Metal–base pairing in DNA

Design and demonstration of a temperature-resistant aptamer structure for highly sensitive mercury ion detection with BioFETs

In this study, we developed a temperature-resistant aptamer coupled with extended gate electric double-layer Field-Effect Transistors (FETs) for highly sensitive mercury ion detection. The design of the temperature-resistant aptamer is based on the thermal and structural properties of the hairpin structure. Two aptamer sequences were designed with different melting temperatures (Tm) and compared for their sensitivity. The hairpin structure of the aptamer with a high melting temperature ensures the stable structure prior to the addition of the mercury ions, which allows the formation of thymine-mercury-thymine (T -Hg2+-T) complex in low concentrations of mercury ions. High sensitivity and low detection limit are achieved at elevated temperatures with the aptamer having a high melting temperature. The elevated temperature facilitates the reaction rate, resulting in high sensitivity and a low detection limit. The aptamer with a high melting temperature hairpin structure has shown a remarkable improvement in the limit of detection with a 4 orders of magnitude increase compared to the one with a low melting temperature. The sensor with the high melting temperature aptamer shows an extremely low detection limit of 4.68 × 10-12 M, surpassing previously reported results. The aptamer with a low melting temperature requires mercury ions to stabilize the hairpin structure by forming a T-Hg2+-T complex. The results show that if the melting temperature is lower than the ambient temperature, it is very difficult to detect low concentrations of mercury ions at the ambient temperature. The selectivity of this sequence was also tested against multiple heavy metals, including arsenic (As), lead (Pb), chromium (Cr), and cadmium (Cd) ions. This study has shown how the structural and thermal properties of the aptamer, and the ambient temperature affect the sensitivity. They are strongly correlated to the performance of the sensors and need to be considered in the design of the sequence.

Recent progress in nanomaterial-based aptamers as biosensors for point of care detection of Hg2+ ions and its environmental applications

Among the foremost persistent heavy metal ions in the ecosystem, mercury (Hg2+) remains intimidating to the environment by producing a catastrophic effect on the environment as well as on mankind due to the exacerbation of anthropogenic activities. Therefore, it has become necessary to develop superlative techniques for its detection even at low concentrations. The conventional approaches for Hg2+ ions are quite laborious, and expensive, and require expertise in operating sophisticated instruments. To overcome these limitations, aptamer-based biosensors emerged as a promising tool for its detection. DNA-based aptamers have evolved as a significant technique by detecting them even in ppb levels. This review outlines the progress in aptamer-based biosensors from the year 2019-2023 by inducing changes in the electrochemical signal or by fluorescent/colorimetric approaches. The electrochemical sensors used nanomaterial electrodes for increasing the sensitivity whereas fluorescent and colorimetric sensors exhibit quenching or strong fluorescence in the presence of Hg2+ ions depending upon the prevailing mechanism or visible color changes. This perturbation in the signals could be attributed to the formation of the T-Hg2+ -T complex with the aptamers in the presence of ions revealing its real-time and biological applications in living or cancerous cells. Furthermore, next-generation biosensors are suggested to bring a paradigm shift to the integration of high-end smartphones, machine learning, artificial intelligence, etc.

Role of Alkali Cations in DNA-Thioflavin T Interaction

This study investigates the role of alkali cations in modulating the interaction between deoxyribonucleic acid (DNA) and Thioflavin T (ThT) in dilute and condensed phases. The emission characteristics of ThT were analyzed in the presence of double-stranded DNA and G-quadruplex structures with a focus on the effects of four cations: sodium, potassium, calcium, and magnesium. The ThT emission in double-stranded DNA was influenced by direct DNA binding and steric hindrance within the hydration shell of DNA, which was modulated by the presence of alkali cations. Lasing spectroscopy experiments further highlighted ThT sensitivity to the spatial arrangement of water molecules in the DNA hydration shell. Lasing was exclusively observed in the presence of Mg2+ in the G-quadruplex structure, suggesting that the parallel propeller configuration of G4 provides an optimal environment for ThT light amplification. This study highlights the critical role of cations in DNA-dye interactions and reaffirms the significance of ThT in biophysical studies.

Antidiabetic Close Loop Based on Wearable DNA-Hydrogel Glucometer and Implantable Optogenetic Cells

Diabetes mellitus and its associated secondary complications have become a pressing global healthcare issue. The current integrated theranostic plan involves a glucometer-tandem pump. However, external condition-responsive insulin delivery systems utilizing rigid glucose sensors pose challenges in on-demand, long-term insulin administration. To overcome these challenges, we present a novel model of antidiabetic management based on printable metallo-nucleotide hydrogels and optogenetic engineering. The conductive hydrogels were self-assembled by bioorthogonal chemistry using oligonucleotides, carbon nanotubes, and glucose oxidase, enabling continuous glucose monitoring in a broad range (0.5-40 mM). The optogenetically engineered cells were enabled glucose regulation in type I diabetic mice via a far-red light-induced transgenic expression of insulin with a month-long avidity. Combining with a microchip-integrated microneedle patch, a prototyped close-loop system was constructed. The glucose levels detected by the sensor were received and converted by a wireless controller to modulate far-infrared light, thereby achieving on-demand insulin expression for several weeks. This study sheds new light on developing next-generation diagnostic and therapy systems for personalized and digitalized precision medicine.

Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction

DNA double helices containing metal-mediated DNA (mmDNA) base pairs are constructed from Ag+ and Hg2+ ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials is impractical without a complete lexical and structural description. Here, the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination is explored. The tensegrity triangle is employed to build a comprehensive structural library of mmDNA pairs via X-ray diffraction and generalized design rules for mmDNA construction are elucidated. Two binding modes are uncovered: N3-dominant, centrosymmetric pairs and major groove binders driven by 5-position ring modifications. Energy gap calculations show additional levels in the lowest unoccupied molecular orbitals (LUMO) of mmDNA structures, rendering them attractive molecular electronic candidates.

Structural and Thermodynamic Control of Supramolecular Polymers and DNA Assemblies with Cyanuric Acid: Influence of Substituents and Intermolecular Interactions

Understanding the interactions and thermodynamic parameters that govern the structure and stability of supramolecular polymers is challenging because of their flexible nature and high sensitivity to weak intermolecular interactions. The application of both experimental and computational analyses reveals the role that substituents on cyanuric acid (Cy), and other nitrogen-containing heterocycles, play in the formation of novel helical supramolecular structures. In this report, we focus on how noncovalent interactions, including steric and stacking interactions, modulate the structural and physical properties of these assemblies. In-depth analyses and several examples of critical steric and electrostatic effects provide insight into the relationship between intermolecular interactions of Cy with nucleic acids and the structure and thermodynamic stability of the supramolecular polymers they form.

Intramolecular Folding of PolyT Oligonucleotides Induced by Cooperative Binding of Silver(I) Ions

Ag⁺-bridged T-Ag⁺-T was recently discovered in a Ag⁺-DNA nanowire crystal, but it was reported that Ag⁺ had little to no affinity to T nucleobases and T-rich oligonucleotides in solution. Therefore, the binding mode for the formation of this type of novel metallo base pair in solution is elusive. Herein, we demonstrate that Ag⁺ can interact with polyT oligonucleotides once the concentration of Ag⁺ in solution exceeds a threshold value. The threshold value is independent of the concentration of the polyT oligonucleotide but is inversely proportional to the length of the polyT oligonucleotide. The polyT oligonucleotides are intramolecularly folded due to their positively cooperative formation and the stack of T-Ag⁺-T base pairs, resulting in the 5'- and 3'-ends being in close proximity to each other. The intramolecular Ag⁺-folded polyT oligonucleotide has a higher thermal stability than the duplex and can be reversibly modulated by cysteine.

N-Methoxy-1,3-oxazinane nucleic acids (MOANAs) - a configurationally flexible backbone modification allows post-synthetic incorporation of base moieties

(2R,3S)-4-(Methoxyamino)butane-1,2,3-triol was converted into a protected phosphoramidite building block and incorporated into the middle of a short DNA oligonucleotide. O1 and O3 of the (2R,3S)-4-(methoxyamino)butane-1,2,3-triol were engaged in phosphodiester linkages, leaving O2 and the methoxyamino function available to form an N-methoxy-1,3-oxazinane ring through reaction with an aldehyde. In modified oligonucleotides thus obtained, the oxazinane ring formally replaces the furanose ring and the aldehyde, the base moiety of natural nucleosides. The feasibility of synthesizing base-modified oligonucleotides by this approach was demonstrated with several aromatic and aliphatic aldehydes featuring various functional groups.

DNA Templated Silver Nanoclusters for Bioanalytical Applications: A Review

Due to their unique programmability, biocompatibility, photostability and high fluorescent quantum yield, DNA templated silver nanoclusters (DNA Ag NCs) have attracted increasing attention for bioanalytical application. This review summarizes the recent developments in fluorescence properties of DNA templated Ag NCs, as well as their applications in bioanalysis. Finally, we herein discuss some current challenges in bioanalytical applications, to promote developments of DNA Ag NCs in biochemical analysis.

Magnesium ions reversibly bind to DNA double stranded helix in thin films

Effects of magnesium (Mg²⁺) ions on the stability and structural properties of double-stranded DNA are vitally important for DNA folding and functional behavior. Complementing our previous study on highly hydrated thin films of DNA with sodium counterions, with no buffer (pH ≈ 6) and surrounded with Mg²⁺ cations, here we use Fourier transform infrared spectroscopy and band shape analysis to explore in detail the vibrational signatures of DNA-magnesium interaction in the case when DNA charges are neutralized solely by Mg²⁺ cations, hereafter called MgDNA. Ion atmosphere has been controlled by the magnesium to phosphate molar concentration ratio r which varied between 0.0067 and 10. For r = 0 we find that spectral features in the base region remain similar as in DNA, whereas changes in the backbone region indicate that the B conformation becomes fully stabilized. With increasing r a pronounced structural reshaping occurs in the phosphate backbone region indicating a blue shift of the asymmetric band, while the symmetric band does not show any displacement in frequency. The band shape analysis of overlapping peaks in the respective phosphate regions demonstrates that the number of constituent modes as well as their positions in frequency do not change, whereas their intensities and bandwidths display disparate changes. The results reflect a variety of local environments at the DNA backbone due to a heterogeneous ion atmosphere with randomly distributed magnesium ions and local patterns of hydrogen bonds which change with increasing r. Remarkably, after crowded r = 10 ion atmosphere is depleted, Mg induced spectral changes vanish and structural features of MgDNA (r ≈ 0) are fully restored. Overall results strongly suggest that in MgDNA on highly hydrated thin films the hydrogen-base pairing remains preserved and that Mg²⁺ ions, similar to sodium ions, retain their mobility and interact with double helix via water-mediated electrostatic forces.

