Ag-DNA Emitter: Metal Nanorod or Supramolecular Complex?

Amino acid-stabilized luminescent gold clusters for sensing pterin and its analogues

Pteridines are important low molecular weight biomarkers used in the diagnostics of inflammation, oxidative stress, phenylketonuria, cancer, etc. In this experimental study, we present a simple and selective approach to determine pteridines (pterin, leucopterin and folic acid) and nucleobase guanine concentration using luminescent gold clusters stabilized by aromatic amino acids. We synthesized several new gold clusters (AA-Au NCs) stabilized by various aromatic amino acids - 3,4-dihydroxy-L-phenylalanine (DOPA), L-tryptophan (Trp), L-tyrosine (Tyr) and L-phenylalanine (Phe), emitting in the violet-green spectral range. Their luminescence appeared to be sensitive to the presence of pterin, leucopterin, folic acid and guanine depending on the stabilizing matrix. Thus, a facile and cost-effective approach for the detection of pteridines is proposed. AA-Au NC-based sensors work according to "turn-off" and "turn-on" mechanisms. The possible physical origins of their luminescence quenching and enhancement are discussed.

Excited States in Single-Stranded and i-Motif DNA with Silver Ions

We have studied the excited states and structural properties for the complexes of cytosine (dC)10 chains with silver ions (Ag+) in a wide range of the Ag+ to DNA ratio (r) and pH conditions using circular dichroism, steady-state absorption, and fluorescence spectroscopy along with the ultrafast fluorescence upconversion technique. We also calculated vertical electronic transition energies and determined the nature of the corresponding excited states in some models of the cytosine-Ag+ complexes. We show that (dC)10 chains in the presence of silver ions form a duplex stabilized by C-Ag+-C bonds. It is also shown that the i-motif structure formed by (dC)10 chains is destabilized in the presence of Ag+ ions. The excited-state properties in the studied complexes depend on the amount of binding ions and the binding sites, which is supported by the calculations. In particular, new low-lying excited states appear when the second Ag+ ion interacts with the O atom of cytosine in the C-Ag+-C pairs. A similar picture is observed in the case when one Ag+ ion interacts with one cytosine via the N7 atom.

Breaching the Fortress: Photochemistry of DNA-Caged Ag106

A DNA strand can encapsulate a silver molecule to create a nanoscale, aqueous stable chromophore. A protected cluster that strongly fluoresces can also be weakly photolabile, and we describe the laser-driven photochemistry of the green fluorophore C4AC4TC3GT4/Ag106+. The embedded cluster is selectively photoexcited at 490 nm and then bleached, and we describe how the efficiency, products, and route of this photochemical reaction are controlled by the DNA cage. With irradiation at 496.5 nm, the cluster absorption progressively drops to give a photodestruction quantum yield of 1.5 (±0.2) × 10-4, ∼103× less efficient than fluorescence. A new λabs = 335 nm chromophore develops because the precursor with 4 Ag0 is converted into a group of clusters with 2 Ag0 - Ag64+, Ag75+, Ag86+, and Ag97+. The 4-7 Ag+ in this series are chemically distinct from the 2 Ag0 because they are selectively etched by iodide. This halide precipitates silver to favor only the smallest Ag64+ cluster, but the larger clusters re-develop when the precipitated Ag+ ions are replenished. DNA-bound Ag106+ decomposes because it is electronically excited and then reacts with oxygen. This two-step process may be state-specific because O2 quenches the red luminescence from Ag106+. However, the rate constant of 2.3 (±0.2) × 106 M-1 s-1 is relatively small, which suggests that the surrounding DNA matrix hinders O2 diffusion. On the basis of analogous photoproducts with methylene blue, we propose that a reactive oxygen species is produced and then oxidizes Ag106+ to leave behind a loose Ag+-DNA skeleton. These findings underscore the ability of DNA scaffolds to not only tune the spectra but also guide the reactions of their molecular silver adducts.

