Supramolecular DNA Three-Way Junction Motifs With a Bridging Metal Center

DNA three-way junction structures with amino acid side chains prepared via post-synthetic amide condensation

DNA three-way junction (3WJ) structures with three amino acid side chains in the core have been synthesized via post-synthetic DNA modification. Amide condensation reactions of oligonucleotides containing 2'-aminouridine with activated esters yielded DNA strands modified with His, Cys and Asp side chains to form modified 3WJs. Even a 3WJ with three negatively charged Asp side chains formed stably at room temperature. Furthermore, DNA hybridization alone placed two (His and Asp) and three (His, Cys, and Asp) side chains within the 3WJs, indicating that the DNA 3WJs are a useful platform for spatial arrangement of amino acid side chains.

Design and Characterization of Compact, Programmable, Multistranded Nonimmunostimulatory Nucleic Acid Nanoparticles Suitable for Biomedical Applications

We report a thorough investigation of the role of single-stranded thymidine (ssT) linkers in the stability and flexibility of minimal, multistranded DNA nanostructures. We systematically explore the impact of varying the number of ssTs in three-way junction motifs (3WJs) on their formation and properties. Through various UV melting experiments and molecular dynamics simulations, we demonstrate that while the number of ssTs minimally affects thermodynamic stability, the increasing ssT regions significantly enhance the structural flexibility of 3WJs. Utilizing this knowledge, we design triangular DNA nanoparticles with varying ssTs, all showing exceptional assembly efficiency except for the 0T triangle. All triangles demonstrate enhanced stability in blood serum and are nonimmunostimulatory and nontoxic in mammalian cell lines. The 4T 3WJ is chosen as the building block for constructing other polygons due to its enhanced flexibility and favorable physicochemical characteristics, making it a versatile choice for creating cost-effective, stable, and functional DNA nanostructures that can be stored in the dehydrated forms while retaining their structures. Our study provides valuable insights into the design and application of nucleic acid nanostructures, emphasizing the importance of understanding stability and flexibility in the realm of nucleic acid nanotechnology. Our findings suggest the intricate connection between these ssTs and the structural adaptability of DNA 3WJs, paving the way for more precise design and engineering of nucleic acid nanosystems suitable for broad biomedical applications.

Triplet Excimer Formation in a DNA Duplex with Silver Ion-Mediated Base Pairs

The dynamics of excited electronic states in self-assembled structures formed between silver(I) ions and cytosine-containing DNA strands or monomeric cytosine derivatives were investigated by time-resolved infrared (TRIR) spectroscopy and quantum mechanical calculations. The steady-state and time-resolved spectra depend sensitively on the underlying structures, which change with pH and the nucleobase and silver ion concentrations. At pH ∼ 4 and low dC20 strand concentration, an intramolecularly folded i-motif is observed, in which protons, and not silver ions, mediate C-C base pairing. However, at the higher strand concentrations used in the TRIR measurements, dC20 strands associate pairwise to yield duplex structures containing C-Ag+-C base pairs with a high degree of propeller twisting. UV excitation of the silver ion-mediated duplex produces a long-lived excited state, which we assign to a triplet excimer state localized on a pair of stacked cytosines. The computational results indicate that the propeller-twisted motifs induced by metal-ion binding are responsible for the enhanced intersystem crossing that populates the triplet state and not a generic heavy atom effect. Although triplet excimer states have been discussed frequently as intermediates in the formation of cyclobutane pyrimidine dimers, we find neither computational nor experimental evidence for cytosine-cytosine photoproduct formation in the systems studied. These findings provide a rare demonstration of a long-lived triplet excited state that is formed in a significant yield in a DNA duplex, demonstrating that supramolecular structural changes induced by metal ion binding profoundly affect DNA photophysics.

Photoreactive silver-containing supramolecular polymers that form self-assembled nanogels for efficient antibacterial treatment

In this study, an efficient synthetic strategy and potential route to obtain a photo-reactive silver-containing cytosine-functionalized polypropylene glycol polymer (Ag-Cy-PPG) was developed by combining a hydrophilic oligomeric polypropylene glycol (PPG) backbone with dual pH-sensitive/photo-reactive cytosine-silver-cytosine (Cy-Ag-Cy) linkages. The resulting photo-responsive Ag-Cy-PPG holds great promise as a multifunctional biomedical material that generates spherical-like nanogels in water; the nanogels exhibit high antibacterial activity and thus may significantly enhance the efficacy of antibacterial treatment. Due to the formation of photo-dimerized Cy-Ag-Cy cross-linkages after UV irradiation, Ag-Cy-PPG converts into water-soluble cross-linked nanogels that possess a series of interesting chemical and physical properties, such as intense and stable fluorescence behavior, highly sensitive pH-responsive characteristics, on/off switchable phase transition behavior, and well-controlled release of silver ions (Ag+) in mildly acidic aqueous solution. Importantly, antibacterial tests clearly demonstrated that irradiated Ag-Cy-PPG nanogels exhibited strong antibacterial activity at low doses (MIC values of < 50 μg/mL) against gram-positive and gram-negative bacterial pathogens, whereas non-irradiated Ag-Cy-PPG nanogels did not inhibit the viability of bacterial pathogens. These results indicate that irradiated Ag-Cy-PPG nanogels undergo a highly sensitive structural change in the bacterial microenvironment due to their relatively unstable π-conjugated structures (compared to non-irradiated nanogels); this change results in a rapid structural response that promotes intracellular release of Ag+ and induces potent antibacterial ability. Overall, this newly created metallo-supramolecular system may potentially provide an efficient route to dramatically enhance the therapeutic effectiveness of antibacterial treatments.

