Aptamers nucleotide. Medical search. Frequent questions

Nucleic acid aptamers are "short single-stranded DNA- or RNA-based oligonucleotides that can selectively bind to small molecular ligands or protein targets with high affinity and specificity, when folded into their unique three-dimensional structure" (1). (ucf.edu)
Aptamers 2016 will be co-hosted with our 2nd symposium on antisense and therapeutic oligonucleotides, Oligo 2016 , on 6th April 2016. (libpubmedia.co.uk)
The assay is many times more sensitive than conventional UV absorbance, and free nucleotides or short oligonucleotides of up to 6 bases do not interfere with the OliGreen ssDNA quantitation assay. (thermofisher.com)
OliGreen reagent assays are routinely used for antisense oligonucleotides, aptamers, genomic DNA isolated under denaturing conditions, PCR primers, sequencing primers, and single-stranded phage DNA. (thermofisher.com)
Aptamers are short single-stranded RNA or DNA oligonucleotides capable of folding into complex 3D structures, enabling them to bind to a large variety of targets ranging from small ions to an entire organism. (encyclopedia.pub)
Aptamers are single-stranded RNA or DNA oligonucleotides that fold up into a distinctive 3D structure capable of binding with high affinity and specificity to small molecules up to entire organisms, with nanomolar range dissociation constants. (encyclopedia.pub)
Nucleic acid-based aptamers were first described in 1990, where the first aptamers were in vitro selected using a random library of single-stranded oligonucleotides sequences [ 1 ] by a selection procedure known as systematic evolution of ligands by exponential enrichment (SELEX). (encyclopedia.pub)
Chemical modifications of aptamer oligonucleotides are needed mainly to enhance their resistance to nuclease degradation and lowering their renal filtration. (encyclopedia.pub)
Although monoclonal antibody therapeutics remain the mainstream in clinical practice, aptamers are synthetic oligonucleotides that encompass antibody-mimicking functions. (tmu.edu.tw)

Oligonucleotide aptamers are well known for their stability and flexibility in conjugating various inflammatory molecules. (iasp-pain.org)
The aptamer is bound to the pore by hybridization to an oligonucleotide that is attached covalently through a disulfide bond to a single cysteine residue near a mouth of the pore. (huji.ac.il)
The first oligonucleotide aptamer was isolated to bind with small molecules [ 2 ] . (encyclopedia.pub)

Studies have shown that small target molecules enable a greater signal gain for low density aptamer packing, while larger proteins as a target generate the greatest signal at intermediate probe packing densities. (wikipedia.org)
The levels of mononuclear cell infiltration, pro-inflammatory cytokine interleukin-1 beta (b), caspase-1 (casp-1), and Nucleotide-binding oligomerization domain, Leucine rich Repeat and Pyrin domain containing proteins 1 and 3 (NALP1 and NALP3) in the prostate of rats were increased seven days after carrageenan injection. (iasp-pain.org)
The genetic information of life on Earth have been conserved in natural nucleotides-A, G, C, T(U) forming two exclusive sets of base pairs A-T(U) & G-C, that complementing to the fundamental processes of DNA replication & RNA transcription by several polymerases and translation to functional proteins via ribosomal reactions. (fortuneonline.org)

The review also outlines the vast applications of UBPs as novel information storage components as well as in creation of semi-synthetic organisms expressing non canonical amino acids, high affinity aptamer generation, PCR based diagnostics and sitespecific labelling of RNAs. (fortuneonline.org)
Here, we report a novel high-affinity CTLA-4-antagonizing DNA aptamer (dissociation constant, 11.84 nM), aptCTLA-4, which was identified by cell-based SELEX and high-throughput sequencing. (tmu.edu.tw)

E-AB sensors are advantageous over previously reported aptamer-based sensors, such as fluorescence generating aptamers, due to their ability to detect target binding in vivo with real-time measurements. (wikipedia.org)
Due to its exceptional stability and unique topology, 93del has been used in many different studies involving DNA G-quadruplexes, such as DNA aptamer and multimer design, as well as DNA fluorescence research. (ntu.edu.sg)
ECHO probes have a fluorescence-labeled nucleotide in which two molecules of thiazole orange or its derivatives are linked covalently. (ne.jp)

The selectivity, low limit of detection, and cost-effectiveness make these nucleic acid aptamers optimal bio-sensors. (ucf.edu)
2014), nucleic acid aptamers (Woo et al. (datexis.com)
Because nucleic acid aptamers have comparable binding affinities with corresponding antibodies, they are regarded as potential candidates for the development of therapeutic agents or diagnostic probes (Brody and Gold, 2000). (datexis.com)