Interrupted DNA and Slow Silver Cluster Luminescence

A DNA-silver cluster conjugate is a hierarchical chromophore with a partly reduced silver core embedded within the DNA nucleobases that are covalently linked by the phosphodiester backbone. Specific sites within a polymeric DNA can be targeted to spectrally tune the silver cluster. Here, the repeated (C₂A)₆ strand is interrupted with a thymine, and the resulting (C₂A)₂-T-(C₂A)₄ forms only Ag₁₀⁶⁺, a chromophore with both prompt (∼1 ns) green and sustained (∼10² μs) red luminescence. Thymine is an inert placeholder that can be removed, and the two fragments (C₂A)₂ and (C₂A)₄ also produce the same Ag₁₀⁶⁺ adduct. In relation to (C₂A)₂T(C₂A)₄, the (C₂A)₂ + (C₂A)₄ pair is distinguished because the red Ag₁₀⁶⁺ luminescence is ∼6× lower, relaxes ∼30% faster, and is quenched ∼2× faster with O₂. These differences suggest that a specific break in the phosphodiester backbone can regulate how a contiguous vs broken scaffold wraps and better protects its cluster adduct.

Quantitative determination of albumin and immunoglobulin in human serum using gold nanoclusters

In this experimental study, we developed a simple and selective approach to determine the concentrations of human serum albumin (HSA) and total amount of immunoglobulins (Ig) in real human serum (HS) sample using luminescent gold nanoclusters (Au NCs). In doing so, Au NCs were grown directly on the HS proteins without any sample pretreatment. We synthesized Au NCs on HSA and Ig and studied their photophysical properties. Using combined fluorescent and colorimetric assay we were able to obtain protein concentrations with a high degree of accuracy relative to techniques currently used in clinical diagnostics. We used method of standard additions to determine both HSA and Ig concentrations in HS by the Au NCs absorbance and fluorescence signals. A simple and cost-effective method developed in this work represents an excellent alternative to the techniques currently used in clinical diagnostics.

Optical, structural and antibacterial properties of silver nanoparticles and DNA-templated silver nanoclusters

Silver nanoparticles (AgNPs) are increasingly considered for biomedical applications as drug-delivery carriers, imaging probes and antibacterial agents. Silver nanoclusters (AgNCs) represent another subclass of nanoscale silver. AgNCs are a promising tool for nanomedicine due to their small size, structural homogeneity, antibacterial activity and fluorescence, which arises from their molecule-like electron configurations. The template-assisted synthesis of AgNCs relies on organic molecules that act as polydentate ligands. In particular, single-stranded nucleic acids reproducibly scaffold AgNCs to provide fluorescent, biocompatible materials that are incorporable in other formulations. This mini review outlines the design and characterization of AgNPs and DNA-templated AgNCs, discusses factors that affect their physicochemical and biological properties, and highlights applications of these materials as antibacterial agents and biosensors.

Tug-of-War between DNA Chelation and Silver Agglomeration in DNA-Silver Cluster Chromophores

Supramolecular chromophores form when a DNA traps silvers that then coalesce into clusters with discrete, molecular electronic states. However, DNA strands are polymeric ligands that disperse silvers and thus curb agglomeration. We study this competition using two chromophores that share three common components: a dimeric DNA scaffold, Ag⁺-nucleobase base pairs, and Ag⁰ chromophores. The DNA host C₄-A₂-iC₄T mimics structural elements in a DNA-cluster crystal structure using a phosphodiester backbone with combined 5' → 3' and 3' → 5' (indicated by "i") directions. The backbone directions must alternate to form the two silver clusters, and this interdependence supports a silver-linked structure. This template creates two chromophores with distinct sizes, charges, and hence spectra: (C₄-A₂-iC₄T)₂/Ag₁₁⁷⁺ with λ_abs/λ_em = 430/520 nm and (C₄-A₂-iC₄T)₂/Ag₁₄⁸⁺ with λ_abs/λ_em = 510/630 nm. The Ag⁺ and Ag⁰ constituents in these partially oxidized clusters are linked with structural elements in C₄-A₂-iC₄T. Ag⁺ alone binds sparsely but strongly to form C₄-A₂-iC₄T/3-4 Ag⁺ and (C₄-A₂-iC₄T)₂/7-8 Ag⁺ complexes, and these stoichiometries suggest that Ag⁺ cross-links pairs of cytosines to form a hairpin with a metallo-C₄/iC₄ duplex and an adenine loop. The Ag⁰ are chemically orthogonal because they can be oxidatively etched without disrupting the underlying Ag⁺-DNA matrix, and their reactivity is attributed to their valence electrons and weaker chelation by the adenines. These studies suggest that Ag⁺ disperses with the cytosines to create an adenine binding pocket for the Ag⁰ cluster chromophores.