Phenanthroline-modified DNA three-way junction structures stabilized by interstrand 3 : 1 metal complexation

Incorporation of interstrand metal complexes into DNA is a versatile strategy for metal-dependent stabilization and structural induction of DNA supramolecular structures. In this study, we have synthesized DNA three-way junction (3WJ) structures modified with phenanthroline (phen) ligands. The phen-modified 3WJ was found to be thermally stabilized (ΔTm = +16.9 °C) by the formation of an interstrand NiII(phen)3 complex. Furthermore, NiII-mediated structure induction of 3WJs was demonstrated with the phen-modified strands and their unmodified counterparts. This study suggests that ligand-modified 3WJs would be useful structural motifs for the construction of metal-responsive DNA molecular systems.

Bipyridine-Modified DNA Three-Way Junctions with Amide linkers: Metal-Dependent Structure Induction and Self-Sorting

DNA three-way junction (3WJ) structures are essential building blocks for the construction of DNA nanoarchitectures. We have synthesized a bipyridine (bpy)-modified DNA 3WJ by using a newly designed bpy-modified nucleoside, U_bpy -3, in which a bpy ligand is tethered via a stable amide linker. The thermal stability of the bpy-modified 3WJ was greatly enhanced by the formation of an interstrand Ni^II (bpy)₃ complex at the junction core (ΔT_m =+17.7 °C). Although the stereochemistry of the modification site differs from that of the previously reported bpy-modified nucleoside U_bpy -2, the degree of the Ni^II -mediated stabilization observed with U_bpy -3 was comparable to that of U_bpy -2. Structure induction of the 3WJs and the duplexes was carried out by the addition or removal of Ni^II ions. Furthermore, Ni^II -mediated self-sorting of 3WJs was performed by using the bpy-modified strands and their unmodified counterparts. Both transformations were driven by the formation of Ni^II (bpy)₃ complexes. The structural induction and self-sorting of bpy-modified 3WJs are expected to have many potential applications in the development of metal-responsive DNA materials.

Metal-responsive reversible binding of triplex-forming oligonucleotides with 5-hydroxyuracil nucleobases

Metal-responsive triplex-forming oligonucleotides (TFOs) were synthesised by incorporating 5-hydroxyuracil (UOH) nucleobases as metal recognition sites. Binding of the UOH-containing TFO to the target natural DNA duplexes was reversibly regulated by the addition and removal of GdIII ions under isothermal conditions.

Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry

This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.

Toehold-Mediated Selective Assembly of Compact Discrete DNA Nanostructures

Production of small discrete DNA nanostructures containing covalent junctions requires reliable methods for the synthesis and assembly of branched oligodeoxynucleotide (ODN) conjugates. This study reports an approach for self-assembly of hard-to-obtain primitive discrete DNA nanostructures-"nanoethylenes", dimers formed by double-stranded oligonucleotides using V-shaped furcate blocks. We scaled up the synthesis of V-shaped oligonucleotide conjugates using pentaerythritol-based diazide and alkyne-modified oligonucleotides using copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) and optimized the conditions for "nanoethylene" formation. Next, we designed nanoethylene-based "nanomonomers" containing pendant adapters. They demonstrated smooth and high-yield spontaneous conversion into the smallest cyclic product, DNA tetragon aka "nano-methylcyclobutane". Formation of DNA nanostructures was confirmed using native polyacrylamide gel electrophoresis (PAGE) and atomic force microscopy (AFM) and additionally studied by molecular modeling. The proposed facile approach to discrete DNA nanostructures using precise adapter-directed association expands the toolkit for the realm of DNA origami.

Silver assisted stereo-directed assembly of branched peptide nucleic acids into four-point nanostars

Branched chiral peptide nucleic acids br(4S/R)-PNA with three arms of PNA-C4 strands were constructed on a central chiral core of 4(R/S)-aminoproline as the branching center. The addition of Ag+ triggered the self-assembly of branched PNAs through the formation of C-Ag+-C metallo base pairing of the three PNA C4 arms leading to non-covalent dendrimers, whose architecture is directed by the C4(R/S)-stereocenter of core 4-aminoproline. The 4S-aminoprolyl core enabled the precise formation of four-pointed nanostars that was not realised with 4R-aminoprolyl or acyclic, achiral aminoethyl glycyl PNA cores. The dendritic assembly of 4 pointed nanostars exhibited net chirality of base stacks in CD spectra, while the base stack assembly from br(4R)-PNA 2 was overall achiral. The results demonstrate that the silver assisted, 4S-aminoproline core stereo selective chiral assembly of branched PNAs manifests into nanostar morphology. The chiral branched PNAs open new vistas in the supramolecular organization of nucleic acids.