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  • present
  • Here, we present a brief survey of the use of aptamers in signaling pathways, in particular of polypeptide growth factors, starting with the published as well as potential applications of aptamers targeting Epidermal Growth Factor Receptor signaling. (mdpi.com)
  • target
  • 7. A method to detect and identify a target protein, the method comprising interacting the peptide aptamer of claim 1 (within the polyprotein) with the target protein and detecting the resulting fluorescence. (patentsencyclopedia.com)
  • important
  • For at least one other aptamer I show that a pseudoknot is the important binding element, but binding is increased in the presence of additional flanking sequence. (umsystem.edu)
  • thrombin
  • The cation dependence of the CD spectra of the vertebrate telomere repeat DNAs is distinctly different from that of the telomere repeats of Tetrahymena and Oxytricha as well as that of the thrombin binding aptamer. (nih.gov)
  • The aptasensor showed a linear response for thrombin in the range of 7.5 pM to 75 pM and a detection limit of 4.5 pM.The aptasensor was regenerated by breaking the complex formed between the aptamer and thrombin using 2.0 M NaCl solution at 42 °C, showing its operation for different cycles.The interference response caused by main proteins in serum has been characterized. (nih.gov)
  • The electrode surface was partially blocked due to formation of aptamer-thrombin complex, resulting in an increase of the interfacial electron-transfer resistance detected by Electrochemical Impedance Spectroscopy (EIS). (nih.gov)
  • The aptasensor was regenerated by breaking the complex formed between the aptamer and thrombin using 2.0 M NaCl solution at 42 °C, showing its operation for different cycles. (nih.gov)
  • b) Aptamer of thrombin (AptThr) , and (c) AptThr-Thr ○ 10 pM [Thr]. (nih.gov)
  • With the optimized concentrations of aptamer and PEG and following the above experimental protocol for the detection of thrombin, the aptasensor response was initially evaluated. (nih.gov)
  • The aptamer of thrombin forms a single-strand oligonucleotide, a chain that recognizes the protein by a three-dimensional folding (quadriplex). (nih.gov)
  • Anti-thrombin aptamers are G-quadruplex-bearing oligonucleotides, which recognizes the exosites of human thrombin. (wikipedia.org)
  • The first anti-thrombin aptamer, TBA, was generated through via SELEX (Systematic Evolution of Ligands by Exponential Enrichment) technology in 1992 by L.C. Bock, J.J. Toole and colleagues. (wikipedia.org)
  • A second thrombin-binding aptamer, HD22, recognizes thrombin exosite II and was discovered in 1997 by NeXstar (now Gilead Sciences). (wikipedia.org)
  • It interacts with the exosite I of human alpha-thrombin, which is the binding site of fibrinogen, so this aptamer acts as an anti-coagulant agent inhibiting the activation of fibrinogen as well as platelet aggregation. (wikipedia.org)
  • Some groups use this property to develop aptamer-based thrombin sensors. (wikipedia.org)
  • ribose sugar
  • A nucleotide is made up of three chemical components: a phosphate, a five-carbon sugar group (this can be either a deoxyribose sugar - which gives us the "D" in DNA - or a ribose sugar - the "R" in RNA), and one of five standard bases (adenine, guanine, cytosine, thymine or uracil). (wikipedia.org)
  • The molecules that piece together to form the six xeno nucleic acids are almost identical to those of DNA and RNA, with one exception: in XNA nucleotides, the deoxyribose and ribose sugar groups of DNA and RNA have been replaced. (wikipedia.org)
  • guanine
  • Here, we report the discovery of riboswitch aptamers for phosphoribosyl pyrophosphate (PRPP) that naturally exist either in singlet arrangements, or occur in tandem with guanine aptamers. (elifesciences.org)
  • Tandem guanine-PRPP aptamers can bind the target ligands, either independently or in combination, to approximate the function expected for an IMPLY Boolean logic gate to regulate transcription of messenger RNAs for de novo purine biosynthesis in bacteria. (elifesciences.org)
  • Critical to this sensitivity is a single difference in the secondary structure of ribonucleotides: in position 74 of the aptamer domain, it has been found that conversion of a cytosine to a uracil changes an aptamer from being guanine sensitive to being adenine sensitive, and vice versa. (wikipedia.org)
  • Such a conversion is owed to the ability of a nucleotide in position 74 to Watson-Crick base pair with the ligand in the binding pocket, and cytosine and uracil's respective ability to preferentially hydrogen-bond with guanine or adenine. (wikipedia.org)
  • The Guanine Riboswitch selectively recognizes guanine, and contains a cytosine ribonucleotide in position 74 of the guanine-binding aptamer domain. (wikipedia.org)
  • bind the target
  • FC5L-S1 and FC45L-S1 were determined to bind codeine with Kd values of 5.51 ± 0.23 μM and 4.18 ± 0.48 μM, respectively (Supplementary Figure 2A and B). These results indicate that the modified mini-aptamers bind the target molecule codeine with affinities similar to the corresponding unmodified mini-aptamers. (nih.gov)
  • base pairs
  • The base stems of the mini-aptamers were modified with an extension of GC base pairs to stabilize the proposed structures of these mini-aptamers. (nih.gov)
