Complexes of DNA bases and Watson-Crick base pairs with small neutral gold clusters

Deqformer: high-definition and scalable deep learning probe design method

Target enrichment sequencing techniques are gaining widespread use in the field of genomics, prized for their economic efficiency and swift processing times. However, their success depends on the performance of probes and the evenness of sequencing depth among each probe. To accurately predict probe coverage depth, a model called Deqformer is proposed in this study. Deqformer utilizes the oligonucleotides sequence of each probe, drawing inspiration from Watson-Crick base pairing and incorporating two BERT encoders to capture the underlying information from the forward and reverse probe strands, respectively. The encoded data are combined with a feed-forward network to make precise predictions of sequencing depth. The performance of Deqformer is evaluated on four different datasets: SNP panel with 38 200 probes, lncRNA panel with 2000 probes, synthetic panel with 5899 probes and HD-Marker panel for Yesso scallop with 11 000 probes. The SNP and synthetic panels achieve impressive factor 3 of accuracy (F3acc) of 96.24% and 99.66% in 5-fold cross-validation. F3acc rates of over 87.33% and 72.56% are obtained when training on the SNP panel and evaluating performance on the lncRNA and HD-Marker datasets, respectively. Our analysis reveals that Deqformer effectively captures hybridization patterns, making it robust for accurate predictions in various scenarios. Deqformer leads to a novel perspective for probe design pipeline, aiming to enhance efficiency and effectiveness in probe design tasks.

Controllable synthesis of fluorescent silver nanoparticles with different length oligonucleotides

Silver nanomaterials have become important research topics in recent years. As a new type of fluorescent material, silver nanomaterials have been applied to fluorescent sensors, bioimaging and materials targeting cancer cells. Here, an approach to the oligonucleotide‐templated controllable formation of fluorescent Ag nanomaterials is reported. In this experiment, silver nanoparticles (NPs) were synthesised from oligonucleotides chains, sodium borohydride (NaBH₄) and silver nitrate (AgNO₃) by changing the molar ratio of DNA to sodium borohydride (NaBH₄) and silver nitrate (AgNO₃). Fluorescent assay and transmission electron microscopy were used to characterise the silver NPs. The optimal selection of DNA chains with different lengths as templates for the synthesis of silver NPs was found. This work successfully develops the capping oligonucleotides scaffolds of silver nanoclusters.

Understanding structural and molecular properties of complexes of nucleobases and Au13 golden nanocluster by DFT calculations and DFT-MD simulation

The characterization of the complexes of biomolecules and nanostructures is highly interesting and benefits the rational development and design of nano-materials and nano-devices in nano-biotechnology. In this work, we have used dispersion corrected density functional theory (DFT-D) as well as DFT based molecular dynamics simulations to provide an atomistic understanding of interaction properties of DNA nucleobases and Au13 nanocluster. Various active sites of interacting molecules considering their relative orientation and distance are explored. Our goal is to stimulate the binding characteristics between two entities and evaluate this through the interaction energy, the charge transfer, the electronic structure, and the specific role of the molecular properties of the nucleobase-Au13 system. The primary outcomes of this comprehensive research illuminated that nucleic bases have potent affinity for binding to the Au cluster being chemisorption type and following the trend: Adenine > Cytosine > Guanine > Thymine. The AIM analysis indicated that the binding nature of the interacting species was predominantly partial covalent and high polar. We discuss the bearing of our findings in view of gene-nanocarrier, biosensing applications as well as nanodevices for sequencing of DNA.

Syntheses and crystal structures of new aurate salts of adenine or guanine nucleobases

Two new gold(III) complexes with adenine or guanine nitrogenous bases as counter-cations were synthesized. These are 6-amino-7H-purine-1,9-diium tetrachloridogold(III) chloride monohydrate, (C₅H₇N₅)[AuCl₄]Cl·H₂O, 1, and 2-amino-6-oxo-6,7-dihydro-1H-purin-9-ium tetrachloridogold(III) hemihydrate, (C₅H₆N₅O)[AuCl₄]·0.5H₂O, 2. Their crystal structures were studied using single-crystal X-ray diffraction and FT-IR spectroscopic techniques. The arrangement of species in the studied crystal structures implies π-stacking interactions, as well as concomitant C-H...π interactions, hydrogen bonds and other types of noncovalent interactions, which were studied qualitatively and quantitatively using the method of molecular Voronoi-Dirichlet polyhedra. The variation of the nitrogenous base from adenine to guanine results in evident differences in the packing of the species in the crystals of 1 and 2. The splitting and shifting of bands in the FT-IR spectra of the title compounds reveals several features representative of noncovalent interactions in their crystal structures.

