Aptamers for allosteric regulation

Abstract

Aptamers are useful for allosteric regulation because they are nucleic acid-based structures in which ligand binding induces conformational changes that may alter the function of a connected oligonucleotide at a distant site. Through this approach, a specific input is efficiently converted into an altered output. This property makes these biomolecules ideally suited to function as sensors or switches in biochemical assays or inside living cells. The ability to select oligonucleotide-based recognition elements in vitro in combination with the availability of nucleic acids with enzymatic activity has led to the development of a wide range of engineered allosteric aptasensors and aptazymes. Here, we discuss recent progress in the screening, design and diversity of these conformational switching oligonucleotides. We cover their application in vitro and for regulating gene expression in both prokaryotes and eukaryotes.

A general approach for rational design of fluorescent DNA aptazyme sensors based on target-induced unfolding of DNA hairpins

“…Functional DNA [1][2][3][4][5][6][7][8] is a class of DNA molecules exhibiting functions beyond genetic information, which was once thought as the solely function of DNA. This interesting class of DNA includes DNAzyme (also called deoxyribozyme or DNA enzyme) that can catalyze chemical reactions in the presence of specific cofactors [1][2][3][4][9][10][11], DNA aptamer that can bind specific targets [2,[4][5][6][7][8]11], and DNA aptazyme that is the combination of the above two [9,12,13].…”

“…This interesting class of DNA includes DNAzyme (also called deoxyribozyme or DNA enzyme) that can catalyze chemical reactions in the presence of specific cofactors [1][2][3][4][9][10][11], DNA aptamer that can bind specific targets [2,[4][5][6][7][8]11], and DNA aptazyme that is the combination of the above two [9,12,13]. Since the first discovery of a DNA aptamer and a DNAzyme in 1990's [14,15], more and more functional DNAs have been identified by combinatorial techniques such as in vitro selection and SELEX (Systematic evolution of ligands by exponential amplification) [14][15][16][17][18].…”

“…Since the first discovery of a DNA aptamer and a DNAzyme in 1990's [14,15], more and more functional DNAs have been identified by combinatorial techniques such as in vitro selection and SELEX (Systematic evolution of ligands by exponential amplification) [14][15][16][17][18]. So far, functional DNA has played increasingly important roles in many research fields such as biosensing, nanoassembly, and catalysis [1][2][3][4][5][6][7][8][9][10][11]19]. Particularly, fluorescent biosensors based on functional DNA have attracted intensive attention in recent years, because of the high specificity and affinity of functional DNAs to their targets as well as the simplicity and nondestructive nature of fluorescence measurement.…”

“…In contrast to the wide applications of DNAzymes and aptamers as biosensors in multiple research fields [1][2][3][4][5][6][7][8]10,11,22,[35][36][37][38][39][40][41][42][43][44], there are considerably less studies on DNA aptazymes for similar applications [9,12,13,45]. Perhaps a major reason for this difference is that, most DNA aptazyme sensors are developed by artificial design using known DNAzymes and aptamers rather than by more efficient combinatorial techniques [46], therefore extensive trial-and-error and optimization procedures are usually required for the identification of a successful aptazyme sensor with target-dependent fluorescence switch.…”

Artificial riboswitches for gene expression and replication control of DNA and RNA viruses

“…Hence, they enable conditional cleavage of RNA, including mRNAs, and fulfill all of the above-mentioned criteria. Moreover, they can be engineered for ON-or OFF-switch activity by modification of the aptamer-ribozyme linking sequences (8)(9)(10). Compared with well-established inducible promoters, as used for example in the Tet system (11), aptazymes are much smaller (approximately 100 bp) and do not require the expression of recombinant, potenSignificance Riboswitches are short RNA sequences for ligand-dependent modulation of gene expression in cis.…”