Solvent and Counteranion Assisted Dynamic Self-Assembly of Molecular Triangles and Tetrahedral Cages

Self-assembly of naked Pd^II ions separately with newly designed bis(3-pyridyl)benzothiadiazole (L1) and bis(3-pyridyl)thiazolo[5,4-d]thiazole (L2) donors separately, under varying experimental conditions, yielded Pd₄L₈ (L= L1 or L2) tetrahedral cages and their homologous Pd₃L₆ (L= L1 or L2) double-walled triangular macrocycles. The resulting assemblies exhibited solvent, temperature, and counteranion induced dynamic equilibrium. Treatment of L1 with Pd(BF₄)₂ in acetonitrile (ACN) resulted in selective formation of a tetrahedral cage [Pd₄(L1)₈](BF₄)₈ (1a), which is in dynamic equilibrium with its homologue triangle [Pd₃(L1)₆](BF₄)₆ (2a) in dimethyl sulfoxide (DMSO). On the other hand, similar self-assembly using L2 instead of L1 yielded an equilibrium mixture of tetrahedral cage [Pd₄(L2)₈](BF₄)₈ (3a) and triangle [Pd₃(L2)₆](BF₄)₆ (4a) forms in both ACN and DMSO. The assembles were characterized by multinuclear NMR and ESI-MS while the structure of the tetrahedral cage (1a) was determined by single crystal X-ray diffraction. Existence of a dynamic equilibrium between the assemblies in solution has been investigated via variable temperature ¹H NMR. The equilibrium constant K = ([Pd₄L₈]³/[Pd₃L₆]⁴) was calculated at each experimental temperature and fitted with the Van't Hoff equation to determine the standard enthalpy (ΔH°) and entropy (ΔS°) associated with the interconversion of the double-walled triangle to tetrahedral cage. The thermodynamic feasibility of structural interconversion was analyzed from the change in ΔG°, which suggests favorable conversion of Pd₃L₆ triangle to Pd₄L₈ cage at elevated temperature for L1 in DMSO and L2 in ACN. Interestingly, similar self-assembly reactions of L1 and L2 with Pd(NO₃)₂ instead of Pd(BF₄)₂ resulted in selective formation of a tetrahedral cage [Pd₄(L1)₈](NO₃)₈ (1b) and double-walled triangle [Pd₃(L2)₆](NO₃)₆ (4b), respectively.

2-Trifluoromethyl-6-mercurianiline Nucleotide, a Sensitive 19F NMR Probe for Hg(II)-mediated Base Pairing

A 2-trifluoromethylaniline C-nucleoside was synthesized, incorporated in the middle of an oligonucleotide, and mercurated. The affinity of the mercurated oligonucleotide toward complementary strands placing each of the canonical nucleobases opposite to the organomercury nucleobase analogue was examined by ultraviolet (UV), circular dichroism (CD), and 19F NMR spectroscopy analyses. According to the UV melting profile analysis, the organomercury nucleobase analogue showed increased affinities in the order T > G > C > A. The CD profiles indicated the typical B-type helix in each case. The 19F resonance signal proved sensitive for the local environmental changes, showing clearly distinct signals for the duplexes with different opposing nucleobases. Furthermore, valuable information on the mercurated oligonucleotide and its binding to complementary strands at varying temperature could be obtained by 19F NMR spectroscopy.

Progress of metal nanoclusters in nucleic acid detection

The development and application of metal nanoclusters (MNCs) in nucleic acid testing in the past 10 years have been summarized. Fluorescence enhancement and red shift can occur when the G-rich sequence gets close to Ag NCs or the complementary DNA strand hybridizes with Ag NCs tail strand, which can be used to identify the nucleic acid. Ag NCs with the abasic site in DNA duplex can distinguish mutant genes such as cancer suppression gene p53. Ag NCs with auxiliary DNA can be used to detect miR-21, miR-16-5p, miR-19b-3p, and miR-141. Cu NCs/Cu NPs can recognize miRNA-155, miR-21, and miR-let-7d without auxiliary DNA. Au NCs can identify H1N1 gene fragments by fluorescence quenching caused by proximity to the G-rich sequence. Besides, Au NCs can recognize miRNA-21 and let-7a. SsDNA MNCs adsorbed on the surface of GO and CNPs oxide can be used to identify HBV and HIV gene fragments. The addition of enzymes or auxiliary amplification technologies is a popular way to improve probe sensitivity. Ag NCs combined with TAIEA has the best performance and can obtain LOD as low as aM for miRNA.

Electronic Level Structure of Novel Guanine Octuplex DNA Single Molecules

Throughout the past few decades, guanine quadruplex DNA structures have attracted much interest both from a fundamental material science perspective and from a technologically oriented perspective. Novel guanine octuplex DNA, formed from coiled quadruplex DNA, was recently discovered as a stable and rigid DNA-based nanostructure. A detailed electronic structure study of this new nanomaterial, performed by scanning tunneling spectroscopy on a subsingle-molecule level at cryogenic temperature, is presented herein. The electronic levels and lower energy gap of guanine octuplex DNA compared to quadruplex DNA dictate higher transverse conductivity through guanine octads than through guanine tetrads.