An electrochemical sensor for attomolar determination of mercury(II) using DNA/poly-L-methionine-gold nanoparticles/pencil graphite electrode

The present work describes an ultrasensitive electrochemical sensor for determination of mercury(II) using deoxyribonucleic acid/poly-L-methionine-gold nanoparticles/pencil graphite electrode (DNA/PMET-AuNPs/PGE). To fabricate this biosensor, L-methionine (L-MET) was electropolymerized on the PGE surface followed by simultaneous electrochemical entrapment of AuNPs. Next, DNA was immobilized on the PMET-AuNPs/PGE by applying a 0.5 V potential. The surface area of modified and unmodified electrodes was determined by chronocoulometric technique. Hg²⁺ was detected in the linear dynamic range of 0.1 aM to 0.1 nM, and the detection limit was determined as 0.004 aM using square wave anodic stripping voltammetry (SWASV) under optimized conditions. The DNA/PMET-AuNPs/PGE demonstrated good selectivity toward Hg²⁺ against other metal ions such as V⁴⁺, Pb²⁺, Cr³⁺, Cd²⁺, Cu²⁺, Zn²⁺, Sn²⁺, In³⁺, Ge⁴⁺, and Fe³⁺. Real samples studies were carried out in sea water and fish samples.

Fluorescent ZnO-Au Nanocomposite as a Probe for Elucidating Specificity in DNA Interaction

In this work, we report the interaction of a fluorescent ZnO-Au nanocomposite with deoxyribonucleic acid (DNA), leading to AT-specific DNA interaction, which is hitherto not known. For this study, three natural double-stranded (ds) DNAs having different AT:GC compositions were chosen and a ZnO-Au nanocomposite has been synthesized by anchoring a glutathione-protected gold nanocluster on the surface of egg-shell-membrane (ESM)-based ZnO nanoparticles. The ESM-based bare ZnO nanoparticles did not show any selective interaction toward DNA, whereas intrinsic fluorescence of the ZnO-Au nanocomposite shows an appreciable blue shift (Δλ_max = 18 nm) in the luminescence wavelength of 520 nm in the presence of ds calf thymus (CT) DNA over other studied DNAs. In addition, the interaction of the nanocomposite through fluorescence studies with single-stranded (ss) CT DNA, synthetic polynucleotides, and nucleobases/nucleotides (adenine, thymine, deoxythymidine monophosphate, deoxyadenosine monophosphate) was also undertaken to delineate the specificity in interaction. A minor blue shift (Δλ_max = 5 nm) in the emission wavelength at 520 nm was observed for single-stranded CT DNA, suggesting the proficiency of the nanocomposite for discriminating ss and ds CT DNA. More importantly, fluorescence signals from the nano-bio-interaction could be measured directly without any modification of the target, which is the foremost advantage emanated from this study compared with other previous reports. The AT base-pair-induced enhancement was also found to be highest for the melting temperature of CT DNA (ΔT_mCT = 6.7 °C). Furthermore, spectropolarimetric experiments followed by calorimetric analysis provided evidence for specificity in AT-rich DNA interaction. This study would lead to establish the fluorescent ZnO-Au nanocomposite as a probe for nanomaterial-based DNA-binding study, featuring its specific interaction toward AT-rich DNA.

