Adaptive Recognition by Nucleic Acid Aptamers

Abstract

Nucleic acid molecules play crucial roles in diverse biological processes including the storage, transport, processing, and expression of the genetic information. Nucleic acid aptamers are selected in vitro from libraries containing random sequences of up to a few hundred nucleotides. Selection is based on the ability to bind ligand molecules with high affinity and specificity. Three-dimensional structures have been determined at high resolution for a number of aptamers in complex with their cognate ligands. Structures of aptamer complexes reveal the key molecular interactions conferring specificity to the aptamer-ligand association, including the precise stacking of flat moieties, specific hydrogen bonding, and molecular shape complementarity. These basic principles of discriminatory molecular interactions in aptamer complexes parallel recognition events central to many cellular processes involving nucleic acids.

Metal‐Induced Specific and Nonspecific Oligonucleotide Folding Studied by FRET and Related Biophysical and Bioanalytical Implications

“…<50 nucleotides) and are present as random coils without a stable secondary structure. [5] Addition of target molecules folds the aptamers into more rigid binding structures (so called adaptive binding), which often accompanies with a reduced end-to-end distance. [5] The adaptive binding property has been used to design fluorescence resonance energy transfer (FRET)-based sensors with end-labeled fluorophores since FRET is known to be sensitive to such distance changes.…”

“…[5] Addition of target molecules folds the aptamers into more rigid binding structures (so called adaptive binding), which often accompanies with a reduced end-to-end distance. [5] The adaptive binding property has been used to design fluorescence resonance energy transfer (FRET)-based sensors with end-labeled fluorophores since FRET is known to be sensitive to such distance changes. Many molecules include adenosine/ATP, [6] cocaine, [7] arginiamide, [8] K I , [9][10][11][12] Mg II /Ca II , [13] Ag I , [14] Hg II , [15,16] thrombin, [17] and (platelet-derived growth factor) PDGF [18,19] have been detected using this method.…”

A review on electronic bio-sensing approaches based on non-antibody recognition elements

“…protein and inorganic molecules). 63,64 Attributed to the folding capability upon binding, 65 the binding affinity and specificity of aptamer/target interactions are comparable to that of antibody/antigen interactions. Hence, nucleic acid aptamers are termed as "chemical antibodies" in various cases.…”

RNA affinity tags for purification of RNAs and ribonucleoprotein complexes

“…With this powerful technique, DNA or RNA ligands with affinity toward the desired target molecules can be selected out of random-sequence DNA or RNA libraries, and the technique has been used to identify RNA ligands (aptamers) that recognize a wide range of target molecules, from small molecules to more complex macromolecules (reviewed in [12][13][14][15]). Two types of aptamers with affinity to Sephadex or streptavidin have been developed, and they are shown to have a potential use as RNA affinity tags [8,9].…”