The binding of the aptamer with the target protein produces a change in impedance of the membrane which is picked up by the electrochemical sensor using an impedance spectroscopy analyzer. (wikipedia.org)
In this work, in silico selection of DNA-aptamers to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was performed using molecular modeling methods. (jyu.fi)
Based on molecular docking results, the only one aptamer (Apt16) was selected from the library as a starting aptamer to the RBD protein. (jyu.fi)
Binding of the each modeled aptamer to the RBD was studied in terms of interactions between residues in protein and nucleotides in the aptamers. (jyu.fi)
Donaldson, J. G., Finazzi, D. & Klausner, R. D. Brefeldin A inhibits Golgi membrane-catalysed exchange of guanine nucleotide onto ARF protein. (nature.com)
Morinaga, N., Tsai, S.-C., Moss, J. & Vaughan, M. Isolation of a brefeldin A-inhibited guanine nucleotide-exchange protein for ADP ribosylation factor (ARF) 1 and ARF3 that contains a Sec7-like domain. (nature.com)
Based on cascade catalysis amplification driven by glucose oxidase (GOx), a sensitive electrochemical impedimetric aptasensor for protein (carcinoembryonic antigen, CEA as tested model) was proposed by using Cu-based metal-organic frameworks functionalized with Pt nanoparticles, aptamer, hemin and GOx (Pt@CuMOFs-hGq-GOx). (unboundmedicine.com)
In the present study, we isolated RNA aptamers specific to influenza NS1 protein. (datexis.com)
Unlike the wild-type 10-mer sequences, which bind 1 protein dimer/duplex, these 22-mer thiophosphate aptamers bind with a stoichiometry of 2 dimers/duplex. (utmb.edu)

Depending on the size and nature of target molecule, different aptamer packing densities favor signal gain. (wikipedia.org)

Aptamers have shown promising ability for detection in the subnanomolar range of nucleic acid targets with specificity down to single nucleotide variations (2). (ucf.edu)
SNP analysis: You can detect difference of a single nucleotide. (ne.jp)

Among the list of the artificial nucleotides, bridged nucleic acids (BNAs) appear to be the most promising new generation BNAs to date in view of the usage for applications. (biosyn.com)
Thus, while inculcating the UBPs in a DNA structure, their aromatic scaffolds must exhibit hydrophobic packing and must have hydrogen bond donor groups for the artificial nucleotides to interact with polymerases for their efficient incorporation in the non-template strand to bind with their UB partner in template strand [1-3]. (fortuneonline.org)

Aptamer target-binding specificity and affinity are obtained using a Darwinian evolution screening technology called systematic evolution of ligands by exponential enrichment (SELEX). (encyclopedia.pub)
The SELEX methodology is quite similar for both DNA and RNA aptamers. (encyclopedia.pub)
The standard SELEX procedure allows the identification of specific RNA binders (aptamers) for the target of interest. (elsevierpure.com)
Herein, we described a strategy integrating high-throughput (HT) sequencing with conventional SELEX followed by bioinformatic analysis to identify aptamers with high binding affinity and target specificity to unravel the sequence-structure motifs of pre-miRNA, which is essential for binding to the recently developed new water-soluble small-molecule CMBL3aL. (elsevierpure.com)

We use 80 nucleotide sequences in our aptamer selection process, with a random region of 40 nucleotides. (neoaptamers.com)
Using DNA and RNA aptamers sequences, targeting ability can be bestowed to the polymerized nucleotides. (duke.edu)
Using a 22-nucleotide-long duplex random library, nanomolar binding, specific 22-mer thiophosphate backbone substitution sequences (at dA positions only) were selected. (utmb.edu)

Objective This study aimed to validate the use of Ca-apt-1, an RNA aptamer, that we generated previously as a probe for immunostaining of Candida albicans in rat tongue paraffin-fixed tissue sections Material and Methods The performance of Ca-apt-1 as a detector molecule was compared with that of anti- C. albicans polyclonal antibody (PcAb), which was used as a positive control. (unair.ac.id)
Here we used an aptamer displacement screen to identify SecinH3, a small molecule antagonist of cytohesins. (nature.com)
The length of an aptamer is not a function of its size but it's ability to bind to a target molecule. (neoaptamers.com)

Many approaches have been introduced to promote the stability of aptamers without altering their binding affinity and specificity against their targets. (encyclopedia.pub)

93del is a 16-nucleotide G-quadruplex-forming aptamer which can inhibit the activity of the HIV-1 integrase enzyme at nanomolar concentration. (ntu.edu.sg)
The selected RNA aptamers bind to NS1 specifically and inhibit the interaction between NS1 and TRIM25. (datexis.com)