Chemical reduction of Ag+ to Ag employing organic electron donors: evaluation of the effect of Ag+-mediated cytosine-cytosine base pairing on the aggregation of Ag nanoparticles

Ag⁺-mediated base pairing is valuable for synthesising DNA-based silver nanoparticles (AgNPs) and nanoclusters (AgNCs). Recently, we reported the formation of a [Ag(cytidine)₂]⁺ complex in dimethyl sulfoxide (DMSO), which facilitated the evaluation of the effect of cytosine-Ag⁺-cytosine (C-Ag⁺-C) base pairing on the degree of AgNP aggregation in solution. As an aprotic solvent, DMSO was expected to dissolve the [Ag(cytidine)₂]⁺ complex, and powerful reducing agents, such as organic electron donors. In this study, the chemical reduction of a cytidine/Ag⁺ system using a powerful reducing agent tetrakis(dimethylamino)ethylene (TDAE) was investigated. ¹H/¹³C/¹⁵N NMR spectroscopic evidence was obtained to identify the iminium dication (TDAE²⁺), which is an oxidised form of TDAE. The results were compared with those obtained using another organic electron donor, tetrathiafulvalene (TTF), which exhibits a relatively lower reduction activity than TDAE. AgNPs prepared via redox reaction between [Ag(cytidine)₂]⁺ and organic electron donors (TDAE and TTF) were characterised using UV-Vis spectroscopy and nanoparticle tracking analysis. It was found that the formation of C-Ag⁺-C base pairing inhibited the aggregation of AgNPs in solution. In addition, in the presence of cytidine, the total concentration of the AgNP solution was affected by the reduction activity of the reducing agent.

Effect of cytosine-Ag+-cytosine base pairing on the redox potential of the Ag+/Ag couple and the chemical reduction of Ag+ to Ag by tetrathiafulvalene

The redox properties of metallo-base pairs remain to be elucidated. Herein, we report the detailed 1H/13C/109Ag NMR spectroscopic and cyclic voltammetric characterisation of the [Ag(cytidine)2]+ complex as isolated cytosine-Ag+-cytosine (C-Ag+-C) base pairs. We also performed comparative studies between cytidine/Ag+ and other nucleoside/Ag+ systems by using cyclic voltammetry measurements. In addition, to evaluate the effect of [Ag(cytidine)2]+ formation on the chemical reduction of Ag+ to Ag, we utilised the redox reaction between Ag+ and tetrathiafulvalene (TTF). We found that Ag+-mediated base pairing lowers the redox potential of the Ag+/Ag couple. In addition, C-Ag+-C base pairing makes it more difficult to reduce captured Ag+ ions than in other nucleoside/Ag+ systems. Remarkably, the cytidine/Ag+ system can be utilised to control the redox potential of the Ag+/Ag couple in DMSO. This feature of the cytidine/Ag+ system may be exploited for Ag nanoparticle synthesis by using the redox reaction between Ag+ and TTF.

Development, Preparation, and Biomedical Applications of DNA-Based Hydrogels

Hydrogels have outstanding research and application prospects in the biomedical field. Among them, the design and preparation of biomedical hydrogels with deoxyribonucleic acid (DNA) as building blocks have attracted increasing research interest. DNA-based hydrogel not only has the skeleton function of hydrogel, but also retains its biological functions, including its excellent selection specificity, structural designability, precise molecular recognition ability, outstanding biocompatibility, and so on. It has shown important application prospects in the biomedical field, such as drug delivery, biosensing, and tissue engineering. In recent years, researchers have made full use of the characteristics of DNA molecules and constructed various pure DNA-based hydrogels with excellent properties through various crosslinking methods. Moreover, via introducing functional molecules or elements, or combining with other functional materials, a variety of multifunctional DNA-based hybrid hydrogels have also been constructed, which expand the breadth and depth of their applications. Here, we described the recent development trend in the area of DNA-based hydrogels and highlighted various preparation methods of DNA-based hydrogels. Representative biomedical applications are also exemplified to show the high performance of DNA-based hydrogels. Meanwhile, the existing problems and prospects are also summarized. This review provided references for the further development of DNA-based hydrogels.

Sequence dependence of Pd(II)-mediated base pairing by palladacyclic nucleobase surrogates

A C-nucleoside derivative of phenylpyridine or the respective palladacycle was incorporated at either 3'- or 5'-terminus of a short oligodeoxynucleotide. Hybridization properties of these modified oligonucleotides were studied in a fluorescence-based competition assay in addition to conventional UV melting temperature analysis and compared with those of a previously prepared analogue featuring the modified nucleoside in the middle of the sequence. With the unpalladated phenylpyridine oligonucleotides, UV melting temperature qualitatively correlated with the ability to displace a strand from a double helix in the competition assay, decreasing in the order 5' > 3' > middle. Corresponding results on the palladacyclic oligonucleotides were more difficult to interpret but both UV melting and competition experiments revealed a decrease in the duplex stability upon palladation in most cases. On the other hand, dependence of the UV melting temperature on the identity of the canonical nucleobase opposite to the modified nucleobase analogue was much more pronounced with the palladacyclic duplexes than with their unpalladated counterparts. Furthermore, UV melting profiles of the palladacyclic duplexes featured an additional transition at a temperature exceeding the melting temperature of the unmodified part of the duplex. Taken together, these results lend support to the idea of Pd(II)-mediated base pairs that are highly stable but incompatible with the geometry of a double helix.