A single nucleobase tunes nonradiative decay in a DNA-bound silver cluster

DNA strands are polymeric ligands that both protect and tune molecular-sized silver cluster chromophores. We studied single-stranded DNA C₄AC₄TC₃XT₄ with X = guanosine and inosine that form a green fluorescent Ag₁₀ ⁶⁺ cluster, but these two hosts are distinguished by their binding sites and the brightness of their Ag₁₀ ⁶⁺ adducts. The nucleobase subunits in these oligomers collectively coordinate this cluster, and fs time-resolved infrared spectra previously identified one point of contact between the C2-NH₂ of the X = guanosine, an interaction that is precluded for inosine. Furthermore, this single nucleobase controls the cluster fluorescence as the X = guanosine complex is ∼2.5× dimmer. We discuss the electronic relaxation in these two complexes using transient absorption spectroscopy in the time window 200 fs-400 µs. Three prominent features emerged: a ground state bleach, an excited state absorption, and a stimulated emission. Stimulated emission at the earliest delay time (200 fs) suggests that the emissive state is populated promptly following photoexcitation. Concurrently, the excited state decays and the ground state recovers, and these changes are ∼2× faster for the X = guanosine compared to the X = inosine cluster, paralleling their brightness difference. In contrast to similar radiative decay rates, the nonradiative decay rate is 7× higher with the X = guanosine vs inosine strand. A minor decay channel via a dark state is discussed. The possible correlation between the nonradiative decay and selective coordination with the X = guanosine/inosine suggests that specific nucleobase subunits within a DNA strand can modulate cluster-ligand interactions and, in turn, cluster brightness.

In vitro investigation of biophysical interactions between Ag(I) complexes of bis(methyl)(thia/selena)salen and ct-DNA via multi-spectroscopic, physicochemical and molecular docking methods along with cytotoxicity study

Four silver(I) (Ag(I)) complexes: 1.PF₆ , 2.PF₆ , 1.ClO₄ and 2.ClO₄ of bis(methyl)thia salen (1) and bis (methyl)selena salen (2) with two different counter anions (PF₆ ^- and ClO₄ ^- ) have been investigated for DNA binding properties. In vitro interactional association between the Ag(I) complexes and ct-DNA has been examined by performing spectroscopic titrations on absorption spectrophotometer and fluorescence spectrophotometer. A competitive binding study has also been done using a fluorescence spectrophotometer with ethidium bromide as a classical intercalator. The spectroscopic methods revealed a major groove. Viscometry and agarose gel electrophoresis experiments have also been performed as physicochemical methods to confirm the binding of complex molecules with DNA. Molecular docking analysis has been executed to obtain the theoretical insight into the mode of binding. The docking study demonstrated the major groove binding of all four complexes to the DNA with electrostatic metal-phosphate interactions (between the metal and the backbone of DNA) and hydrophobic interactions. Cytotoxicity of the complexes has been studied on the Human Fibroblast foreskin (HFF) cell line. The cytotoxicity results showed positive gesture for moving ahead to the next level of screening; the values were above 10 μM which are appreciated for the normal cell lines.

Studies on the interactions of Ag(i) with DNA and their implication on the DNA-templated synthesis of silver nanoclusters and on the interaction with complementary DNA and RNA sequences

Silver nanoclusters (AgNCs) prepared by the reduction of silver ions in the presence of DNA oligonucleotides have attracted great interest as potential diagnostic tools for their tunable and high fluorescent properties. In this work, three DNA sequences that consist of a 12-nucleotide long probe sequence at the 5′-end linked to the complementary sequence to three miRNAs are studied. First, the interaction of these sequences with Ag(i) was characterized by means of circular dichroism spectroscopy. By applying multivariate methods to the analysis of spectroscopic data, two complexes with different Ag(i) : DNA ratios were resolved. Secondly, the impact of several experimental variables, such as temperature, borohydride concentration and reaction time, on the formation of AgNCs templated by these three sequences was studied. Finally, the fluorescence properties of the duplexes formed by DNA probes with complementary DNA or miRNA sequences were studied. The results presented here highlight the role of the secondary structure adopted by the DNA probe on the fluorescence properties of DNA-stabilized AgNCs which, in turn, affect the development of methods for miRNA detection.

