flow cytometry, including with DOX conjugation, where a strong binding affinity towards the transferrin receptor on glioblastoma cells was observed. Next, the internalization and drug retention of aptamer-conjugates was visualized over a hour period through confocal microscopy. With aptamer-DOX internalisation and drug retention visualised, the results of this study show that this conjugate would make an ideal therapeutic candidate for future studies. Selection of aptamers for detection of blood coagulation status. In clinical coagulation diagnostics, there is an urgent need for reliable testing devices to determine the coagulation status, especially during or after extracorporeal procedures. Infrequent and inaccurate measurements can lead to life-threatening complications, such as bleeding or thrombosis. Conventional coagulation tests require long turnaround times and costly equipment. Thus, they are inappropriate for on-site use. For an accurate diagnosis, it is essential to measure multiple biomarkers simultaneously. This project aims to implement a microfluidic sensor using aptamers for the assessment of blood coagulation status in real time. For this purpose, aptamers against proteins involved in blood coagulation, beta-thromboglobulin, plasminogen, and fibrinogen are selected. To select aptamers, systematic evolution of ligands by exponential enrichment is used. Every round, protein-DNA complex is bound to mixed cellulose ester membrane and aptamer candidates are amplified by polymerase chain reaction PCR. Before proceeding with the next round, the quality of the products is ensured by polyacrylamide gel electrophoresis. After multiple rounds, binding assays are performed and demonstrated the accumulation of putative aptamers against corresponding targets via real-time PCR. Selected aptamer pools are analyzed by Next-Generation-Sequencing and next, clustered aptamer sequences will be further tested regarding their binding affinity. The successful selection of beta-thromboglobulin, plasminogen, and fibrinogen-specific aptamers and their incorporation into biosensors could enable the real-time monitoring of blood coagulation. Characterization of an aptamer inhibitor for hot start RTX, a novel reverse transcriptase. AptOx2 3, JGraswich. RNA amplification is critical in modern biochemistry, and it is very important that the reactions used to amplify RNA are accurate. RT in its current form is an inaccurate process, as most reverse transcriptases lack an exonuclease domain to proofread base pairing. This process is commonly paired with polymerase chain reaction amplification with exonuclease proofreading to improve accuracy and yield. Consequently, a single enzyme reaction would be highly desirable. RT reactions performed by RTX show evidence of reduced errors compared to traditional reverse transcriptases, however further improvements can be made by using an aptamer for a hot start application. Aptamers have previously been shown to have high potential for polymerase inhibition, as evidenced by AptaTaq, an aptamer inhibitor for Taq polymerase. Binding affinities for these applications are often on the same order of antibodies. It is also important that aptamers are resistant to degradation and relatively inexpensive to produce, making them both efficient and accessible for this purpose. In the presence of an inhibitory aptamer, RTX will be unable to bind targets at room temperature, consequently lowering mispriming incidents. Following ten rounds of aptamer selection, recurring sequences have been found in the pool via Sanger sequencing. Samples are currently being prepared for NGS, and an inhibition assay will be run on promising candidates identified via NGS. Additional testing will be done to examine the difference in transcriptional errors between RTX and the hot start RTX-aptamer complex once acceptable candidates have been identified and characterized. A novel synthetic caffeine-binding riboswitch. The ligand binding capacity of aptamers can be utilized in a wide variety of ways. One of the evolutionary oldest ones might be the ability of RNA aptamers to recognize a ligand and thereby activating a functional RNA element. In this work, a synthetic RNA aptamer for caffeine with regulatory activity was identified and optimized. Two candidates with regulatory activity were then identified in a subsequent screen of individual transformants of S. The structure of an identified riboswitch was characterized by inline-probing and mutational studies to optimize its regulatory activity were performed. Afterwards, a caffeine-dependant hammerhead aptazyme was developed by replacing the P3 stem of the extended hammerhead ribozyme with the identified binding domain of the caffeine-riboswitch. The aptazyme exhibited a 2. The caffeine-binding domain was also fused to the DHBI binding