Functional Nucleic Acids as Molecular Recognition Elements for Small Organic and Biological Molecules

The abundance of small molecules in biological systems, the wide-spread usage of synthetic small molecules as drugs and biological probes, and the escalation of industrial pollutants in our environment, underscore the importance of detection of small molecules for many disciplines. Functional nucleic acids (FNAs) are single-stranded DNA or RNA sequences that are capable of carrying out ligand binding (aptamers), catalysis (nucleic acid enzymes) or both functions (aptazymes). Many FNAs have been shown to be suitable molecular recognition elements for small-molecule targets. In this article, we will present a focused review on FNAs for small molecule binding and detection. First, we will discuss the technique of "in vitro selection" by which artificial FNAs can be isolated from random-sequence DNA or RNA pools. This will be followed by a survey of aptamers for small molecules isolated to date. Next, the diverse functions of natural aptamers, as part of riboswitches (metabolite-sensing RNA regulatory systems that exist in many organisms) will be explored. Efforts in creating aptazymes will also be presented. Finally, we will examine numerous applications of aptamers and aptazymes in the development of fluorescent, colorimetric and electrochemical biosensors and discuss some emerging applications concerning FNAs. Keywords: Functional nucleic acid, aptamer, ribozyme, DNAzyme, aptazyme, riboswitch, biosensor, in vitro selection, SELEX, amino acids, steroids, carbohydrates, nucleotides, organic drugs, dyes, carcinogens, IN VITRO SELECTION (SELEX) TECHNIQUE, RT-PCR (for RNA-based selec-tion), RNA-cleaving DNAzyme, elution, structure-switching, L-arginine, L-citrulline, L-dopamine, L-isoleucine, D-tryptophan, L-tyrosine, L-valine, L-tyrosinamide, 7-methyl-guanosine, 8-oxo-deoxyguanosine, adenosine 5'-triphosphate, guanosine 5'-triphosphate (GTP), cyclic adenosine mono-phosphate, biotin, coenzyme A, cya-nocobalamin (vitamin B12), riboflavin, flavin adenine dinucleo-tide, flavin mononucleotide, nicotina-mide mononucleotide, S-adenosylmethionine, S-adenosylhomocysteine, steroids 17-estradiol, cholic acid, thyroxine hormone, ochratoxin A (a mycotoxin), chloramphenicol, kanamycin, livi-domycin, neomycin, streptomycin, tetracycline, tobramycin, viomycin