* The secondary structure may not be accurate because of MFOLD limitations on chemistries other than RNA/DNA.
2'-F-RNA Mouse P68 RNA Helicase (Ddx5) Protein 30.8 nM (reported value)For selection: 5 nmol of aptamer pool in 200 µl of PBS, injected systemically and allowed to circulate for 20 minutes
For binding assay: 10 mM Tris-HCl (pH 7.0), 150 mM NaCl, 10% (v/v) glycerol, 2.5 µg/ml tRNA. 10 minute incubation at 37°C
For affinity purification: 20 mM HEPES (pH 7.4), 150 mM NaCl, 2 mM CaCl2, 0.1% BSA, 0.1 µM tRNA at 4°C for 2 hoursN/A
Has better affinity for HA-tagged version of human p68 protein (13.8 nM), but only has an affinity of 190 nM for HA-tagged Tenascin CD. ATPase activity was significantly decreased in the presence of aptamer 14-16. IC50 of aptamer was 0.78 µM compared to that of the library (3.63 µM).
An additional “U” nucleotide is present at position 55 in supplementary Figure 1-b and in the later-published version of the paper available at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2795795/. This sequence was used to predict the secondary structure.
Aptagen develops and manufactures aptamers (synthetic antibodies) which are ligands of RNA, DNA, and peptide oligos that bind to a variety of target antigens. Aptamers (synthetic antibodies) are sometimes referred to as "chemical antibodies or DNA antibodies." Aptazymes are aptamers (synthetic antibodies) with enzymatic activity. A subclass of aptazymes called molecular switches is analogous to molecular beacons for fluorescent detection of analytes in test samples. Examples include allosteric ribozymes, also known as riboswitches.
Allosteric ribozymes (or riboswitches) have been engineered to act like molecular switches turning "on" or "off" in the presence or absence of effectors. Ribozyme catalysis is modulated by rapid conformational changes imparted by an effector molecule binding to an aptamer domain apart from the catalytic site. The aptamer domain is a structural region of several nucleotides that binds specifically to its cognate effector molecule. With the advent of allosteric RNA switches and aptazymes, it was soon recognized that the precise molecular recognition and high degree of selectively exhibited by these molecules make them ideal biosensor elements which can be immobilized on a solid support for microarray analysis and biosensor applications. Compared to other types of biosensor recognition elements such as proteins, antibodies, and oligonucleotides, which are commonly used in microarrays to detect a narrow assortment of targets, RNA allosteric elements are better suited for the detection of a wide variety of analytes in a complex mixture, since unlike proteins, antibodies, and oligonucleotides, they are not limited by the types of targets they can bind. As described before, the ability to rapidly develop RNA molecular switches using one pot selection techniques against a vast array of targets permits the rapid development of biochips capable of analyzing and fingerprinting a complex mixture of chemical and biological targets. The versatility and utility of these molecular switches have been employed in biochips which are able to detect specific targets from a complex mixture containing metal ions, enzyme cofactors, metabolites, serum biomarkers, drug analytes, and strains of E coli strain from culture media.
Aptagen, LLC is a biotechnology company offering aptamer (synthetic antibody) products and services as research reagents, diagnostic and biomarker discovery tools, as well as for use in drug discovery and targeted delivery for therapeutics, and bioindustrial applications. We have 20 years of experience in developing aptamers (synthetic antibodies) for all types of downstream applications.