What are the properties of the target molecule to which the aptamer will bind?
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The target molecule to which an aptamer binds typically exhibits high specificity and affinity. Aptamers can bind to a variety of targets, including proteins, small molecules, and even specific amino acids. Aptamers designed for protein interactions can have affinities ranging from picomolar to nanomolar levels, similar to monoclonal antibodies. In the case of theophylline, aptamers can detect concentrations as low as 0.5 µM with high specificity. Aptamers can also be engineered to target specific regions of proteins, such as the spike receptor-binding domain of SARS-CoV-2, with high stability and affinity, making them a potential therapeutic option. Overall, aptamers exhibit remarkable binding properties that make them versatile tools for various applications in molecular recognition and detection.
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06 Jul 2023 | The target molecule for aptamer binding in the study is phenylalanine. Aptamers recognize phenylalanine moieties, enabling specific peptide retention and differentiation from structurally similar amino acids like tyrosine and tryptophan. |
| The target molecule for the peptide aptamer is the spike receptor-binding domain of SARS-CoV-2. It exhibits high affinity, stability, and specificity similar to ACE2, crucial for viral entry inhibition. | |
1 Citations | The target molecule for the aptamer is theophylline, with the system detecting concentrations as low as 0.5 µM in 15 minutes, showcasing high affinity and specificity. |
| The properties of the target molecule for aptamer binding are estimated through conformational structure prediction, molecular docking, and molecular dynamic simulation, enhancing aptamer development efficiency. | |
| The aptamer binds to the target protein-small molecule complex, disrupting the DNA polymerase aptamer probe's inhibitory structure, allowing DNA polymerase activity and subsequent fluorescence enhancement. |
Related Questions
What are aptamer?5 answersAptamers are small oligonucleotides that can fold into unique three-dimensional shapes and bind to a wide array of targets with high affinity and selectivity. They are considered as "chemical antibodies" and possess several advantages such as easy synthesis, convenient modification, high programmability, and good biocompatibility. Aptamers have been extensively utilized in various fields including environmental monitoring, clinical diagnosis, therapeutics, and biomedicine. They have shown promise in applications such as biosensors, pathogen detection, new drug development, nanotechnology, and cancer theranostics. Aptamers are screened in vitro through a process called selective expansion of ligands by exponential enrichment (SELEX). They have the potential to revolutionize immunotheranostics by targeting immune checkpoint molecules and contributing to the development of new strategies in cancer immunotherapy.
Binding interaction between Oligonucleotide and Target mRNA. What is the current research status and future research directions?4 answersThe current research status on the binding interaction between oligonucleotides and target mRNA involves the use of natural antisense transcripts (NATs) and antisense oligonucleotides (ASOs). NATs are noncoding RNA molecules that regulate gene expression by interacting with mRNA. Single-stranded sense oligonucleotides corresponding to mRNA sequences can decrease mRNA levels by interfering with mRNA-NAT interactions. On the other hand, AntagoNAT oligonucleotides, which are complementary to NATs, can increase specific mRNA levels. ASOs, which are single-stranded nucleic acid strings, can selectively modify protein synthesis by binding complementary mRNA sequences. They can be designed to have specific properties such as cellular uptake, toxicity, nuclease resistance, and binding affinity to target mRNA. Future research directions include the development of personalized, allele-specific ASO therapies for neurodegenerative diseases. Additionally, there is ongoing research on using small compounds to inhibit protein-RNA interactions, which could have therapeutic implications for cancer treatment.
How do Aptamers bind?4 answersAptamers are short nucleic acid sequences that can bind to target molecules with high affinity and specificity. They can bind to target proteins and other biomolecules through hydrogen bonds and hydrophobic interactions, forming complexes with the target molecules. The binding mechanisms of aptamers involve the secondary and tertiary structures of the nucleic acids, which determine their three-dimensional conformation. Aptamers can be designed as cyclic peptides to enhance their conformational rigidity and increase the strength of binding interactions. The binding capabilities of aptamer sequences can be validated using various analytical methodologies such as isothermal titration calorimetry, mass spectrometry, and nuclear magnetic resonance spectroscopy. Aptamers can specifically bind to small molecules, such as natural and synthetic cannabinoids, with nanomolar dissociation constants.
What are the examples where aptamer is used as drug?5 answersAptamers have been used as drugs in various applications. For example, in the treatment and diagnosis of breast cancer, aptamers have been utilized as a method for specifically targeting tumors. In colon cancer treatment, a nanosponge therapeutic medication system called AS1411@antimiR-21@Dox has been developed using aptamers for targeted drug delivery. Aptamer-conjugated nucleotide analog drugs have also been explored for cancer-targeting therapies, such as clofarabine, ara-guanosine, gemcitabine, and floxuridine. Aptamers have shown promise in targeted drug delivery (TDD) for cancer treatment, with advantages including high binding affinity and specificity, low immunogenicity, and customizable chemical composition. Additionally, aptamers have been used as targeting ligands for the functionalization of nanomaterials in order to enhance efficacy and develop carrier systems for targeted cancer therapy.
How do aptamers bind targets?3 answersAptamers bind to their targets through high affinity and specificity. They are short, single-stranded oligonucleotides (RNA/DNA) that can fold into a three-dimensional shape with useful binding properties. Aptamers are usually developed through a process called Systematic Evolution of Ligands by Exponential Enrichment (SELEX), which involves repeated rounds of selection and amplification from a random-sequence oligonucleotide library. These aptamers can be raised against various targets, including ions, small molecules, proteins, enzymes, and even intact/living cells. The binding affinity between aptamers and their targets can be determined using techniques such as Enzyme-Linked Oligonucleotide Assay (ELONA) and MicroScale Thermophoresis (MST). Aptamers can also be modified to enhance their drug delivery capabilities, resulting in aptamer-drug conjugates (ApDCs) with higher drug loading capacity and targeted cancer therapy potential. Additionally, an integrated digital PCR-fluorescence activated sorting based SELEX (IFS-SELEX) strategy has been developed for rapid screening of aptamers against fluorescent targets, streamlining the aptamer selection process.
Why must we use binding buffer such as PBS for pre-incubating aptamers with bacteria cells?5 answersBinding buffers such as PBS are used for pre-incubating aptamers with bacteria cells because they provide the optimal conditions for the binding process. The use of PBS helps to maintain the pH and ionic strength necessary for the aptamers to interact with the cell surface molecules. Additionally, PBS can help to stabilize the aptamers and prevent their degradation during the incubation process. The binding buffer also helps to minimize non-specific interactions between the aptamers and other components in the sample, allowing for more specific and accurate binding to the target cells. Overall, the use of a binding buffer such as PBS ensures that the aptamers can effectively bind to the bacteria cells and facilitates the selection and detection processes.