Aptameric sensors based on structural change for diagnosis
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Aptamers are nucleic acids that can bind to various molecules. Because they have some features that are lacking in antibodies, aptamers could serve as alternatives to antibodies. For the purpose of biosensing, we focused on aptamers that undergo structural changes on binding to their target molecules. We constructed an aptamer-based bound/free (B/F) separation system that uses a designed aptamer named the "capturable aptamer". The capturable aptamer changes its structure upon recognizing its target molecule thereby exposing a specific single-strand region. The oligonucleotide that is complementary to this exposed region, named the "capture DNA" is immobilized on a support. This design permits the exclusive capture by the capture DNA of the aptamer bound to its target, and subsequent removal of any unbound aptamer and contaminants by B/F separation. The removal of unbound contaminants or aptamers results in highly sensitive detection at similar levels to those achievable by sandwich-based immunoassay. We describe the construction of a thrombin-detection system by using a capturable aptamer, and we discuss the potential of capturable aptamers in clinical diagnostics.Keywords:
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This chapter contains sections titled: Introduction Structure of Nucleic Acids Oligonucleotide Derivatives for Targeting Nucleic Acids Targeting of Specific Sequences in RNA and DNA with Oligonucleotide Derivatives Oligonucleotide-Based Techniques and Molecular Devices Affinity Modification of Nucleic Acids and Proteins with Reactive Derivatives of Oligonucleotides Derivatives of Oligonucleotides as Inhibitors of Nucleic Acids and Proteins Conclusions
Nucleic acid structure
Molecular beacon
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As antibody's substitute,aptamer has wide perspective on veterinary drugs detection,clinic diagnose,targeted therapy.Aptamer-based biosensers had been prepared with aptamers binding to biosensors.The concept of aptamer,its advantages,and principle,detectability,application of the different aptamer-based biosensors,which are fluorescence biosensors,electrochemical biosensors,colorimetric sensors,SERS biosensors and SPR biosensors were summarized.The perspective of aptamer-based biosensors were reviewed on detection of veterinary drug residue,and diagnosis of animal diseases.
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DNA lesions such as 1,N6-ethenoadenine (εA) and 3,N4-ethenocytosine (εC) are ubiquitously present in genomes of different organisms and show increasing levels upon exposure to mutagenic substances or under conditions of chronic inflammations and infections. To facilitate investigations of the mutagenic properties and repair mechanisms of etheno-base adducts, access to oligonucleotides bearing these lesions at defined positions is of great advantage. In this study, we report a new synthetic strategy to sequence-specifically generate etheno-adducts in a single-stranded unmodified DNA sequence making use of a DNA-templated approach that positions the alkylating agent close in space to the respective target base. In contrast to solid-phase synthesis of modified oligonucleotides such DNA-templated methods can be applied to single-stranded nucleic acids of unrestricted lengths. The modular nature of the system allows straightforward adaptation to different sequences.
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To explore thermofluorimetric analysis (TFA) in detail, we compared two related aptamers. The first, LINN2, is a DNA aptamer previously selected against EGFR recombinant protein. In this work we selected a second aptamer, KM4, against EGFR-overexpressing A549 cells. The two aptamers were derived from the same pool and bind the same target but behave differently in TFA. Our results suggest four overall conclusions about TFA of aptamers: 1. Some aptamers show reduced fluorescence upon target binding suggesting that target-bound aptamer is not always fluorescent. 2. Many aptamers do not obey the intuitive assumptions that aptamer–target interactions stabilize a folded conformation. 3. TFA may be most appropriate for aptamers with significant double-stranded structure. 4. Kinetic effects may be significant and the order of operations in preparing samples should be carefully optimized.
Aptamer
SELEX Aptamer Technique
Target protein
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Aptamers are nucleic acids that can bind to various molecules. Because they have some features that are lacking in antibodies, aptamers could serve as alternatives to antibodies. For the purpose of biosensing, we focused on aptamers that undergo structural changes on binding to their target molecules. We constructed an aptamer-based bound/free (B/F) separation system that uses a designed aptamer named the "capturable aptamer". The capturable aptamer changes its structure upon recognizing its target molecule thereby exposing a specific single-strand region. The oligonucleotide that is complementary to this exposed region, named the "capture DNA" is immobilized on a support. This design permits the exclusive capture by the capture DNA of the aptamer bound to its target, and subsequent removal of any unbound aptamer and contaminants by B/F separation. The removal of unbound contaminants or aptamers results in highly sensitive detection at similar levels to those achievable by sandwich-based immunoassay. We describe the construction of a thrombin-detection system by using a capturable aptamer, and we discuss the potential of capturable aptamers in clinical diagnostics.
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Aptamers have emerged as research hotspots of the next generation due to excellent performance benefits and application potentials in pharmacology, medicine, and analytical chemistry. Despite the numerous aptamer investigations, the lack of comprehensive data integration has hindered the development of computational methods for aptamers and the reuse of aptamers. A public access database named AptaDB, derived from experimentally validated data manually collected from the literature, was hence developed, integrating comprehensive aptamer-related data, which include six key components: (i) experimentally validated aptamer-target interaction information, (ii) aptamer property information, (iii) structure information of aptamer, (iv) target information, (v) experimental activity information, and (vi) algorithmically calculated similar aptamers. AptaDB currently contains 1350 experimentally validated aptamer-target interactions, 1230 binding affinity constants, 1293 aptamer sequences, and more. Compared to other aptamer databases, it contains twice the number of entries found in available databases. The collection and integration of the above information categories is unique among available aptamer databases and provides a user-friendly interface. AptaDB will also be continuously updated as aptamer research evolves. We expect that AptaDB will become a powerful source for aptamer rational design and a valuable tool for aptamer screening in the future. For access to AptaDB, please visit http://lmmd.ecust.edu.cn/aptadb/.
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Interface (matter)
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When aptamers first emerged almost two decades ago, most were RNA species that bound and tagged or inhibited simple target ligands. Very soon after, the 'selectionologists' developing aptamer technology quickly realized more potential for the aptamer. In recent years, advances in aptamer techniques have enabled the use of aptamers as small molecule inhibitors, diagnostic tools and even therapeutics. Aptamers are now being employed in novel applications. We review, herein, some of the recent and exciting applications of aptamers in cell-specific recognition and delivery.
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