Variables affecting the fluorescent properties of DNA-stabilized silver nanoclusters are studied. The secondary structure of the AgNC-stabilizing DNA sequence dramatically affects the analytical signal behind the hybridization reaction.

Passivating Nucleobases Bring Charge Transfer Character to Optically Active Transitions in Small Silver Nanoclusters

DNA-wrapped silver nanoclusters (DNA-AgNCs) are known for their efficient luminescence. However, their emission is highly sensitive to the DNA sequence, the cluster size, and its charge state. To get better insights into photophysics of these hybrid systems, simulations based on density functional theory (DFT) are performed. Our calculations elucidate the effect of the structural conformations, charges, solvent polarity, and passivating bases on optical spectra of DNA-AgNCs containing five and six Ag atoms. It is found that inclusion of water in calculations as a polar solvent media results in stabilization of nonplanar conformations of base-passivated clusters, while their planar conformations are more stable in vacuum, similar to the bare Ag₅ and Ag₆ clusters. Cytosines and guanines interact with the cluster twice stronger than thymines, due to their larger dipole moments. In addition to the base-cluster interactions, hydrogen bonds between bases notably contribute to the structure stabilization. While the relative intensity, line width, and the energy of absorption peaks are slightly changing depending on the cluster charge, conformations, and base types, the overall spectral shape with five well-resolved bands at 2.5-5.5 eV is consistent for all structures. Independent of the passivating bases and the cluster size and charge, the low energy optical transitions at 2.5-3.5 eV exhibit a metal to ligand charge transfer (MLCT) character with the main contribution emerging from Ag-core to the bases. Cytosines facilitate the MLCT character to a larger degree comparing to the other bases. However, the doublet transitions in clusters with the open shell electronic structure (Ag₅ and Ag₆⁺) result in appearance of additional red-shifted (<2.5 eV) and optically weak band with negligible MLCT character. The passivated clusters with the closed shell electronic structure (Ag₅⁺ and Ag₆) exhibit higher optical intensity of their lowest transitions with much higher MLCT contribution, thus having better potential for emission, than their open shell counterparts.

Comparative study of gold and silver interactions with amino acids and nucleobases

Metal nanoclusters (NCs) have gained much attention in the last decade. In solution, metal nanoclusters can be stabilized by proteins, and, thus, exhibit many advantages in biocatalysis, biosensing, and bioimaging. In spite of much progress in the synthesis of polypeptide-stabilized gold (Au) clusters, their structure, as well as amino acid-cluster and amino acid-Au+ interactions, remain poorly understood. It is not entirely clear which amino acid (AA) residues and sites in the protein are preferred for binding. The understanding of NC-protein interactions and how they evolve in the polypeptide templates is the key to designing Au NCs. In this work, binding of gold ion Au+ and diatomic neutral gold nanocluster Au2 with a full set of α-proteinogenic amino acids is studied using Density Functional Theory (DFT) and the ab initio RI-MP2 method in order to find the preferred sites of gold interaction in proteins. We demonstrated that the interaction of gold cations and clusters with protonated and deprotonated amino acid residues do not differ greatly. The binding affinity of AAs to the Au2 cluster increases in the following order: Cys(-H+) > Asp(-H+) > Tyr(-H+) > Glu(-H+) > Arg > Gln, His, Met ≫ Asn, Pro, Trp > Lys, Tyr, Phe > His(+H+) > Asp > Lys(+H+) > Glu, Leu > Arg(+H+) > Ile, Val, Ala > Thr, Ser > Gly, Cys, which agrees with the available experimental data that gold cluster synthesis occurs in a wide range of pH - amino acid residues with different protonation states are involved in this process. The significant difference in the binding energy of metal atoms with nucleobases and amino acids apparently means that unlike on DNA templates, neutral metal atoms are strongly bound to amino acid residues and can't freely diffuse in a polypeptide globula. This fact allows one to conclude that formation of metal NCs in proteins occurs through the nucleation of reduced Au atoms bound to the neighboring amino acid residues, and the flexibility of the amino acid residue side-chains and protein chain as a whole plays a significant role in this process.

