Oligonucleotide or peptide molecules that bind specific targets
Left: Unbound aptamer. Right: the aptamer bound to its target protein. The protein is in yellow. Parts of the aptamer that change shape when it binds its target are in blue, while the unchanging parts are in orange. The parts of the aptamer that contact the protein are highlighted in red.Breast cancer cells incubated with aptamers that bind selectively to biomarkers on the cancer cells, but not to healthy cells. Aptamers are linked to Alexa Fluor 594, a molecule that glows red under UV light. This type of test allows a doctor or researcher to identify cancer cells in a tissue sample from a patient.
Aptamers are oligomers of artificial ssDNA, RNA, XNA, or peptide that bind a specific target molecule, or family of target molecules. They exhibit a range of affinities (KD in the pM to μM range),[1][2] with variable levels of off-target binding[3] and are sometimes classified as chemical antibodies. Aptamers and antibodies can be used in many of the same applications, but the nucleic acid-based structure of aptamers, which are mostly oligonucleotides, is very different from the amino acid-based structure of antibodies, which are proteins. This difference can make aptamers a better choice than antibodies for some purposes (see antibody replacement).
Aptamers are used in biological lab research and medical tests. If multiple aptamers are combined into a single assay, they can measure large numbers of different proteins in a sample. They can be used to identify molecular markers of disease, or can function as drugs, drug delivery systems and controlled drug release systems. They also find use in other molecular engineering tasks.
Most aptamers originate from SELEX, a family of test-tube experiments for finding useful aptamers in a massive pool of different DNA sequences. This process is much like natural selection, directed evolution or artificial selection. In SELEX, the researcher repeatedly selects for the best aptamers from a starting DNA library made of about a quadrillion different randomly generated pieces of DNA or RNA. After SELEX, the researcher might mutate or change the chemistry of the aptamers and do another selection, or might use rational design processes to engineer improvements. Non-SELEX methods for discovering aptamers also exist.
Researchers optimize aptamers to achieve a variety of beneficial features. The most important feature is specific and sensitive binding to the chosen target. When aptamers are exposed to bodily fluids, as in serum tests or aptamer therapeutics, it is often important for them to resist digestion by DNA- and RNA-destroying proteins. Therapeutic aptamers often must be modified to clear slowly from the body. Aptamers that change their shape dramatically when they bind their target are useful as molecular switches to turn a sensor on and off. Some aptamers are engineered to fit into a biosensor or in a test of a biological sample. It can be useful in some cases for the aptamer to accomplish a pre-defined level or speed of binding. As the yield of the synthesis used to produce known aptamers shrinks quickly for longer sequences,[4] researchers often truncate aptamers to the minimal binding sequence to reduce the production cost.
^Rhodes, Andrew; Smithers, Nick; Chapman, Trevor; Parsons, Sarah; Rees, Stephen (2001-10-05). "The generation and characterisation of antagonist RNA aptamers to MCP-1". FEBS Letters. 506 (2): 85–90. doi:10.1016/S0014-5793(01)02895-2. ISSN 0014-5793. PMID 11591377. S2CID 36797240.
^Stoltenburg, Regina; Nikolaus, Nadia; Strehlitz, Beate (2012-12-30). "Capture-SELEX: Selection of DNA Aptamers for Aminoglycoside Antibiotics". Journal of Analytical Methods in Chemistry. 2012: e415697. doi:10.1155/2012/415697. ISSN 2090-8865. PMC 3544269. PMID 23326761.
^Crivianu-Gaita V, Thompson M (November 2016). "Aptamers, antibody scFv, and antibody Fab' fragments: An overview and comparison of three of the most versatile biosensor biorecognition elements". Biosensors & Bioelectronics. 85: 32–45. doi:10.1016/j.bios.2016.04.091. PMID 27155114.
^"DNA Oligonucleotide Synthesis". Millipore Sigma. Retrieved 4 July 2022.
Aptamers are oligomers of artificial ssDNA, RNA, XNA, or peptide that bind a specific target molecule, or family of target molecules. They exhibit a range...
synthetically derived RNA aptamer born out of the need for a way of studying the role of RNAs at the cellular level. This aptamer was created using Systematic...
ligands. These single-stranded DNA or RNA are commonly referred to as aptamers. Although SELEX has emerged as the most commonly used name for the procedure...
immuno-RCA, the ssDNA RCA primer can be conjugated to the 3' end of a DNA aptamer as well. The primer tail can be amplified through rolling circle amplification...
Known examples of smart ligands include DNA smart aptamers; however, RNA and peptide smart aptamers can also be developed. Smart ligands can find a set...
pair to DNA aptamer generation by in vitro selection (SELEX) and demonstrated the genetic alphabet expansion significantly augment DNA aptamer affinities...
increased scalability and consistency in manufacture compared to standard aptamer molecules. Optimer ligands are composed of single-stranded DNA or RNA polymers...
alongside Paul Weiss and Anne M. Andrews. Her doctoral research considered aptamer-functionalised field effect transistors for serotonin and dopamine sensing...
green. For example, Zhao et al., demonstrated the use of malachite green aptamer in microcantilever based sensors to detect low concentration of malachite...
IL-1α and the aptamer. Huang et al. uses ACE to investigate protein-protein interactions using aptamers. A α-thrombin binding aptamer was labeled with...
linker synthesized with an alpha-1,3-gal-gal bond on one end and a DNA aptamer devised to bind specifically to the strain of influenza you have on the...
12-dimethylbenzanthracene), a mutagen. Moreover, HSF1 inhibition by a potent RNA aptamer attenuates mitogenic (MAPK) signaling and induces cancer cell apoptosis...
known different activity depending on enantiomeric form, Aptamers (L-ribonucleic acid aptamers): "That makes mirror-image biochemistry a potentially lucrative...
specifically bind antigens. They consist of artificial peptides or proteins, or aptamer-based nucleic acid molecules with a molar mass of about 3 to 20 kDa. Antibody...
and streptavidin proteins. DNA and other nucleic acids are the basis of aptamers, synthetic oligonucleotide ligands for specific target molecules used in...
important for aptamer generation. Citartan, Marimuthu; et al. (December 2011). "Asymmetric PCR for good quality ssDNA generation towards DNA aptamer production"...
released in the process. Furthermore, polymerases can be inhibited with aptamers that denature upon heating. A fifth variant is a polymerase adsorbed on...
an aptamer rather than an antibody. This could be seen as similar to a Southern blot, however the interaction is between a DNA molecule (the aptamer) and...
Novartis purchased the rights to market Ophthotech's Fovista (an anti-PDGF aptamer, also being investigated for use in combination with anti-VEGF treatments)...
its aptamer, which forms as many as five base-paired substructures. PreQ1-III riboswitch has a distinct structure and is also larger in aptamer size...
materials used in sensor development are molecularly imprinted polymers and aptamers. A chemical sensor array is a sensor architecture with multiple sensor...
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