Organomercury Nucleic Acids: Past, Present and Future

Synthetic efforts towards nucleosides, nucleotides, oligonucleotides and nucleic acids covalently mercurated at one or more of their base moieties are summarized, followed by a discussion of the proposed, realized and abandoned applications of this unique class of compounds. Special emphasis is given to fields in which active research is ongoing, notably the use of HgII -mediated base pairing to improve the hybridization properties of oligonucleotide probes. Finally, this minireview attempts to anticipate potential future applications of organomercury nucleic acids.

Enzymatic construction of metal-mediated nucleic acid base pairs

Artificial metal base pairs have become increasingly important in nucleic acids chemistry due to their high thermal stability, water solubility, orthogonality to natural base pairs, and low cost of production. These interesting properties combined with ease of chemical and enzymatic synthesis have prompted their use in several practical applications, including the construction of nanomolecular devices, ions sensors, and metal nanowires. Chemical synthesis of metal base pairs is highly efficient and enables the rapid screening of novel metal base pair candidates. However, chemical synthesis is limited to rather short oligonucleotides and requires rather important synthetic efforts. Herein, we discuss recent progress made for the enzymatic construction of metal base pairs that can alleviate some of these limitations. First, we highlight the possibility of generating metal base pairs using canonical nucleotides and then describe how modified nucleotides can be used in this context. We also provide a description of the main analytical techniques used for the analysis of the nature and the formation of metal base pairs together with relevant examples of their applications.

Functional Nucleic Acid Nanomaterials: Development, Properties, and Applications

Functional nucleic acid (FNA) nanotechnology is an interdisciplinary field between nucleic acid biochemistry and nanotechnology that focuses on the study of interactions between FNAs and nanomaterials and explores the particular advantages and applications of FNA nanomaterials. With the goal of building the next-generation biomaterials that combine the advantages of FNAs and nanomaterials, the interactions between FNAs and nanomaterials as well as FNA self-assembly technologies have established themselves as hot research areas, where the target recognition, response, and self-assembly ability, combined with the plasmon properties, stability, stimuli-response, and delivery potential of various nanomaterials can give rise to a variety of novel fascinating applications. As research on the structural and functional group features of FNAs and nanomaterials rapidly develops, many laboratories have reported numerous methods to construct FNA nanomaterials. In this Review, we first introduce some widely used FNAs and nanomaterials along with their classification, structure, and application features. Then we discuss the most successful methods employing FNAs and nanomaterials as elements for creating advanced FNA nanomaterials. Finally, we review the extensive applications of FNA nanomaterials in bioimaging, biosensing, biomedicine, and other important fields, with their own advantages and drawbacks, and provide our perspective about the issues and developing trends in FNA nanotechnology.

Structure and luminescence of DNA-templated silver clusters

DNA serves as a versatile template for few-atom silver clusters and their organized self-assembly. These clusters possess unique structural and photophysical properties that are programmed into the DNA template sequence, resulting in a rich palette of fluorophores which hold promise as chemical and biomolecular sensors, biolabels, and nanophotonic elements. Here, we review recent advances in the fundamental understanding of DNA-templated silver clusters (Ag N -DNAs), including the role played by the silver-mediated DNA complexes which are synthetic precursors to Ag N -DNAs, structure-property relations of Ag N -DNAs, and the excited state dynamics leading to fluorescence in these clusters. We also summarize the current understanding of how DNA sequence selects the properties of Ag N -DNAs and how sequence can be harnessed for informed design and for ordered multi-cluster assembly. To catalyze future research, we end with a discussion of several opportunities and challenges, both fundamental and applied, for the Ag N -DNA research community. A comprehensive fundamental understanding of this class of metal cluster fluorophores can provide the basis for rational design and for advancement of their applications in fluorescence-based sensing, biosciences, nanophotonics, and catalysis.

Self-assembled metallasupramolecular cages towards light harvesting systems for oxidative cyclization

Designing artificial light harvesting systems with the ability to utilize the output energy for fruitful application in aqueous medium is an intriguing topic for the development of clean and sustainable energy. We report here facile synthesis of three prismatic molecular cages as imminent supramolecular optoelectronic materials via two-component coordination-driven self-assembly of a new tetra-imidazole donor (L) in combination with 180°/120° di-platinum(ii) acceptors. Self-assembly of 180° trans-Pt(ii) acceptors A1 and A2 with L leads to the formation of cages Pt4 L 2(1a) and Pt8 L 2(2a) respectively, while 120°-Pt(ii) acceptor A3 with L gives the Pt8 L 2(3a) metallacage. PF6 - analogues (1b, 2b and 3b) of the metallacages possess a high molar extinction coefficient and large Stokes shift. 1b-3b are weakly emissive in dilute solution but showed aggregation induced emission (AIE) in a water/MeCN mixture as well as in the solid state. AIE active 2b and 3b in aqueous (90% water/MeCN mixture) medium act as donors for fabricating artificial light harvesting systems via Förster resonance energy transfer (FRET) with organic dye rhodamine-B (RhB) with high energy efficiency and good antenna effect. The metallacages 2b and 3b represent an interesting platform to fabricate new generation supramolecular aqueous light harvesting systems with high antenna effect. Finally, the harvested energy of the LHSs (2b + RhB) and (3b + RhB) was utilized successfully for efficient visible light induced photo-oxidative cross coupling cyclization of N,N-dimethylaniline (4) with a series of N-alkyl/aryl maleimides (5) in aqueous acetonitrile with dramatic enhancement in yields compared to the reactions with RhB or cages alone.