On the photophysics of electrochemically generated silver nanoclusters: spectroscopic and theoretical characterization

Ligand-free atomic silver nanoclusters (AgNCs) were successfully synthesized following the electrochemical procedure developed by Lopez-Quintela and col. (D. Buceta, N. Busto, G. Barone, J. M. Leal, F. Domínguez, L. J. Giovanetti, F. G. Requejo, B. García and M. A. López-Quintela, Angew. Chem., Int. Ed., 2015, 54, 7612-7616), who have identified the presence of Ag₂ and Ag₃ AgNCs. The goal of this work was to get information on the photophysics of these AgNCs, which was achieved by combining information from excitation/emission matrix (EEM) and time resolved emission spectroscopy (TRES) along with DFT/TD-DFT calculations. This procedure allowed deconvolving the emission and excitation spectra of the AgNC mixture, with further assignment of each transition and lifetime associated to Ag₂, Ag₃⁺ and Ag₄²⁺ clusters. This deconvolution together with theoretical calculations allowed suggesting for the first time the radiative and non-radiative excited state deactivation mechanism for these clusters.

Micro RNA Sensing with Green Emitting Silver Nanoclusters

Micro RNA (miR) are regulatory non-coding RNA molecules, which contain a small number of nucleotides ~18-28 nt. There are many various miR sequences found in plants and animals that perform important functions in developmental, metabolic, and disease processes. miRs can bind to complementary sequences within mRNA molecules thus silencing mRNA. Other functions include cardiovascular and neural development, stem cell differentiation, apoptosis, and tumors. In tumors, some miRs can function as oncogenes, others as tumor suppressors. Levels of certain miR molecules reflect cellular events, both normal and pathological. Therefore, miR molecules can be used as biomarkers for disease diagnosis and prognosis. One of these promising molecules is miR-21, which can serve as a biomarker with high potential for early diagnosis of various types of cancer. Here, we present a novel design of miR detection and demonstrate its efficacy on miR-21. The design employs emissive properties of DNA-silver nanoclusters (DNA/AgNC). The detection probe is designed as a hairpin DNA structure with one side of the stem complimentary to miR molecule. The binding of target miR-21 opens the hairpin structure, dramatically modulating emissive properties of AgNC hosted by the C12 loop of the hairpin. "Red" fluorescence of the DNA/AgNC probe is diminished in the presence of the target miR. At the same time, "green" fluorescence is activated and its intensity increases several-fold. The increase in intensity of "green" fluorescence is strong enough to detect the presence of miR-21. The intensity change follows the concentration dependence of the target miR present in a sample, which provides the basis of developing a new, simple probe for miR detection. The detection strategy is specific, as demonstrated using the response of the DNA/AgNC probe towards the scrambled miR-21 sequence and miR-25 molecule. Additionally, the design reported here is very sensitive with an estimated detection limit at ~1 picomole of miR-21.

Synthetic Biology: A Solution for Tackling Nanomaterial Challenges

Bioengineers have mastered practical techniques for tuning a biomaterial's properties with only limited information on the relationship between the material's structure and function. These techniques have been quintessential to engineering proteins, which are most often riddled with ill-defined structure-function relationships. In this Perspective, we review bioengineering approaches aimed at overcoming the elusive protein structure-function relation. We extend these principles to engineering synthetic nanomaterials, specifically applying the underlying theory to optical sensors based on single-stranded DNA-wrapped single-walled carbon nanotubes (ssDNA-SWCNTs). Bioengineering techniques such as directed evolution, computational design, and noncanonical synthesis are reviewed in the broader context of nanomaterials engineering. We further provide an order-of-magnitude analysis of empirical approaches that rely on random or guided searches for designing new nanomaterials. The underlying concepts presented in these approaches can be further extended to a broad range of engineering fields confronted with empirical design strategies, including catalysis, metal-organic frameworks (MOFs), pharmaceutical dosing, and optimization algorithms.