domain of the iSpinach fluorogenic aptamer and fluorescence measured in vitro. Targeting highly homologous Flavivirus NS1 proteins with supremely specific Clickmers. Flaviviruses are arthropod-borne pathogenic ssRNA viruses. Their RNA genome encodes a polyprotein which is cleaved by host and viral proteases into 3 structural and 7 non-structural proteins. The non-structural protein 1 NS1 is highly conserved across flavivirus species. Hexameric NS1 glycoprotein is secreted from infected cells, modulating the hosts immune response by interacting with the complement system and contributing to immune evasion as well as vascular leakage. It is therefore not only a promising diagnostic biomarker for infection but also a potential candidate for a therapeutic approach. The Clickmers show supreme specificity and can be used to detect NS1 from human serum in clinically relevant concentrations. With their outstanding specificity the NS1 Clickmers could aid in differential diagnosis of Flavivirus infections. Clickmers can bind to NS1 in presence of serum as well as full blood and show, in contrast to many NS1 Antibodies, no cross-reactivity towards Thrombin and Plasminogen. These properties can be advantageous in therapeutic approaches targeting NS1. With an in silico algorithm prototype we are now performing docking simulations and k-mer analysis to understand the role of DNA sequence plus modifications in target binding. We aim for a machine learning assisted fast and efficient in silico optimization of Clickmers through identification and modulation of binding sequence motifs and the required modifications. Flavonoids are natural polyphenolic compounds found in plants. One of these flavonoids is naringenin which have been shown to possess numerous beneficial effects on human health including antioxidant and anti-inflammatory properties. With this method structure-switching aptamers against the free molecule are selected and we used next-generation sequencing NGS analysis to identify the aptamers after 10 cycles of selection. The affinities of the aptamers were determined using microscale thermophoresis MST and we investigated the secondary structures of the aptamers using SHAPE probing. Building on the Capture-SELEX principle, we developed a strand displacement assay to measure naringenin concentrations in vitro. In this assay, the binding of naringenin to the aptamer displaces the Cy3-labelled capture-oligonucleotide CO and allows it to hybridize with a Cy5-labelled anti-CO, creating a FRET signal between the oligonucleotides. As a result. Naringenin can be produced through the metabolic engineering of microorganisms using tyrosine as a precursor. To optimize the microbial production, we are working on using our naringenin aptamers to develop a Twister-based aptazyme for in vivo sensing of naringenin bioproduction. The increasing occurrence of antibiotic-resistant bacteria is a growing threat for the public health worldwide. Combined with big pharmaceutical companies leaving the field of antibiotic compound development, bacterial infection could become the number one cause of death by To address this growing threat, we designed a high-throughput pipeline for the development of inhibitory RNA aptamers against proteins DIRA. The pipeline consists of two parts: an initial screening for binding affinity via systematic evolution of ligands by exponential enrichment SELEX and a subsequent microfluidic screening for enzymatic activity which selects for inhibitory capabilities of the RNA sequences. The combination of these methods allows for a fast and effective development of inhibitory RNA aptamers against any given protein. Since bacteria expressing metallo—lactamases are particularly difficult to treat, we selected the Sao Paolo metallo—lactamase 1 SPM-1 as the first target for our pipeline. First, we started with a randomized RNA pool and obtained an enriched pool of target-binding sequences. Second, we further selected the pre-selected pool for inhibition of the target protein activity via the microfluidic pipeline. The sequence was further characterized and reduced to a minimal binding motif that was only 37 nucleotides long and still served as an effective inhibitor. In the next step this minimal aptamer will be linked to a bacterial siderophore and tested for its in-vivo efficiency. With the functional minimal aptamer, we have proven the effectiveness of our pipeline and are theoretically capable of quickly developing inhibitory RNA aptamers against any given protein. CCL22 inhibition by aptamers inhibit immune cell chemotaxis in vivo. CCL17 mainly induces chemotaxis towards T cells and thus promotes inflammation. The half-life of AJ2m was determined being 2 hours in mouse serum. The systemic application i. To further investigate the therapeutic potential of AJ2 we applied a skin