Metal-Mediated Base Pairing of Rigid and Flexible Benzaldoxime Metallacycles

Oligonucleotides incorporating a central C-nucleoside with either a rigid or flexible benzaldoxime base moiety have been synthesized, and the hybridization properties of their metallacyclic derivatives have been studied by UV melting experiments. In all cases, the metallated duplexes were less stable than their unmetallated counterparts, and the metallacyclic nucleobases did not show a clear preference for any of the canonical nucleobases as a base-pairing partner. With palladated oligonucleotides, increased flexibility translated to less severe destabilization, whereas the opposite was true for the mercurated oligonucleotides; this reflects the greater difficulties in accommodating a rigid PdII -mediated base pair than a rigid HgII -mediated base pair within the base stack of a double helix.

Electronic Level Structure of Silver-Intercalated Cytosine Nanowires

Metal-mediated base-paired DNA has long been investigated for basic scientific pursuit and for nanoelectronics purposes. Particularly attractive in these domains is the Ag⁺-intercalated polycytosine DNA duplex. Extensive studies of this molecule have led to our current understanding of its self-assembly properties, high thermodynamic and structural stability, and high longitudinal conductivity. However, a high-resolution morphological characterization of long Ag⁺-intercalated polycytosine DNA has hitherto not been carried out. Furthermore, the electronic level structure of this molecule has not been studied before. Here we present a scanning tunneling microscopy and spectroscopy study of this intriguing nanowire. Its temperature-independent morphological and electronic properties suggest substantial stability, while its emergent electronic levels and energy gap provide the basis for its high conductivity.

1,8-Dimercuri-6-Phenyl-1H-Carbazole as a Monofacial Dinuclear Organometallic Nucleobase

A C-nucleoside with 6-phenyl-1H-carbazole as the base moiety has been synthesized and incorporated in the middle of an oligonucleotide. Mercuration of this modified residue at positions 1 and 8 gave the first example of an oligonucleotide featuring a monofacial dinuclear organometallic nucleobase. The dimercurated oligonucleotide formed stable duplexes with unmodified oligonucleotides placing either cytosine, guanine, or thymine opposite to the organometallic nucleobase. A highly stabilizing (ΔT_m =7.3 °C) Hg^II -mediated base pair was formed with thymine. According to DFT calculations performed at the PBE0DH level of theory, this base pair is most likely dinuclear, with the two Hg^II ions coordinated to O2 and O4 of the thymine base.

Role of the backbone of nucleic acids in the stability of Hg2+-mediated canonical base pairs and thymine–thymine mispair: a DFT study

Metal-mediated base pairs have attracted attention in nucleic acid research and molecular devices. Herein, we report a systematic computational study on Hg²⁺-mediated base pairs with canonical and TT mispair dimers. The computed results revealed that the model _DTT_D (thymine–thymine with DNA backbone) mispair is more energetically favored than the canonical base pairs. The _DTTTT_D mispair dimer is more energetically stable by ∼36.0 kcal mol⁻¹ than the corresponding canonical _DATGC_D base pairs. The Hg⋯Hg metallophilic interaction was observed with the _DTTTT_D mispair and not the canonical base pairs. The _DATGC_D (adenine: thymine, guanine: cytosine) base pairs were significantly perturbed upon interaction with the mercury ion; however, the TTTT mispairs were aligned upon interaction with the Hg²⁺ ion. The _DTTTT_D mispair adopts a B-type conformation with proper alignment of its nucleobases along the axis. The MESP calculations showed a larger V_min value for the interacting nitrogen centers of the thymine nucleobase, supporting its stronger binding with the Hg²⁺ ion compared to the other nucleobases. The role of the backbone is crucial in nucleic acids to determine many useful properties, and PNAs have been exploited extensively in the literature. Thus, this study was further extended to metal-mediated PNA-containing dimer mispairs such as _DTTTT_P (thymine–thymine dimer model with hybrid DNA and PNA backbone) and _PTTTT_P (thymine–thymine dimer model with PNA backbone). The calculated results showed that the _PTTTT_P PNA mispair is thermodynamically more stable than the canonical dimers. The enthalpy calculated for _DTTTT_D and _PTTTT_P at the B3LYP-D3/6-31G* level of theory showed that _PTTTT_P is ∼3.0 kcal mol⁻¹ more stable than _DTTTT_D. The metallophilic interaction of Hg²⁺ ions in the _PTTTT_P mispair was not observed; however, the metal ions interact with the nitrogen of the thymine bases, presumably enhancing the stability of this mispair by strong electrostatic interactions. These interactions arise due to the P-type conformations of PNAs, which lack metallophilic interactions between the metal ions and can adopt a wider and more unwounded helix. The interaction of the mispair dimers with the explicit water molecules also showed a similar stability trend to that observed with the implicit solvation model. The metallophilic interaction (Hg⋯Hg) was found to be conserved in _DTTTT_D. The AIM analysis performed for these dimers revealed that the interactions are primarily electrostatic in nature. The UV-vis absorption spectra of the mispair systems calculated at the B3LYP-D3/6-31G* level of theory using the TD-DFT method in the aqueous phase suggested that the absorption maximum is located at a longer wavelength in the case of _PTTTT_P compared to the corresponding _DTTTT_D and can be a signature to identify the formation of metal-mediated nucleic acid systems.

