Highly Specific Recognition of Guanosine Using Engineered Base-Excised Aptamers

AMP Aptamer Programs DNA Tile Cohesion without Canonical Base Pairing

Tile-based DNA self-assembly provides a versatile approach for the construction of a wide range of nanostructures for various applications such as nanomedicine and advanced materials. The inter-tile interactions are primarily programmed by base pairing, particularly Watson-Crick base pairing. To further expand the tool box for DNA nanotechnology, herein, we have designed DNA tiles that contain both ligands and aptamers. Upon ligand-aptamer binding, tiles associate into geometrically well-defined nanostructures. This strategy has been demonstrated by the assembly of a series of DNA nanostructures, which have been thoroughly characterized by gel electrophoresis and atomic force microscopy. This new inter-tile cohesion could bring new potentials to DNA self-assembly in the future. For example, the addition of free ligand could modulate the nanostructure formation. In the case of biological ligands, DNA self-assembly could be related to the presence of certain ligands.

Harnessing the CRISPR-Cas13d System for Protein Detection by Dual-Aptamer-Based Transcription Amplification

CRISPR-based biosensing technology has been emerging as a revolutionary diagnostic tool for many disease-related biomarkers. In particular, RspCas13d, a newly identified RNA-guided Cas13d ribonuclease derived from Ruminococcus sp., has shown great promise for accurate and sensitive detection of RNA due to its RNA sequence-specific recognition and robust collateral trans-cleavage activity. However, its diagnostic utility is limited to detecting nucleic-acid-related biomarkers. To address this limitation, herein we present a proof-of-concept demonstration of a target-responsive CRISPR-Cas13d sensing system for protein biomarkers. This system was rationally designed by integrating a dual-aptamer-based transcription amplification strategy with CRISPR-Cas13d (DATAS-Cas13d), in which the protein binding initiates in-vitro RNA transcription followed by the activation of RspCas13d. Using a short fluorescent ssRNA as the signal reporter and cardiac troponin I (cTnI) as the model analyte, the DATAS-Cas13d system showed a wide linear range, low detection limit, and high specificity for the detection of cTnI in buffer and human serum. Thanks to the facile integration of various bioreceptors into the DATAS-Cas13d system, the method could be adapted to detecting a broad range of clinically relevant protein biomarkers, and thus broaden the medical applications of Cas13d-based diagnostics.

G-quadruplex apurinic site-programmed chiral cyanine assemblies for specifically recognizing guanosine and guanine

DNA-tuned dye assemblies have received considerable attention toward developing various devices. Owing to easy conformation implementation, G-quadruplexes (G4s) have been extensively used as initiators to grow dye assemblies with controllable chiralities. However, programmed chirality regulation of dye assemblies for a given G4 sequence has not been realized in a straightforward manner. In this work, we replaced a middle guanine in the G-tracts of a human telomeric G4 with an apurinic site (AP site) to meet the programmed dye assemblies. Although all of the AP site replacements altered the G4 conformation from the hybrid to the antiparallel folding, the handedness of pinacyanol (PIN) assemblies grown on the AP site-containing G4 was programmably regulated. The G4 with the AP site at the 5'-most G-tract grew right-handed assemblies, while that with the AP site at the 3'-most G-tract grew left-handed assemblies. The handedness of assemblies almost totally mirrored each other within 450-700 nm. Interestingly, we found that the AP site provided a specific binding site for guanosine and guanine, and this binding event sensitively broke the chiral assemblies. Thus, dye assembly-based sensors can be easily established based on the chiral responses with a high selectivity and sensitivity. Our work first demonstrates the AP site programmed chirality regulation of G4-grown dye assemblies and will find wide application in chiral devices.

Aptamer-based strategies for recognizing adenine, adenosine, ATP and related compounds

Adenine is a key nucleobase, adenosine is an endogenous regulator of the immune system, while adenosine triphosphate (ATP) is the energy source of many biological reactions. Selective detection of these molecules is useful for understanding biological processes, biochemical reactions and signaling. Since 1993, various aptamers have been reported to bind to adenine and its derivatives. In addition, the adenine riboswitch was later discovered. This review summarizes the efforts for the selection of RNA and DNA aptamers for adenine derivatives, and we pay particular attention to the specificity of binding. In addition, other molecular recognition strategies based on rational sequence design are also introduced. Most of the work in the field was performed on the classic DNA aptamer for adenosine and ATP reported by the Szostak group. Based on this aptamer, some representative applications such as the design of fluorescent, colorimetric and electrochemical biosensors, intracellular imaging, and ATP-responsive materials are also described. In addition, we critically review the limit of the reported aptamers and also important problems in the field, which can give future research opportunities.