cream containing fluorescently labeled AJ2 ex vivo on mouse skin and visualized penetration of the aptamer by confocal microscopy. AJ2 was observed to penetrate the ear skin and was localized in the epidermis and dermis. Our study validates CCL22 as therapeutic target using an aptamer-based approach. The CCLbinding aptamer AJ2 inhibits chemokine-mediated chemotaxis and, thus, represents a promising tool for the treatment of allergic and inflammatory diseases. More than million people have been registered as infected with SARS-COV-2, challenging the capacity of our healthcare systems due to the broad spectrum of clinical presentation, i. Demanding the development of novel strategies to stratify patient populations to predict prognosis, guide treatment management, and focus resources. The molecular composition of blood reflects our physiology, health state, lifestyle etc. Fjelstrup et al. We hypothesised that the technology could identify disease-specific patterns for COVID, allowing diagnosis and prediction of disease severity by measuring fluctuations in the plasma proteome. The developed assay predicts the day mortality in females with high sensitivity and specificity with an AUC of 0. The technology possesses the potential to serve as a health-state measuring and prediction tool for treatment management. Aptamer function, specificity and selectivity are widely a consequence of the 3-dimensional structures they adopt when binding a ligand and understanding the specific mechanisms by which structure and function are related within aptamers can open avenues for specific biosensor and therapeutic design. Previous research had selected an aptamer to bind the neurotransmitter dopamine with a sub-micromolar-scale affinity in a counter selection process against similar analogues. Initially thought to undergo ligand-induced structural change to form a G-quadruplex however, recent 2D NMR studies contraindicate a G-quadruplex. Several mutations were made to a DA Mut3 Del7 variant of the aptamer to probe this alternate structure and interestingly it appeared that the removal of several bases that are thought to partially occupy the binding site for dopamine, resulted in a fold stronger binding. Proton exchange rate experiments were performed to determine the rate of imino proton exchange with surrounding solvent to determine the degree by which a base may be protected or buried within the greater aptamer structure in the bound state. This can further lend support to the proposed tertiary structure for this aptamer and further explain observations made regarding the binding studies of these variants of the dopamine-binding aptamer. One of the most exciting areas of synthetic biology is to control cellular behaviour using engineered genetic circuits. The expression levels of the corresponding genes need to be regulated and fine-tuned to avoid unbalanced gene expression and the accumulation of toxic intermediates. Synthetic RNA-based systems have increasingly been used for the regulation of gene expression and can be employed for the control of translation initiation, pre-mRNA splicing, RNA self-cleavage as well as fluorogenic aptamers. Due to their structural properties, riboswitches provide a convenient basis for the development of ligand-dependent, controllable systems. We were able to achieve a Finally, we were able to engineer a minimal regulating sequence with retained switching behaviour. The high mortality rates are mostly linked to the absence of early clinical symptoms and that the cancer is usually detected in later stages. Due to this lack of early clinical symptoms, there is a great need for early diagnostic and prognostic biomarkers. Early biomarkers would also aid in treatment options and detection of reoccurrence. Once the cancer has metastasised into other organs or to surrounding lymph nodes, this excludes surgery as a treatment option and further treatments are far less effective. Endoscopy and biopsy are currently considered the gold standard for diagnostics in OC but both are invasive and are often carried out at later stages of cancer. There is a general lack of knowledge surround the biology in OC and therefore aptamers and epigenetics has been a major area of research in terms of biomarker discovery. There is currently a lack of aptamers targeting early OC specifically and a potential novel aptamer will be used in conjunction with an epigenetic panel to produce a novel, non-invasive method for OC diagnostics. Flow cytometry has also been used to determine the binding potential of current OC associated aptamers e. This work shows that an aptamer can be generated using these methods and its diagnostic potential will continue to be investigated. Selection and development of aptamers against Anaplasma phagocytophilum , a tick-borne, zoonotic bacterium. Anaplasma phagocytophilum