title: Allosteric aptamers: targeted reversibly attenuated probes.
abstract: Aptamers are unique nucleic acids with regulatory potentials that differ markedly from those of proteins. A significant feature of aptamers not possessed by proteins is their ability to participate in at least two different types of three-dimensional structure: a single-stranded folded structure that makes multiple contacts with the aptamer target and a double-helical structure with a complementary nucleic acid sequence. We have made use of this structural flexibility to develop an aptamer-based biosensor (a targeted reversibly attenuated probe, TRAP) in which hybridization of a cis-complementary regulatory nucleic acid (attenuator) controls the ability of the aptamer to bind to its target molecule. The central portion of the TRAP, between the aptamer and the attenuator, is complementary to a target nucleic acid, such as an mRNA, which is referred to as a regulatory nucleic acid (regNA) because it regulates the activity of the aptamer in the TRAP by hybridization with the central (intervening) sequence. The studies reported here of the ATP-DNA TRAP suggest that, as well as inhibiting the aptamer, the attenuator also acts as a structural guide, much like a chaperone, to promote proper folding of the TRAP such that it can be fully activated by the regDNA. We also show that activation of the aptamer in the TRAP by the complementary nucleic acid at physiological temperatures is sensitive to single-base mismatches. Aptamers that can be regulated by a specific nucleic sequence such as in an mRNA have potential for many in vivo applications including regulating a particular enzyme or signal transduction pathway or imaging gene expression in vivo.
authors.affiliation: Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA.
authors.forename: Xiangyu
authors.initials: X
authors.lastname: Cong
authors.forename: Marit
authors.initials: M
authors.lastname: Nilsen-Hamilton
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry*; D000494:Allosteric Regulation / Q000235:genetics; D020137:Base Pair Mismatch; D002151:Calorimetry; D015335:Molecular Probes / Q000138:chemical synthesis / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D016376:Oligonucleotides, Antisense / Q000737:chemistry; D018075:RNA, Complementary / Q000737:chemistry; D012333:RNA, Messenger / Q000737:chemistry; D012045:Regulatory Sequences, Nucleic Acid; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D015335:Molecular Probes; D009841:Oligonucleotides; D016376:Oligonucleotides, Antisense; D018075:RNA, Complementary; D012333:RNA, Messenger; D000255:Adenosine Triphosphate