Layer-by-Layer-Assembled AuNPs-Decorated First-Generation Poly(amidoamine) Dendrimer with Reduced Graphene Oxide Core as Highly Sensitive Biosensing Platform with Controllable 3D Nanoarchitecture for Rapid Voltammetric Analysis of Ultratrace DNA Hybridization

The structure and electrochemical properties of layer-by-layer-assembled gold nanoparticles (AuNPs)-decorated first-generation (G1) poly(amidoamine) dendrimer (PD) with reduced graphene oxide (rGO) core as a highly sensitive and label-free biosensing platform with a controllable three-dimensional (3D) nanoarchitecture for the rapid voltammetric analysis of DNA hybridization at ultratrace levels were characterized. Mercaptopropinoic acid (MPA) was self-assembled onto Au substrate, then GG1PD formed by the covalent functionalization between the amino terminals of G1PD and carboxyl terminals of rGO was covalently linked onto MPA, and finally AuNPs were decorated onto GG1PD by strong physicochemical interaction between AuNPs and -OH of rGO in GG1PD, which was characterized through different techniques and confirmed by computational calculation. This 3D controllable thin-film electrode was optimized and evaluated using [Fe(CN)₆]^3-/4- as the redox probe and employed to covalently immobilize thiol-functionalized single-stranded DNA as biorecognition element to form the DNA nanobiosensor, which achieved fast, ultrasensitive, and high-selective differential pulse voltammetric analysis of DNA hybridization in a linear range from 1 × 10^-6 to 1 × 10^-13 g m^-1 with a low detection limit of 9.07 × 10^-14 g m^-1. This work will open a new pathway for the controllable 3D nanoarchitecture of the layer-by-layer-assembled metal nanoparticles-functionalized lower-generation PD with two-dimensional layered nanomaterials as cores that can be employed as ultrasensitive and label-free nanobiodevices for the fast diagnosis of specific genome diseases in the field of biomedicine.

DNA metallization: principles, methods, structures, and applications

This review summarizes the research activities on DNA metallization since the concept was first proposed in 1998, covering the principles, methods, structures, and applications.

The key role of Au-substrate interactions in catalytic gold subnanoclusters

The development of gold catalysis has allowed significant levels of activity and complexity in organic synthesis. Recently, the use of very active small gold subnanoclusters (Au_n, n < 10) has been reported. The stabilization of such nanocatalysts to prevent self-aggregation represents a true challenge that has been partially remediated, for instance, by their immobilization in polymer matrices. Here, we describe the transient stabilization of very small gold subnanoclusters (Au_n, n < 5) by alkyl chains or aromatic groups appended to the reactive π bond of simple alkynes. The superior performance toward Brønsted acid-free hydration of medium to long aliphatic alkynes (1-hexyne and 1-docecyne) and benzylacetylene with respect to phenylacetylene is demonstrated experimentally and investigated computationally. A cooperative network of dispersive Au···C–H and/or Au···π interactions, supported by quantum mechanical calculations and time-resolved luminescence experiments, is proposed to be at the origin of this stabilization.

Stabilization of gold nanoclusters in order to prevent their self-aggregation remains a great challenge. Here, the authors describe transient stabilization of very small catalytic gold subnanoclusters by alkyl chains or aromatic groups appended to the reactive π bond of simple alkynes.

Luminescent Silver-Purine Double Helicate: Synthesis, Self-Assembly and Antibacterial Action

The synthesis, self-assembly and antibacterial activity of a luminescent silver-purine double helicate is reported. The structure of the newly synthesized silver-supported helicate [C₃₆ H₂₄ N₁₆ O₄ Cl₅ Ag₁ ] was unambiguously characterized by single-crystal X-ray crystallography. It exhibited a bright bluish-green emission (λ_max =460 nm), when excited with 380 nm light. Microscopic investigations showed that the complex has a propensity to self-assemble into nanospheres. The antibacterial activity of this silver-containing helicate was studied against both Gram-positive and Gram-negative bacteria. MIC (minimal inhibitory concentration) values showed that the complex is very active against Gram-negative bacteria. Further internalization of the silver complex into E. coli bacteria was mapped with the help of microscopic techniques. These results are significant as silver was recently found to enhance antibiotic action against Gram-negative bacteria, raising hope in countering severe bacterial infections.

