Conformational studies of 10-23 DNAzyme in solution through pyrenyl-labeled 2'-deoxyadenosine derivatives

Two kinds of DNA enzyme-powered bidirectional one-dimensional DNA walking nanomachine for payload release and biosensing

Herein, we present a target-triggered bidirectional one-dimensional (1D) DNA walking nanomachine, built from a well-designed track, which could simultaneously move two different DNA walkers to the opposite direction along the track and release payload. This track is composed of a DNA walker station (chain S3) in the middle of track for storing two kinds of DNA walker (W1 and W2), and corresponding two kinds of payload conjugated DNA stators (chain S1, S2 and S4, S5) for the moving of walker on the two flanks of chain S3 respectively. Moreover, the chain S3 also serves as a target-assisted amplification platform based on a catalytic hairpin assembly (CHA)-like strategy. In the presence of target (nucleic acid), the dynamic assembly between hairpin (HP) and S3 is triggered for multiple recycling of target and releasing of W1 and W2. Since the W1 and W2 respectively correspond to 8-17 DNAzyme and 10-23 DNAzyme, they could cleave the RNA substrates with sequence specificity to move towards two opposite directions along the track at the same time, accompanying the release of payloads. Such a 1D DNA walking nanomachine is not only could propel the walker to move in two directions respectively but also improve the locomotion efficiency compared to the traditional single-directional 1D DNA walking nanomachine with the same amounts of stators. This concept of inducing the locomotion manner change on a 1D DNA device may provide a thought to facilitate the development of DNA dynamic nanomachines and intelligent nanosensors.

Boronic Acid-Mediated Activity Control of Split 10-23 DNAzymes

The 10-23 DNAzyme is an artificially developed Mg2+ -dependent catalytic oligonucleotide that can cleave an RNA substrate in a sequence-specific fashion. In this study, new split 10-23 DNAzymes made of two nonfunctional fragments, one of which carries a boronic acid group at its 5' end, while the other has a ribonucleotide at its 3' end, were designed. Herein it is demonstrated that the addition of Mg2+ ions leads to assembly of the fragments, which in turn induces the formation of a new boronate internucleoside linkage that restores the DNAzyme activity. A systematic evaluation identified the best-performing system. The results highlight key features for efficient control of DNAzyme activity through the formation of boronate linkages.

Molecular Features and Metal Ions That Influence 10-23 DNAzyme Activity

Deoxyribozymes (DNAzymes) with RNA hydrolysis activity have a tremendous potential as gene suppression agents for therapeutic applications. The most extensively studied representative is the 10-23 DNAzyme consisting of a catalytic loop and two substrate binding arms that can be designed to bind and cleave the RNA sequence of interest. The RNA substrate is cleaved between central purine and pyrimidine nucleotides. The activity of this DNAzyme in vitro is considerably higher than in vivo, which was suggested to be related to its divalent cation dependency. Understanding the mechanism of DNAzyme catalysis is hindered by the absence of structural information. Numerous biological studies, however, provide comprehensive insights into the role of particular deoxynucleotides and functional groups in DNAzymes. Here we provide an overview of the thermodynamic properties, the impact of nucleobase modifications within the catalytic loop, and the role of different metal ions in catalysis. We point out features that will be helpful in developing novel strategies for structure determination and to understand the mechanism of the 10-23 DNAzyme. Consideration of these features will enable to develop improved strategies for structure determination and to understand the mechanism of the 10-23 DNAzyme. These insights provide the basis for improving activity in cells and pave the way for developing DNAzyme applications.

Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.