Collective Response in DNA-Stabilized Silver Cluster Assemblies from First-Principles Simulations

We investigate fluorescence resonant energy transfer and concurrent electron dynamics in a pair of DNA-stabilized silver clusters. For this purpose we introduce a methodology for the simulation of collective optoelectronic properties of coupled molecular aggregates starting from first-principles quantum chemistry, which can be further applied to a broad range of coupled molecular systems to study their electro-optical response. Our simulations reveal the existence of low-energy coupled excitonic states, which enable ultrafast energy transport between subunits, and give insight into the origin of the fluorescence signal in coupled DNA-stabilized silver clusters, which have been recently experimentally detected. Hence, we demonstrate the possibility of constructing ultrasmall energy transmission lines and optical converters based on these hybrid molecular systems.

tRNA as a stabilizing matrix for fluorescent silver clusters: photophysical properties and IR study

In this experimental study fluorescent silver clusters on a tRNA matrix were synthesized for the first time. Two types of fluorescent complexes emitting in the green (550 nm) and red (635 nm) regions of the visible spectrum were obtained. Using FTIR spectroscopy, we identified possible binding sites for the clusters, which appeared to be within the helical regions of tRNA. It was also shown that tRNA retained its double helical structure after the cluster formation, which is essential for its functionality.

Glucose Sensor Using Redox Active Oligonucleotide-Templated Silver Nanoclusters

Redox active, photoluminescent silver nanoclusters templated with oligonucleotides were developed for glucose sensing. The silver nanoclusters had a photoluminescent emission at 610 nm that reversibly changed to 530 nm upon oxidation. The reversible emission change was measured with photoluminescent spectroscopy and used to detect H₂O₂, which is a by-product of the reaction of glucose with glucose oxidase. The ratio of the un-oxidised emission peak (610 nm) and the oxidised analogue (530 nm) was used to measure glucose concentrations up to 20 mM, well within glucose levels found in blood. Also, the reversibility of this system enables the silver nanoclusters to be reused.

Two-stage DNA compaction induced by silver ions suggests a cooperative binding mechanism

The interaction between silver ions and DNA plays an important role in the therapeutic use of silver ions and in related technologies such as DNA sensors. However, the underlying mechanism has not been fully understood. In this study, the dynamics of Ag⁺-DNA interaction at a single-molecule level was studied using magnetic tweezers. AgNO₃ solutions with concentrations ranging from 1 μM to 20 μM led to a 1.4-1.8 μm decrease in length of a single λ-DNA molecule, indicating that Ag⁺ has a strong binding with DNA, causing the DNA conformational change. The compaction process comprises one linear declining stage and another sigmoid-shaped stage, which can be attributed to the interaction mechanism. Considering the cooperative effect, the sigmoid trend was well explained using a phenomenological model. By contrast, addition of silver nanoparticle solution induced no detectable transition of DNA. The dependence of the interaction on ionic strength and DNA concentration was examined via morphology characterization and particle size distribution measurement. The size of the Ag⁺-DNA complex decreased with an increase in Ag⁺ ionic strength ranging from 1 μM to 1 mM. Morphology characterization confirmed that silver ions induced DNA to adopt a compacted globular conformation. At a fixed [AgNO₃]:[DNA base pairs] ratio, increasing DNA concentration led to increased sizes of the complexes. Intermolecular interaction is believed to affect the Ag⁺-DNA complex formation to a large extent.

Silver-Stabilized Guanine Duplex: Structural and Optical Properties

Recent experimental duplexes of DNA stabilized by Ag cations, pairing homostrands of guanine-guanine, cytosine-cytosine, adenine-thymine, and thymine-thymine, display much higher stability than the Watson-Crick paired DNA duplexes; these broaden the range of applications for DNA nanotechnology. Here we focus on silver-stabilized guanine duplexes in water. Using hybrid quantum mechanics/molecular mechanics simulations, we propose an atomic structure for the Ag⁺-mediated guanine duplex with two nucleobases per strand, G₂-Ag₂⁺-G₂. We then compare experimental and time-dependent density functional theory-simulated electronic circular dichroism (ECD) spectra to validate our results. Both experimental and simulated ECD share two negative peaks around 220 and 280 nm, with no positive signal in the measured wavelength range. We found that the left- or right-handed disposition of bases in the structure has a decisive effect on the signs of the ECD. We conclude that G₂-Ag₂⁺-G₂ is left-hand-oriented, and extrapolation of this orientation to longer strands gives rise to a left-hand-oriented parallel helix stabilized by interplanar H bonds.