DNA-stabilized Ag-Au bimetallic clusters: the effects of alloying and embedding on optical properties

Global geometry optimization and time-dependent density functional theory calculations have been used to study the structural evolution and optical properties of AgnAun (n = 2-6) nanoalloys both as individual clusters and as clusters stabilized with the fragments of DNA of different size. We show that alloying can be used to control and tune the level of interaction between the metal atoms of the cluster and the organic fragments of the DNA ligands. For instance, gold and silver atoms are shown to exhibit synergistic effects in the process of charge transfer from the nucleobase to the cluster, with the silver atoms directly connected to the nitrogen atoms of cytosine increasing their positive partial charge, while their more electronegative neighbouring gold atoms host the excess negative charge. This allows the geometrical structures and optical absorption spectra of small bimetallic clusters to retain many of their main features upon aggregation with relatively large DNA fragments, such as a cytosine-based 9-nucleotide hairpin loop, which suggests a potential synthetic route to such hybrid metal-organic compounds, and opens up the possibility of bringing the unique tunable properties of bimetallic nanoalloys to biological applications.

Interaction of nucleobases with silicon doped and defective silicon doped graphene and optical properties

The interaction of nucleobases (NBs) with the surface of silicon doped graphene (SiGr) and defective silicon doped graphene (dSiGr) has been studied using electronic structure methods.

Carbon dioxide interaction with isolated imidazole or attached on gold clusters and surface: competition between σ H-bond and π stacking interaction

Using first principle methodologies, we investigate the subtle competition between σ H-bond and π stacking interaction between CO2 and imidazole either isolated, adsorbed on a gold cluster or adsorbed on a gold surface. These computations are performed using MP2 as well as dispersion corrected density functional theory (DFT) techniques. Our results show that the CO2 interaction goes from π-type stacking into σ-type when CO2 interacts with isolated imidazole and Au clusters or surface. The balance between both types of interactions is found when an imidazole is attached to a Au20 gold cluster. Thus, the present study has great significance in understanding and controlling the structures of weakly-bound molecular systems and materials, where hydrogen bonding and van der Waals interactions are competing. The applications are in the fields of the control of CO2 capture and scattering, catalysis and bio- and nanotechnologies.

RNABP COGEST: a resource for investigating functional RNAs

Structural bioinformatics of RNA has evolved mainly in response to the rapidly accumulating evidence that non-(protein)-coding RNAs (ncRNAs) play critical roles in gene regulation and development. The structures and functions of most ncRNAs are however still unknown. Most of the available RNA structural databases rely heavily on known 3D structures, and contextually correlate base pairing geometry with actual 3D RNA structures. None of the databases provide any direct information about stabilization energies. However, the intrinsic interaction energies of constituent base pairs can provide significant insights into their roles in the overall dynamics of RNA motifs and structures. Quantum mechanical (QM) computations provide the only approach toward their accurate quantification and characterization. ‘RNA Base Pair Count, Geometry and Stability’ (http://bioinf.iiit.ac.in/RNABPCOGEST) brings together information, extracted from literature data, regarding occurrence frequency, experimental and quantum chemically optimized geometries, and computed interaction energies, for non-canonical base pairs observed in a non-redundant dataset of functional RNA structures. The database is designed to enable the QM community, on the one hand, to identify appropriate biologically relevant model systems and also enable the biology community to easily sift through diverse computational results to gain theoretical insights which could promote hypothesis driven biological research.

Database URL:http://bioinf.iiit.ac.in/RNABPCOGEST

Binding to gold nanoclusters alters the hydrogen bonding interactions and electronic properties of canonical and size-expanded DNA base pairs

Structural perturbations, in terms of size expansion and metal binding, lead to exciting electronic properties which can be exploited in designing novel nano-electronic devices.

Nucleobases tagged to gold nanoclusters cause a mechanistic crossover in the oxidation of CO

A mechanistic crossover is observed upon using nucleobase tagged gold clusters as catalysts favoring the Eley–Rideal mechanism, over the conventional Langmuir–Hinshelwood pathway followed using pristine gold clusters during CO oxidation.