is a tick-borne, zoonotic bacterium of great interest in animal and human health. This lack of knowledge results from the difficulty to isolate and cultivate A. Aptamers are innovative and powerful tools in infectiology employed as valuable substitutes to antibodies. These oligonucleotides are able to bind with high affinity and specificity to a wide variety of targets e. Thereby, our team is working on the selection of aptamers directed against A. The first step consisted in selecting aptamers against infected cell lysates by performing 12 rounds of SELEX. The progress of selection was monitored by quantitative PCR and NGS sequencing and demonstrated an enrichment of sequences from round 6. Three different oligonucleotides were chosen for further binding and specificity studies. The first results are promising as they suggest that certain sequences could be specific to proteins expressed during infection or to A. Aptamers specific to molecules expressed during the infection will help to better understand the interaction between A. Aptamers specific to A. In this context, several objectives will be pursued: to better explore epidemiological cycles, to understand the mechanisms involved in virulence and species barriers and to identify new potential vaccine and therapeutic targets in the longer term. Selection of sialic acid-modified aptamers targeting influenza A virus. Traditional influenza therapies face challenges due to the constantly evolving nature of the virus, which can lead to drug resistance and reduced recognition by the immune system. In this context, aptamers show great promise as new alternatives for neutralizing influenza viruses. However, reported aptamers targeting influenza hemagglutinin are limited by the restricted chemical space of their canonical nucleobases. To address this issue, this study introduces a modified SELEX method using sialic acid for RNA modification, with the aim of improving selection of high affinity aptamers to viral hemagglutinin, and potentially other influenza virus proteins, for virus neutralization. The results consistently show high transcription yields using sialic acid modifications and preservation of modified nucleotides after multiple SELEX rounds. Sialic acid-modified aptamers with low nanomolar affinities to influenza A H1N1 virus hemagglutinin have been selected, and further research will examine the effect of these modifications on RNA-target interaction. This study highlights the potential of utilizing natural influenza ligands to broaden the chemical space of RNA aptamers targeting influenza. The analysis of the affinity and stability of modifications of the glucose-binding and cocaine-binding aptamers. Aptamers are selected to bind to their ligands, usually with high affinity and selectivity for their targets. Due to this aptamers can be used as sensing molecules in several different biosensor applications. Previously published research by the Stojanovic group selected an aptamer to bind glucose, but not any structurally related carbohydrates. The K d of this aptamer-ligand interaction is only 10mM, which is much lower than the nM affinities seen in other aptamer-ligand systems. This is of physiological relevance as the blood glucose concentration usually falls between 4 mM to 11 mM, meaning it can be used in possible in vivo applications. Glucose is a difficult molecule to select an aptamer for as there are no strong epitopes present of glucose for DNA bases to interact with. NMR spectroscopy is suited to study weaker aptamer-ligand interactions such as these due to the greater concentrations required for NMR relative to other methods. The stability of high affinity glucose binding modifications will be studied using differential scanning calorimetry DSC similar to an analysis performed on the cocaine-binding aptamer. The cocaine-binding aptamer is a DNA aptamer selected to bind cocaine and is composed of three stems constructed around a three-way junction with 2 A-G mismatches at the centre. DSC is being used to investigate the thermostability of the cocaine-binding aptamer as a function of how many base pairs are in stem one. The length of stem one can change how tightly the aptamer binds a ligand, and how well defined the free state of the aptamer is. This was done with the hope of determining which stem one variant is the most thermodynamically stable. Optoribogenetics: Light dependent control of cellular processes through PAL-aptamer platform. One such photoreceptor is PAL which was identified in the a gram-positive actinobacterium Nakamurella multipartite. Herein, aptamer Upon light irradiation, PAL binds to the aptamer thus blocking the translation and reduction of Luciferase expression in the cells. Here, PAL changes its conformation when exposed to blue light, which triggers the binding of the aptamer