Hg²⁺-mediated PNA–PNA mispair duplex (_PTTTT_P) is more energetically favoured compared to DNA–DNA mispair duplex (_DTTTT_D).

Discovery of and Insights into DNA "Codes" for Tunable Morphologies of Metal Nanoparticles

The discovery and elucidation of genetic codes has profoundly changed not only biology but also many fields of science and engineering. The fundamental building blocks of life comprises of four simple deoxyribonucleotides and yet their combinations serve as the carrier of genetic information that encodes for proteins that can carry out many biological functions due to their unique functionalities. Inspired by nature, the functionalities of DNA molecules have been used as a capping ligand for controlling morphology of nanomaterials, and such a control is sequence dependent, which translates into distinct physical and chemical properties of resulting nanoparticles. Herein, an overview on the use of DNA as engineered codes for controlling the morphology of metal nanoparticles, such as gold, silver, and Pd-Au bimetallic nanoparticles is provided. Fundamental insights into rules governing DNA controlled growth mechanisms are also summarized, based on understanding of the affinity of the DNA nucleobases to various metals, the effect of combination of nucleobases, functional modification of DNA, the secondary structures of DNA, and the properties of the seed employed. The resulting physical and chemical properties of these DNA encoded nanomaterials are also reviewed, while perspectives into the future directions of DNA-mediated nanoparticle synthesis are provided.

Construction and characterization of metal ion-containing DNA nanowires for synthetic biology and nanotechnology

DNA is an attractive candidate for integration into nanoelectronics as a biological nanowire due to its linear geometry, definable base sequence, easy, inexpensive and non-toxic replication and self-assembling properties. Recently we discovered that by intercalating Ag+ in polycytosine-mismatch oligonucleotides, the resulting C-Ag+-C duplexes are able to conduct charge efficiently. To map the functionality and biostability of this system, we built and characterized internally-functionalized DNA nanowires through non-canonical, Ag+-mediated base pairing in duplexes containing cytosine-cytosine mismatches. We assessed the thermal and chemical stability of ion-coordinated duplexes in aqueous solutions and conclude that the C-Ag+-C bond forms DNA duplexes with replicable geometry, predictable thermodynamics, and tunable length. We demonstrated continuous ion chain formation in oligonucleotides of 11-50 nucleotides (nt), and enzyme ligation of mixed strands up to six times that length. This construction is feasible without detectable silver nanocluster contaminants. Functional gene parts for the synthesis of DNA- and RNA-based, C-Ag+-C duplexes in a cell-free system have been constructed in an Escherichia coli expression plasmid and added to the open-source BioBrick Registry, paving the way to realizing the promise of inexpensive industrial production. With appropriate design constraints, this conductive variant of DNA demonstrates promise for use in synthetic biological constructs as a dynamic nucleic acid component and contributes molecular electronic functionality to DNA that is not already found in nature. We propose a viable route to fabricating stable DNA nanowires in cell-free and synthetic biological systems for the production of self-assembling nanoelectronic architectures.

Covalently Palladated Oligonucleotides Through Oxidative Addition of Pd0

An 11-mer oligonucleotide incorporating a central (2-iodobenzoylamino)methyl residue has been synthesized and palladated by oxidative addition of Pd₂ (dba)₃ . UV melting profiles of the duplexes formed by the palladated oligonucleotide with its natural complements were biphasic and the higher melting temperatures (T_m ) exhibited considerable hysteresis. CD spectra, in turn, resembled those of canonical B-type double helices. Two-step denaturation, with the "low-T_m " melting involving only canonical base pairs and the "high-T_m " melting involving also dissociation of a Pd^II -mediated base pair, appears the most likely explanation for the observed UV melting profiles. As the latter step in all cases takes place at a higher temperature than denaturation of natural duplexes of the same length, the putative Pd^II -mediated base pairs are stabilizing.

Addressing the properties of "Metallo-DNA" with a Ag(i)-mediated supramolecular duplex

The silver-nucleoside complex [Ag(i)-(N3-cytidine)₂]⁺, 1, self-assembles to form a supramolecular metal-mediated base-pair array highly analogous to those seen in metallo-DNA.

The silver-nucleoside complex [Ag(i)-(N3-cytidine)₂], 1, self-assembles to form a supramolecular metal-mediated base-pair array highly analogous to those seen in metallo-DNA. A combination of complementary hydrogen-bonding, hydrophobic and argentophilic interactions drive the formation of a double-helix with a continuous silver core. Electrical measurements on 1 show that despite having Ag···Ag distances within <5% of the metallic radii, the material is electrically insulating. This is due to the electronic structure which features a filled valence band, an empty conduction band dominated by the ligand, and a band gap of 2.5 eV. Hence, as-prepared, such Ag(i)-DNA systems should not be considered molecular nanowires but, at best, proto-wires. The structural features seen in 1 are essentially retained in the corresponding organogel which exhibits thixotropic self-healing that can be attributed to the reversible nature of the intermolecular interactions. Photo-reduced samples of the gel exhibit luminescence confirming that these poly-cytidine sequences appropriately pre-configure silver ions for the formation of quantum-confined metal clusters in line with contemporary views on DNA-templated clusters. Microscopy data reveals the resulting metal cluster/particles are approximately spherical and crystalline with lattice spacing (111) similar to bulk Ag.