Role of size and shape selectivity in interaction between gold nanoclusters and imidazole: a theoretical study

We present a theoretical study on the structure, stability, spectra and electronic properties of imidazole (Im) adsorbed on gold nanoclusters (Aun, n = 2, 4, 6, 8, 10, and 20). These computations were performed using various density functional theories with and without inclusion of Grimme's (D3) dispersion correction. For small clusters, we also carried out wavefunction-based ab initio (MP2 and SCS-MP2) computations for comparison. Vibrational, atoms in molecules (AIM) and natural bond orbital (NBO) analyses clearly reveal the occurrence of charge transfer (CT) through covalent (N1-Au) and noncovalent interactions that play important roles in the stability of the Im@Aun complexes with anchor assisted H-bonds (Cα-H · Au). Therefore, gold clusters can act as H-bond acceptors with biomolecules for development of new materials and applications. Our study establishes also the ability and reliability of PBE0 and M05-2X functionals compared to B3LYP and PBE for an accurate description of covalent and noncovalent interactions between Im and gold clusters since they lead to close agreement with MP2. Finally, we show that the Au8 cluster may be viewed as large enough to mimic the 3D gold surface.

The gold-hydrogen bond, Au-H, and the hydrogen bond to gold, Au∙∙∙H-X

In the first part of this review, the characteristics of Au-H bonds in gold hydrides are reviewed including the data of recently prepared stable organometallic complexes with gold(I) and gold(III) centers. In the second part, the reports are summarized where authors have tried to provide evidence for hydrogen bonds to gold of the type Au∙∙∙H-X. Such interactions have been proposed for gold atoms in the Au(-I), Au(0), Au(I), and Au(III) oxidation states as hydrogen bonding acceptors and H-X units with X = O, N, C as donors, based on both experimental and quantum chemistry studies. To complement these findings, the literature was screened for examples with similar molecular geometries, for which such bonding has not yet been considered. In the discussion of the results, the recently issued IUPAC definitions of hydrogen bonding and the currently accepted description of agostic interactions have been used as guidelines to rank the Au∙∙∙H-X interactions in this broad range of weak chemical bonding. From the available data it appears that all the intra- and intermolecular Au∙∙∙H-X contacts are associated with very low binding energies and non-specific directionality. To date, the energetics have not been estimated, because there are no thermochemical and very limited IR/Raman and temperature-dependent NMR data that can be used as reliable references. Where conspicuous structural or spectroscopic effects have been observed, explanations other than hydrogen bonding Au∙∙∙H-X can also be advanced in most cases. Although numerous examples of short Au∙∙∙H-X contacts exist in the literature, it seems, at this stage, that these probably make only very minor contributions to the energy of a given system and have only a marginal influence on molecular conformations which so far have most often attracted researchers to this topic. Further, more dedicated investigations will be necessary before well founded conclusions can be drawn.

DNA-hosted fluorescent gold nanoclusters: sequence-dependent formation

Various DNAs were employed as hosts to investigate the sequence-dependent formation of fluorescent Au nanoclusters (Au NCs) in aqueous solution. By comparison among hairpin DNAs (HP-DNAs) with a pristine stem segment and varied loop sequences, we found that the emission behavior of the HP-DNA-hosted Au NCs is dependent on the loop sequences. The most efficient host to produce fluorescent Au NCs is the cytosine loop. However, relative to the cytosine and guanine loops, the loop composed of thymine as well as adenine produces Au NCs with a much weaker emission. Additionally, the emission behavior of Au NCs hosted by the single-stranded DNAs (ss-DNAs) with an identical base composition to the corresponding HP-DNAs still exhibits a cytosine-rich dependence. The fully matched DNAs seem to be less efficient than the corresponding loop and ss-DNA structures. Furthermore, the emission properties of HP-DNA-hosted Au NCs can be modulated by the loop length. The sequence-dependent formation of fluorescent Au NCs is believed to be caused by differences in binding nucleophilicity of the DNA heterocyclic nitrogen and exocyclic keto groups to the hydrolyzed Au(III) species. This work demonstrates the role of sequence in producing Au NCs that could serve as promising fluorescent nanoprobes in biosensing and DNA-hosted Au nanomaterials.