These unnatural nucleotides are chemically synthesized to bind each other via non-standard hydrogen bonding, hydrophobic interactions and other shape complementing patterns [2,5]. (fortuneonline.org)
Aptamers have been selected that bind tightly to the nuclear factor for human IL6 (NF-IL6), a basic leucine zipper transcription factor involved in the induction of acute-phase responsive and cytokine gene promotors in response to inflammation. (utmb.edu)

We are developing a platform for targeted and sustained delivery of anti-metabolic nucleotide analogs for chemotherapy. (duke.edu)
In addition to the well-known method of conjugating chemotherapeutic drugs to biopolymers and synthetic polymers, our lab also works on polymerization of nucleotide analogs using enzymatic routes. (duke.edu)

There has been a growing interest in developing chemically modified nucleotides for diagnostics or therapeutics. (biosyn.com)
Modified aptamers may show improved chemical diversity relative to aptamers composed entirely of natural DNA or RNA nucleotides and expand their applications in diagnostics, therapeutics, and nanotechnology [ 1 ] . (encyclopedia.pub)
The use of aptamers in large arrays for molecular diagnostics. (colorado.edu)

For Apt16/RBD complex, molecular dynamic and quantum chemical calculations revealed the pairs of nucleotides and amino acids whose contribution to the binding between aptamer and RBD is the lar gest. (jyu.fi)

In the synthesis process for an aptamer there is failure to appropriate add the next nucleotide approximately 0.8% of the time. (neoaptamers.com)
The cost of aptamer synthesis is based on the cost of the components used to create it. (neoaptamers.com)

Additionally, chemical modifications, in some cases, may increase the aptamer-binding affinity [ 13 ] . (encyclopedia.pub)

Aptamers to components of the replication complex are therefore useful molecular tools for studying viral replication and also have potential as diagnostic molecules in the future. (whiterose.ac.uk)
A new computational approach to aptamer in silico selection is based on a cycle of simulations, including the stages of molecular modeling, molecular docking, molecular dynamic simulations, and quantum chemical calculations. (jyu.fi)
The procedure of 1) aptamer structure modeling/modification, 2) molecular docking, 3) molecular dynamic simulations, 4) quantum chemical calculations was performed sev-eral times. (jyu.fi)
The proposed computational approach to selection and refinement of aptamers is universal and can be used for wide range of molecular ligands and targets. (jyu.fi)
Functional nucleic acids (FNAs), including naturally occurring ribozymes and riboswitches as well as artificially created DNAzymes and aptamers, have been popular molecular toolboxes for diverse applications. (mcmaster.ca)
We exploit different DNA polymerases and molecular biology tools to generate oligomers of nucleotide drugs. (duke.edu)

Previous structural analyses of 93del using NMR spectroscopy have shown that the aptamer forms an interlocked G-quadruplex structure in K+ solution. (ntu.edu.sg)
To confirm the fidelity of this approach, we investigated the binding of CMBL3aL to the identified motifs by surface plasmon resonance (SPR) spectroscopy and its potential regulatory activity on dicer-mediated cleavage of the obtained aptamers and endogenous pre-miRNAs comprising the identified motif in its hairpin loop. (elsevierpure.com)

Moreover, introducing chemical modifications into nucleic acid libraries increases the interaction capabilities of aptamers and thereby their target spectrum [ 12 ] . (encyclopedia.pub)
Focused aptamer libraries are constructed in accordance with a proteome (i.e., complex mixture of native biomolecules). (duke.edu)

Targets on which aptamer selection is conducted against are diverse, ranging from ions to whole living cells. (encyclopedia.pub)

An electrochemical aptamer-based (E-AB) biosensor has the ability to generate an electrochemical signal in response to specific target binding in vivo The signal is measured by a change in Faradaic current passed through an electrode. (wikipedia.org)
Aptamers need to be stabilized for in vivo use against nuclease degradation, and their small size makes them susceptible to renal filtration. (encyclopedia.pub)

Aptamer: You can detect the small molecules by ECHO-installed aptamer. (ne.jp)

Through sandwich-type reaction of target CEA and CEA aptamers (Apt1 and Apt2), the obtained Pt@CuMOFs-hGq-GOx as signal transduction probes (STPs) was captured to the modified electrode interface. (unboundmedicine.com)
In ECHO probes, a hybridization-dependent fluorescent nucleotide regulated by the H-aggregation of thiazole orange organic dyes (D 514 ) is incorporated into specific sequence contexts and serves as fluorescent detection readout for target nucleic acids. (ne.jp)

Our study demonstrates the developmental pipeline of a functional CTLA-4-targeting aptamer and suggests a translational potential for aptCTLA-4. (tmu.edu.tw)