Parallel Guanine Duplex and Cytosine Duplex DNA with Uninterrupted Spines of AgI-Mediated Base Pairs

Hydrogen bonding between nucleobases produces diverse DNA structural motifs, including canonical duplexes, guanine (G) quadruplexes, and cytosine (C) i-motifs. Incorporating metal-mediated base pairs into nucleic acid structures can introduce new functionalities and enhanced stabilities. Here we demonstrate, using mass spectrometry (MS), ion mobility spectrometry (IMS), and fluorescence resonance energy transfer (FRET), that parallel-stranded structures consisting of up to 20 G-Ag^I-G contiguous base pairs are formed when natural DNA sequences are mixed with silver cations in aqueous solution. FRET indicates that duplexes formed by poly(cytosine) strands with 20 contiguous C-Ag^I-C base pairs are also parallel. Silver-mediated G-duplexes form preferentially over G-quadruplexes, and the ability of Ag⁺ to convert G-quadruplexes into silver-paired duplexes may provide a new route to manipulating these biologically relevant structures. IMS indicates that G-duplexes are linear and more rigid than B-DNA. DFT calculations were used to propose structures compatible with the IMS experiments. Such inexpensive, defect-free, and soluble DNA-based nanowires open new directions in the design of novel metal-mediated DNA nanotechnology.

2,6-Dimercuriphenol as a Bifacial Dinuclear Organometallic Nucleobase

A C-nucleoside having 2,6-dimercuriphenol as the base moiety has been synthesized and incorporated into an oligonucleotide. NMR and UV melting experiments revealed the ability of this bifacial organometallic nucleobase surrogate to form stable dinuclear Hg^II -mediated base triples with adenine, cytosine, and thymine (or uracil) in solution as well as within a triple-helical oligonucleotide. A single Hg^II -mediated base triple between 2,6-dimercuriphenol and two thymines increased both Hoogsteen and Watson-Crick melting temperatures of a 15-mer pyrimidine⋅purine*pyrimidine triple helix by more than 10 °C relative to an unmodified triple helix of the same length. This novel binding mode could be exploited in targeting certain pathogenic nucleic acids as well as in DNA nanotechnology.

A dinuclear Cu(i)-mediated complex: Theoretical studies of the G2Cu2 4+ cluster ion

Recently, the T-Hg(ii)₂-A base pair containing two equivalents of Hg(ii) has been prepared and characterized experimentally, which implies that there might exist considerable stable metal-mediated base pairs holding two neighbouring metal centers. Here we report a quantum chemical study on geometries, electronic structures, and bonding of various G₂Cu₂ ⁴⁺ (G = guanine) isomers including one di-copper(i) unit. Different density functional methods [Becke 3-parameter-Lee-Yang-Parr, Perdew-Becke-Ernzerhof, Becke-Perdew, Density Functional Theory with Dispersion Corrections (DFT-D)] assign ambiguous relative energies to these isomers with the singlet and triplet states. High-level ab initio [domain-based local pair natural orbital (DLPNO) coupled-cluster with single and double excitations and DLPNO-coupled-cluster with single, double, and perturbative triple excitations] calculations confirm that the lowest-lying isomer of the G₂Cu₂ ⁴⁺ ion has C _2h symmetry with the singlet state and is comparable to the singly and doubly charged homologues (G₂Cu₂ ⁺ and G₂Cu₂ ²⁺). The extended transition state (ETS)-natural orbitals for the chemical valence (ETS-NOCV) calculations point out that it has larger instantaneous interaction energy and bond dissociation energy than the corresponding singly and doubly charged complexes due to its relatively stronger attractive energies and weaker Pauli repulsion. The orbital interactions in the quadruply charged cluster chiefly come from Cu₂ ⁴⁺ ← G⋯G π donations. The results may help the understanding of the bonding properties of other potential metal-base pair complexes with the electron transfer.

Palladacyclic Conjugate Group Promotes Hybridization of Short Oligonucleotides

Short oligonucleotides with cyclopalladated benzylamine moieties at their 5'-termini have been prepared to test the possibility of conferring palladacyclic anticancer agents sequence-selectivity by conjugation with a guiding oligonucleotide. Hybridization of these oligonucleotides with natural counterparts was studied by UV and CD (circular dichroism) melting experiments in the absence and presence of a competing ligand (2-mercaptoethanol). Cyclopalladated benzylamine proved to be strongly stabilizing relative to unmetalated benzylamine and modestly stabilizing relative to an extra A•T base pair. The stabilization was largely abolished in the presence of 2-mercaptoethanol, suggesting direct coordination of Pd(II) to a nucleobase of the complementary strand. In all cases, fidelity of Watson-Crick base pairing between the two strands was retained. Hybridization of the cyclopalladated oligonucleotides was characterized by relatively large negative enthalpy and entropy, consistent with stabilizing Pd(II) coordination partially offset by the entropic penalty of imposing conformational constraints on the flexible diethylene glycol linker between the oligonucleotide and the palladacyclic moiety.