  • The FC5 mini-aptamer (FC5L) was stabilized by extending the existing 3 bp stem with two GC base pairs (Figure 7B), based on the assumption that a few nucleotides present on each end of the original mini-aptamer are unessential for codeine-binding. (nih.gov)
  • Similarly, the FC45 mini-aptamer (FC45L) was stabilized by extending the base stem formed by the 5′-CUU and 3′-GGG pairing with two GC base pairs (Figure 8B), excluding several nucleotides from the 5′ end. (nih.gov)
  • Hence, the number of total base pairs is equal to the number of nucleotides in one of the strands (with the exception of non-coding single-stranded regions of telomeres). (wikipedia.org)
  • gene
  • Knocking down gene function with an RNA aptamer expressed as part of an intron. (nih.gov)
  • They also show that natural cells use allosteric ribozymes to regulate gene expression, a mechanism commonly used in engineered aptamers but not previously observed in nature. (wikipedia.org)
  • therapeutic
  • Ex-vivo studies on pig corneal models showed therapeutic efficacy of the aptamer in reducing productive infection over a period of 168 hours. (arvojournals.org)
  • In-vivo experiments on mice models exhibited significant decrease in ocular infection through prophylactic, therapeutic and neutralization treatment of corneal tissue with the DNA aptamer. (arvojournals.org)
  • Such an aptamer is intended for use as a targeting agent with both therapeutic and diagnostic application (theragnostic). (beckman-foundation.org)
  • conserved transcription
  • We used this system to express an aptamer against the heat shock factor 1 (HSF1), a conserved transcription factor responsible for mobilizing specific genomic expression programs in response to stressful conditions such as elevated temperature. (nih.gov)
  • naturally
  • Using a genetic code of six XNAs rather than the four naturally occurring DNA nucleotide bases yields endless opportunities for genetic modification and expansion of chemical functionality. (wikipedia.org)
  • Each three nucleotide codon is translated into one of twenty naturally occurring amino acids. (wikipedia.org)
  • therefore
  • Therefore, these results support the proposed secondary structures of the FC5 and FC45 mini-aptamers (Figure 6) and that their codeine-binding affinities were minimally affected by extending the original base stems. (nih.gov)
  • polymerase
  • Since sgRNAs are usually expressed by RNA polymerase III, which limits the length of the RNA domain that can be inserted, CRISPR-Display incorporates RNA polymerase II to permit expression of longer transcripts (~80-250 nucleotides) to overcome this limitation. (wikipedia.org)
  • The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA, and RNA polymerase transcribes DNA into RNA. (wikipedia.org)
  • chains
  • Nucleic acids are chains of nucleotides, which are composed of three parts: a phosphate backbone, a pentose sugar, either ribose or deoxyribose, and one of four nucleobases. (wikipedia.org)
  • absence
  • Freshly cut pig corneas were infected with HSV-1 GFP virus and its spread was monitored over a period of 10 days in the presence and absence of the aptamer. (arvojournals.org)
  • In the absence of adenine, the aptamer domain of the riboswitch instead associates with the riboswitch expression platform, leading to transcription termination. (wikipedia.org)
  • high
  • The binding properties of these aptamers, including equilibrium and kinetic rate constants, were determined through a rapid, high-throughput approach using surface plasmon resonance (SPR) analysis to measure real-time binding. (nih.gov)
  • structures
  • These assays were also employed to confirm the proposed secondary structures of the mini-aptamers. (nih.gov)
  • Proposed secondary structures from mfold of (A) the original FC5 mini-aptamer (FC5L), (B) the FC5 mini-aptamer with a stabilized base stem (FC5L-S1), (C) the FC5 mini-aptamer with a stabilized base stem composed of randomly-selected nucleotides (FC5L-S2). (nih.gov)
  • Following the modification, the structures of these stabilized mini-aptamers were further analyzed in mfold using the DotPlot Partition Function, which confirms these structures to be the most favorable ones to adopt among others. (nih.gov)
  • PreQ1-I has a distinctly small aptamer, ranging from 25 to 45 nucleotides long, compared to the structures of PreQ1-II riboswitch and preQ1-III riboswitch. (wikipedia.org)
  • selection
  • In order to select for the best binding aptamers, the stringency of the selection process was gradually increased by decreasing the concentration of both target and library to a final concentration of 40 pM and 2.5 nM respectively, in round 16. (nih.gov)
  • genes
  • A) Effect of aptamer monomer (M) on the level of HS genes measured by conventional RT-PCR. (nih.gov)
  • HS (20 min at 39°C). (B) Effect of both aptamer monomer (M) and dimer (D) on the level of HS genes measured by RT-qPCR. (nih.gov)
  • These genes were not induced by HS and were not inhibited by the aptamer.Figure 4. (nih.gov)
  • natural
  • The artificial nucleotides featured two fused aromatic rings which formed a (d5SICS-dNaM) complex mimicking the natural (dG-dC) base pair. (wikipedia.org)
  • small
  • Convergent evolution to an aptamer observed in small populations on DNA microarrays. (ox.ac.uk)