DNA as UV light-harvesting antenna

The ordered structure of UV chromophores in DNA resembles photosynthetic light-harvesting complexes in which quantum coherence effects play a major role in highly efficient directional energy transfer. The possible role of coherent excitons in energy transport in DNA remains debated. Meanwhile, energy transport properties are greatly important for understanding the mechanisms of photochemical reactions in cellular DNA and for DNA-based artificial nanostructures. Here, we studied energy transfer in DNA complexes formed with silver nanoclusters and with intercalating dye (acridine orange). Steady-state fluorescence measurements with two DNA templates (15-mer DNA duplex and calf thymus DNA) showed that excitation energy can be transferred to the clusters from 21 and 28 nucleobases, respectively. This differed from the DNA-acridine orange complex for which energy transfer took place from four neighboring bases only. Fluorescence up-conversion measurements showed that the energy transfer took place within 100 fs. The efficient energy transport in the Ag-DNA complexes suggests an excitonic mechanism for the transfer, such that the excitation is delocalized over at least four and seven stacked bases, respectively, in one strand of the duplexes stabilizing the clusters. This result demonstrates that the exciton delocalization length in some DNA structures may not be limited to just two bases.

DNA-protected silver emitters: charge dependent switching of fluorescence

The relationship between the state of charge and spectroscopy of DNA-protected silver emitters is not yet well understood. This remains one of the major issues to unveil in order to fully disentangle the spectroscopic features of these novel systems. It is a well known fact that a fluorescence response arises upon chemical reduction of silver cations attached to DNA, leading to neutral (or partially oxidized) "bright" clusters. It is important to note that the absence of fluorescence in completely ionic complexes is universal in the sense that it does not depend on any experimental variable. This suggests that its origin may be founded on the nature of the interaction between DNA bases and silver cations. Nevertheless, to the best of our knowledge, no explanation exists for this charge dependent switching between dark completely ionic complexes and bright (neutral or partially oxidized) clusters. In this brief report we address this experimental fact on the basis of the electronic structure of the complex as a function of its charge and quantum dynamical simulations of the processes following photoexcitation. These data provide a dynamical picture of the correlation between charge and fluorescence.

Silver-Mediated Double Helix: Structural Parameters for a Robust DNA Building Block

The DNA double helix is a versatile building block used in DNA nanotechnology. To potentiate the discovery of new DNA nanoscale assemblies, recently, silver cations have been introduced to pair DNA strands by base-Ag⁺-base bonding rather than by Watson-Crick pairing. In this work, we study the classical dynamics of a parallel silver-mediated homobase double helix and compare it to the dynamics of the antiparallel double helix. Our classical simulations show that only the parallel double helix is highly stable through the 100 ns simulation time. A new type of H-bond previously proposed by our collaboration and recently observed in crystal-determined helices drives the physicochemical stabilization. Compared to the natural B-DNA form, the metal-mediated helix has a contracted axial base pair rise and smaller numbers of base pairs per turn. These results open the path for the inclusion of this robust metal-mediated building block into new nanoscale DNA assemblies.

Probing the Absorption and Emission Transition Dipole Moment of DNA Stabilized Silver Nanoclusters

Using single molecule polarization measurements, we investigate the excitation and emission polarization characteristics of DNA stabilized silver nanoclusters (C24-AgNCs). Although small changes in the polarization generally accompany changes to the emission spectrum, the emission and excitation transition dipoles tend to be steady over time and aligned in a similar direction, when immobilized in PVA. The emission transition dipole patterns, observed for C24-AgNCs in defocused wide field imaging, match that of a single emitter. The small changes to the polarization and spectral shifting that were observed could be due to changes to the conformation of the AgNC or the DNA scaffold. Although less likely, an alternative explanation could be that several well aligned spectrally similar emitters are present within the DNA scaffold which, due to Förster resonance energy transfer (FRET) processes such as energy hopping, energy transfer, and singlet-singlet annihilation, behave as a single emitter. The reported results can provide more insight in the structural and photophysical properties of DNA-stabilized AgNCs.