The symposium will address therapeutic, diagnostic, analytical as well as basic research applications of aptamers and invites proposals for podium (now closed! (libpubmedia.co.uk)

We also found that viral replication was suppressed in the presence of aptamers, which suggests that the selected RNA aptamers can be developed as a useful therapeutic agent in future. (datexis.com)

Here, we propose to organize this aptamer into a split-aptamer system and determine the limit of detection and selectivity for a target gene in Mycobacterium tuberculosis . (ucf.edu)
Aptamer-based nanopores have the potential to be integrated into arrays for the parallel detection of multiple analytes. (huji.ac.il)

When the probe surface neighboring an aptamer is blocked by an adjacent aptamer, the redox tag on the target-bound aptamer will not have room to come into contact with the electrode, therefore failing to report target binding. (wikipedia.org)
Helms, J. B. & Rothman, J. E. Inhibition by brefeldin A of a Golgi membrane enzyme that catalyses exchange of guanine nucleotide bound to ARF. (nature.com)
CEA aptamer loaded onto Pt@CuMOFs was bound with hemin to form hemin@G-quadruplex (hGq) with mimicking peroxidase activity. (unboundmedicine.com)

Several groups have developed synthetic unnatural nucleotides that can form unnatural base pairs with their complementary synthetic bases. (fortuneonline.org)

The extra nucleotides on a longer aptamer are not involved in the binding event and can reduce both the rate of complex formation by getting in the way, and the rate of complexes coming apart by reducing the stability of the aptamer structure. (neoaptamers.com)

View a selection of Aptamers 2016 photos on the INSOAP website . (libpubmedia.co.uk)
Aptamer selection against novel infections is a complicated and time-consuming approach. (jyu.fi)

RiboGreen reagent does not detect significant sample contamination by free nucleotides and thus more accurately measures the amount of intact RNA in potentially degraded samples. (thermofisher.com)

Chemical Modifications of Aptamers" Encyclopedia , https://encyclopedia.pub/entry/16686 (accessed December 05, 2023). (encyclopedia.pub)

We show that the binding of thrombin to a 15-mer DNA aptamer, which forms a cation-stabilized quadruplex, alters the ionic current through the pore. (huji.ac.il)
The FNA species to be discussed include ribozymes, riboswitches, G‐quadruplex‐based peroxidase mimicking DNAzymes, RNA‐cleaving DNAzymes, and aptamers. (mcmaster.ca)

aptamer interactions. (huji.ac.il)

Four electrode method has also been demonstrated in an electrochemical nanoporous alumina membrane sensor, where the aptamer was grafted onto the membrane and not on the electrode. (wikipedia.org)

Upon target binding, the aptamer changes structure by folding, bringing the redox reporter closer to the gold electrode. (wikipedia.org)
This approach could be beneficial in cases where the electric field of the electrode can change the aptamer structure or the biointerface which may decrease the sensing ability. (wikipedia.org)
To gain further insights on the structure of this unique aptamer, we have determined several high-resolution crystal structures of 93del and its variants. (ntu.edu.sg)
However, more effort is needed to identify and characterize the sequence-structure motifs in the aptamers important for binding to the target. (elsevierpure.com)

The aptamer probe packing density, the nature of the self-assembling monolayer, and the ACV frequency are factors that affect detecting and measuring of signal. (wikipedia.org)
The concentration of aptamer and the surface chemistry of the self-assembling monolayer (SAM) enable variations of desired probe packing density. (wikipedia.org)
The concentration of aptamer in solution that incubates a clean probe is found to be proportional to the density of aptamers that are immobilized on the probe. (wikipedia.org)

It also explores aspects of biomolecular engineering and various bioconjugation methods to confer nuclease resistance to the nucleotide oligomers. (duke.edu)

Anatomy1

Organisms4

Chemicals and Drugs51

Analytical, Diagnostic and Therapeutic Techniques and Equipment22

Phenomena and Processes48

Disciplines and Occupations2

Technology, Industry, Agriculture3

Information Science4

Oligonucleotides9

Oligonucleotide3

Proteins3

High-affinity2

Fluorescence3

Nucleic acid aptamers3

Protein9

Different aptamer1

Single nucleotide2

Artificial nucleotides2

SELEX4

Sequences3

Molecule3

Specificity1

Inhibit2

Bind2

Analogs2

Diagnostics3

Amino acids1

Synthesis2

Affinity1

Molecular6

Spectroscopy2

Libraries2

Targets1

Vivo2

Small molecules1

Probes2

Functional1

Diagnostic1

Therapeutic1

Detection2

Bound3

Synthetic1

Stability1

Selection2

Detect1

20231

Quadruplex2

Interactions1

Membrane1

Structure4

Probe3

Resistance1