An Oligo-Library-Based Approach for Mapping DNA-DNA Triplex Interactions In Vitro

Recent Progress of Triplex DNA Formation and Its Applications

Recently, much attention has been focused on oligonucleotide drugs that precisely control the gene expression. Among these, triplex-forming oligonucleotides (TFOs) represent common antigene strategies because they bind specifically to the major groove position of genomic DNA to form a triplex DNA structure. Thus far, this promising triplex formation technique represents a successful strategy with strong application prospects for gene manipulation applications (e.g., cancer, Huntington's disease, inflammatory disease, etc.), analytical detection (e.g., nucleic acid, small molecules, etc.), and nanotechnology (e.g., molecular machines, etc.). This review summarizes in detail the full range of potential applications described above, particularly the various chemical modification strategies that have facilitated the stepwise advancement of TFO-based oligonucleotide drugs in recent years to improve the effectiveness, specificity, and applicability of triplex DNA and synergistically promote the effectiveness of triplex DNA.

5-Substituted Flavones-Another Class of Potent Triplex DNA-Specific Ligands as Antigene Enhancers

In the field of drug development, the quest for novel compounds that bind to DNA with high affinity and specificity never ends. In the present work, we report the newest development in this field, namely, triplex DNA-specific binding ligands based on the 5-substituted flavone scaffold in our lab. Biophysical studies showed that the newly synthesized flavone derivatives (depending on the side chains) bind to triplex DNA with binding affinities better than or similar to 5-substituted 3,3',4',7-tetramethoxyflavonoids. These compounds selectively stabilize triplex DNA while having little effect on duplex DNA, as verified by various biophysical methods. A detailed structural analysis suggested that the binding of these compounds to triplex DNA depends on the type of amino groups in the side chains and the length of the side chains. Viscosity studies suggested that these ligands bind to triplex DNA via intercalation. A representative ligand, compound 4b, showed a positive inhibitory effect on the activity of a restriction endonuclease (DraI) via ligand-mediated triplex formation. Several of these compounds exhibited excellent cytotoxicity toward various cancer cell lines (HT-29, HCT116, and HL-60), as indicated by the MTT assay. The work presented here is part of a continued effort from our laboratory to explore the novel structural motifs of natural product flavonoids for the development of triplex-specific ligands as antigene enhancers.

RNA-DNA triplexes: molecular mechanisms and functional relevance

Interactions of RNA with DNA are principles of gene expression control that have recently gained considerable attention. Among RNA-DNA interactions are R-loops and RNA-DNA hybrid G-quadruplexes, as well as RNA-DNA triplexes. It is proposed that RNA-DNA triplexes guide RNA-associated regulatory proteins to specific genomic locations, influencing transcription and epigenetic decision making. Although triplex formation initially was considered solely an in vitro event, recent progress in computational, biochemical, and biophysical methods support in vivo functionality with relevance for gene expression control. Here, we review the central methodology and biology of triplexes, outline paradigms required for triplex function, and provide examples of physiologically important triplex-forming long non-coding RNAs.

Integration of DNA-RNA-triplex-based regulation of transcription into molecular logic gates

In recent years, increasing numbers of noncoding RNA molecules were identified as possible components of endogenous DNA-RNA hybrid triplexes involved in gene regulation. Triplexes are potentially involved in complex molecular signaling networks that, if understood, would allow the engineering of biological computing components. Here, by making use of the enhancing and inhibiting effects of such triplexes, we demonstrate in vitro the construction of triplex-based molecular gates: 'exclusive OR' (XOR), 'exclusive NOT-OR' (XNOR), and a threshold gate, via transcription of a fluorogenic RNA aptamer. Precise modulation was displayed by the biomolecular-integrated systems over a wide interval of transcriptional outputs, ranging from drastic inhibition to significant enhancement. The present contribution represents a first example of molecular gates developed using DNA-RNA triplex nanostructures.

TripDesign: A DNA Triplex Design Approach Based on Interaction Forces

A DNA triplex has the advantages of improved nanostructure stability and pH environment responsiveness compared with single-stranded and double-stranded nucleic acids. However, sequence stability and low design efficiency hinder the application of DNA triplexes. Therefore, a DNA triplex design approach (TripDesign) based on interaction forces is proposed. First, we present the stacking force constraint, torsional stress constraint, and G-quadruplex motif constraint and then use an improved memetic algorithm to design triplex sequences under combinatorial constraints. Finally, to quantify the process of triplex formation, we also explore the minimum length of the triplex-forming oligos (TFOs) required to form the triplex and the factors that produce depletion in cyclic pH-jump experiments. The experimental results show that the sequences produced by TripDesign have high stability and reversibility, and the proposed approach achieves efficient and automatic sequence design. In addition, this study characterizes multiple basic parameters of DNA triplex formation and promotes the wider application of DNA triplexes in nanotechnology.

Molecular and experimental tools to design synthetic enhancers

Understanding the grammar of enhancers and how they regulate gene expression is key for both basic research and for the pharma and biotech industries. The design and characterization of synthetic enhancers can expand the known regulatory space. This is achieved by the utilization of DNA Oligo Libraries (OLs), which facilitates screening of as many as millions of synthetic enhancer variants simultaneously. This review includes the latest commercial DNA OL synthesis technology and its capabilities, and a general 'know-how' guide for the design, construction, and analysis of OL-based synthetic enhancer characterization experiments. Specifically, we focus on synthetic-enhancer-based massively parallel reporter assay, Sort-seq methodologies (e.g. flow cytometry, deep sequencing), and a brief description of machine learning-based attempts for OL-analysis and follow-up validation experiments.