and activates gene expression of Blue Fluorescent Protein BFP in mammalian Cells. This system allows for reversible and tunable regulation of gene expression with minimal genetic engineering and low background activity in the dark. Successful development of such a system will add up to the existing gene expression tool box and provides a new approach for investigating complex cellular processes with spatiotemporal precision. Currently, the detection of L-BMAA is challenging and often unreliable, thus, the development of analytical techniques for its detection in aquatic environments is imperative. Molecular recognition elements MREs , such as aptamers, provide the required analyte specificity for bioanalytical applications. Chosen rounds were sent for sequencing using the Illumina next-generation sequencing technology and analyzed using a combination of bioinformatic tools. The GO-SELEX method did not show significant changes in the pool composition or motif enrichment whereas the MB-SELEX method did show a significant shift in the base distribution, which was further supported by the presence of G-rich conserved motifs that were enriched across the selection. A total of 6 candidates were chosen to screen for binders. Preliminary results obtained with the SYBR Green SG fluorescent assay suggest the potential binding of two of these aptamers, with affinities within the low micromolar range. The successful identification of these sequences will set a precedent as the first selected aptamers against the cyanotoxin L-BMAA. AptOx23, S Schellinck. Martins 1,4. It is well accepted that detailed knowledge of aptamer-ligand structures would benefit our fundamental understanding of these systems and would benefit the design and optimisation of aptamers towards affinity and selectivity, thus contributing to the development of real-world applications. To contribute to filling the current knowledge gap, we are currently focussing on NMR spectroscopic investigations of the structure-switching TESS. NMR spectroscopy allows to acquire molecular level information about conformational changes and intermolecular interactions, making it a powerful technique for studying aptamer-ligand interactions. At this nucleotide length, the original aptamer presents challenges both for synthesis and NMR spectroscopy. We will present and discuss recent results that provide the first detailed molecular view on this aptamer and its interaction with the testosterone target. Development of computational methods for aptamer design for biomedical applications. Biomolecular simulations have long been an important part of the drug discovery and development process, with techniques such as docking, virtual screening, molecular dynamics and quantum mechanics being routinely used in the study of the interaction and selection of small molecular drugs with their target proteins or enzymes. More recently, the application of these techniques in aptamer selection and aptamer engineering has algo become a reality. Such methods can help to understand aptamer-target interaction and to rationally introduce modifications in selected aptamers to modulate their affinity, specificity or ability to carry other molecules. Here, we present a computational protocol developed by us for the selection of specific aptamers for protein recognition. The protocol combines protein-DNA docking, atomistic molecular dynamics simulations and free energy calculations, including the conformation variability of the protein and aptamer in the selection process. As a proof of concept, the protocol was applied to a set of 20 ssDNA aptamers comprised by 50 nucleotides each previously experimentally identified from the most prevalent sequences present in the pool obtained after 8 rounds of systematic evolution of ligands by EXponential enrichment SELEX for Cathepsin B, a protein overexpressed in prostate cancer cells. The computational protocol was able to identify the aptamer with the highest affinity towards Cathepsin B and to predict its interaction mode and dominant interactions with Cathepsin B with atomic level detail. In conclusion, this protocol can be used in the selection of aptamers for the recognition of specific protein targets and in rational customization of specific aptamers for improved protein affinity or specificity, working as a useful tools in understanding and engineering molecular recognition. Binding affinity of structure-switching aptamers as a function of NaCl concentration. The goal of this research is to see how structure-switching aptamers behave towards ligand binding as a function of NaCl concentration. Many intermolecular forces contribute to the binding of the ligand to the aptamer such as Van der Waals, hydrogen bonding and electrostatic interactions. Since structure-switching aptamers are unfolded or loosely folded when