Interactions of coinage metal clusters with histidine and their effects on histidine acidity; theoretical investigation

Understanding the nature of interaction between metal nanoparticles and biomolecules such as amino acids is important in the development and design of biosensors. In this paper, binding of M(3) clusters (M = Au, Ag and Cu) with neutral and anionic forms of histidine amino acid was studied using density functional theory (DFT-B3LYP). It was found that the interaction of histidine with M(3) clusters is governed by two major bonding factors: (a) the anchoring N-M and O-M bonds and (b) the nonconventional N-H···M and O-H···M hydrogen bonds. The nature of these chemical bonds has been investigated based on quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses. In the next step, the effects of Au, Ag and Cu metal clusters on the gas-phase acidity of weak organic acid (histidine) have been explored. The acidity of isolated histidine was compared with the acidity of its Au(3)-, Ag(3)- and Cu(3)-complexed species. Results indicate that upon complexation with M(3) clusters (at 298 K), the gas-phase acidity (GPA) of histidine varies from 339.5 to 312.3, 315.0, and 313.7 kcal mol(-1) for Au(3)-, Ag(3)- and Cu(3)-His complexes, respectively (i.e., its dissociation becomes much less endothermic). These values indicate that a weak organic acid can be converted to a super acid when it is complexed with metal clusters. Also, in order to investigate the acidity value of the imidazole moiety in histidine, histidine methyl ester (His-OMe) was selected. Similarly, the acidity of this compound was compared with the acidity of their Au(3), Ag(3) and Cu(3)-complexed species. After complexation with M(3) clusters at 298 K, the gas-phase acidity (GPA) of His-OMe varies from 333.0 to 280.0, 304.2 and 291.5 kcal mol(-1), respectively. Moreover, pK(a) values were determined in water for isolated and complexed species of His and His-OMe. The resulting pK(a) values were found to decrease upon complexation with M(3) clusters.

Theoretical investigation on DNA/RNA base pairs mediated by copper, silver, and gold cations

B3LYP density functional based computations were performed in order to characterize the interactions present in some Cu(+), Ag(+), and Au(+) metal ion-mediated DNA and RNA base pairs from both structural and electronic points of view. Examined systems involve as ligands canonical Watson-Crick, Hoogsteen and Wobble base pairs. Two artificial Hoogsteen base pairs were also taken into account. Binding energy values indicate that complexes involving silver cations are less stable than those in which copper or gold are present, and propose a similar behaviour for these two latter ions. The nature of the bond linking metal ions and bases was described by the NBO analysis that suggests metal coordinative interactions to be covalent. An evaluation of the dispersion contributions for the investigated systems was performed with the B3LYP-D3 functional.

Interaction of cytidine 5'-monophosphate with Au(111): an in situ infrared spectroscopic study

The interaction of cytidine 5'-monophosphate (CMP) with gold surfaces is studied by means of in situ infrared spectroscopy and cyclic voltammetry at the Au(111)|aqueous solution interface. Similar to other nucleic acid components, cytidine 5'-monophosphate is chemisorbed on the surface at positive potentials, and the amount of adsorbed CMP increases with the potential. Subtractively normalized interfacial Fourier-transform infrared spectroscopy (SNIFTIRS) is used to identify the adsorbed and desorbed species. Upon electrochemical desorption, the molecules released in solution are unprotonated on the N3 atom. Striking similarities are found between the spectrum of adsorbed CMP and the solution spectrum of protonated CMP. The origin of such similarities is discussed. The results strongly suggest that chemisorption occurs through the N3 atom of the pyrimidine ring. A comparison is drawn with cytidine, whose electrochemical and spectroscopic behaviors are also investigated.

Probing differential Ag+-nucleobase interactions with isothermal titration calorimetry (ITC): Towards patterned DNA metallization

DNA has been successfully used as a scaffold for the fabrication of metallic nanowires, primarily based on the electrostatic complexation and reduction of the metal cations on the negatively charged sugar-phosphate backbone. Here, we probe the differential binding affinities of nucleobases for silver ions using sensitive isothermal titration calorimetry (ITC) measurements of the reaction enthalpies, which go in order: C > G > A > or = T. Using the disparity between the interaction of cytosine (strong binding) and thymine (weak binding) with silver ions, we have successfully generated silver nanoparticle doublets and triplets on custom-made oligonucleotides, C(30)-T(40)-C(30) and C(20)-T(20)-C(20)-T(20)-C(20), respectively. Thus, a new and simple method of generating metallized DNA wires is presented, based entirely on the nucleotide sequence of DNA. The concept could be extended to other cations and complex DNA sequences in order to achieve intricately patterned DNA constructs.