in the free-state and only become structured when bound to their corresponding target ligand, the contribution of electrostatic forces is the primary interest for this research. Non-structure-switching aptamers have been studied previously in the Johnson lab as a function of NaCl concentration and it was shown that aptamer affinity increased towards their ligand when NaCl concentration was decreased. Since structure-switching aptamers become more structured when binding to their target, we want to see if there is a parallel relationship with non-structure-switching aptamers under the same conditions. This will be investigated by analyzing the binding affinity K a as a function of NaCl concentration through isothermal titration calorimetry ITC with various structure-switching aptamers. This includes MN19 and DAMut3, which are variants of the cocaine-binding aptamer and the dopamine-binding aptamer. The slope of this data provides an indication of the electrostatic contribution for the affinity of the aptamer towards its ligand. Overall, we can see if structure-switching aptamers function similarly to non-structure-switching aptamers under the same conditions or if they can be differentiated from them. Sireethorn Tungsirisurp , Nunzianda Frascione. DNA aptamers are short, single-stranded oligonucleotides developed with selective binding interactions for specific targets. Aptamers are selected through a laborious process systematic evolution of ligands by exponential enrichment, SELEX and their target binding properties are characterised using various techniques. Subsequently, various biophysical techniques were used to experimentally characterise the aptamer binding properties against the receptor binding domain RBD protein. Moreover, circular dichroism CD was used for structural studies of the aptamer and aptamer-target complex. Different in silico simulations were also used to further characterise the DNA aptamers and their target interactions. It is believed that this combinative workflow of experimental and simulations will allow a more in-depth assessment of aptamer-target interactions and appropriate aptamer-based biosensing design. These three-dimensional structures can bind to their target molecules with high affinity and specificity. Two major sequence families consisting of 18 hit sequences for CD19 and 13 hit sequences for CD20 were identified based on defined fold-enrichment values. Non-essential bases from CD and CD20 full-length aptamers were removed to minimize the aptamers to their smallest functional size. Their co-localization on the cell surface with the respective mAb was demonstrated using microscopy. This study establishes LIGS as a state-of-the-art screening technology that can partition highly specific aptamers against complex targets, such as cell surface receptors proteins expressed in their natural state. Keitaro Yoshimoto 1, 2. Nucleic Acids, 16, , LinkBIO Co. Aptamers Oxford, UK. Open-access, peer-reviewed. JAptamers JAptamers. An open-access publisher. Posters and Poster Guidelines Thank you for considering presenting your work as a poster at Aptamers Digital poster preparation and submission Page size: Prepare your poster as you would normally do for printing. You can prepare your poster in sizes A1 or A0, as the page size is not important for digitally presented posters. DO NOT name your poster files as, e. Such files will be automatically rejected. Poster submission: All poster presenters, whether attending virtually or in-person, are required to submit a digital version of their poster. Late posters may not be included in the conference programme. Please ensure you send us the very final version of your poster as well as your poster abstract , as once published, it cannot be replaced. Poster presentation Flash-talks: Poster presenters will have the optional opportunity to introduce their poster in a short, 90 second flash presentation using PowerPoint slides during their allocated break. Therefore, if you have a Twitter account, do include your Twitter handle in your poster. Do tag AptamerSociety and JAptamers in your tweets. Upload Your Digital Poster and Flash-Talk Slides Presenters in Bold If your abstract has been accepted for presentation but it does not appear in the list below, please let us know as soon as possible by emailing AptamersOxford gmail. Development of a label-free electrochemical cortisol aptasensor and automated plug-and-play sensor preparation strategy based on consumer-grade materials and processes AptOx23, ADobrea Alexandra Dobrea 1,2 , Rami Ghannam 1 , Damion K. Johnson Department of Chemistry, York University, Toronto, ON, Canada The goal of this research is to see how structure-switching aptamers behave towards ligand binding as a function of NaCl concentration. Join Our Emailing List. This field should be left blank.