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 Au
2
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 Au
2
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.
Our calculations showed that amino acids stabilize gold nanoclusters; binding energy between organics and gold is higher than between organics and silver.
Tyrosine (Tyr) is involved in the synthesis of neurotransmitters, catecholamines, thyroid hormones, etc. Multiple pathologies are associated with impaired Tyr metabolism. Silver nanoclusters (Ag NCs) ...can be applied for colorimetric, fluorescent, and surface-enhanced Raman spectroscopy (SERS) detection of Tyr. However, one should understand the theoretical basics of interactions between Tyr and Ag NCs. Thereby, we calculated the binding energy (E
) between Tyr and Ag
(n = 1-8; q = 0-2) NCs using the density functional theory (DFT) to find the most stable complexes. Since Ag NCs are synthesized on Tyr in an aqueous solution at pH 12.5, we studied Tyr
, semiquinone (SemiQ
), and Tyr
. Ag
and Ag
had the highest E
. The absorption spectrum of Tyr
significantly red-shifts with the attachment of Ag
, which is prospective for colorimetric Tyr detection. Ag
interacts with all functional groups of SemiQ
(phenolate, amino group, and carboxylate), which makes detection of Tyr possible due to band emergence at 1324 cm
in the vibrational spectrum. The ground state charge transfer between Ag and carboxylate determines the band emergence at 1661 cm
in the Raman spectrum of the SemiQ
-Ag
complex. Thus, the prospects of Tyr detection using silver nanoclusters were demonstrated.
Binding of silver ion (Ag
+
) and two atomic neutral silver cluster (Ag
2
) with a set of amino acids has been studied using Density Functional Theory (DFT) and ab initio MP2 method. We show that ...binding energy with Ag
2
is higher for deprotonated anionic amino acids. Cysteine, aspartic acid, and tyrosine with deprotonated side chain exhibit the highest binding energy (
G
bind
) values among all the amino acids: − 30.1 kcal mol
−1
, − 30.7 kcal mol
−1
, and − 30.9 kcal mol
−1
, respectively. Binding energies of deprotonated cysteine, glutamic acid, tyrosine, and aspartic acid with silver ion Ag
+
are reported here for the first time. Natural bond orbital (NBO) analysis has also been performed to calculate charge transfer, natural populations, occupancies, and Wiberg bond indices of the amino acid–Ag
2
complexes. Atoms-in-molecules (AIM) theory was used to establish the nature of interactions. It was shown that, in most cases, the bonds between amino acid and Ag
2
cluster are partially electrostatic and partially covalent.
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•Interactions between pterin (Ptr) and Ag clusters have been explored using quantum chemistry.•It has been established that Ptr-Ag32+ complex is the most favorable one.•Presence of Ag ...clusters significantly red-shifts the absorption spectrum of Ptr.•SERS detection has potential benefits in both acidic and alkaline pH.
Metal nanoclusters (NCs) are widely present today in biosensing, bioimaging, and diagnostics due to their small size, great biocompatibility, and sensitivity to the biomolecular environment. Silver (Ag) NCs often possess intense fluorescence, photostability, and low photobleaching, which is in high demand during the detection of organic molecules. Pterins are small compounds, which are used in medicine as biomarkers of oxidative stress, cardiovascular diseases, neurotransmitter synthesis, inflammation and immune system activation. It is experimentally possible to detect pterin (Ptr) through the adsorption on Ag colloid. We optimized geometries and evaluated the binding energy in Ptr-Agnq complexes (n = 1–6; q = 0, +1, +2) using quantum chemistry methods. Different Ptr atoms were preferential for silver attachment depending on NC charge and size. The highest Eb was obtained for the complexes between the Ptr0 and Ag32+ (-50.8 kcal mol−1), between Ptr-1 and Ag32+ (-64.8 kcal mol−1), which means that these complexes should be formed preferably in aqueous solutions in acidic and alkaline media, respectively. The colorimetric detection of pterin with silver clusters does not seem to be promising. However, intense S0→S1 transitions of Ag5+ complexes look promising for luminescent Ptr detection. SERS detection of pterin is better to be done at pH > 8 since deprotonated pterin Raman undergo more dramatic changes upon addition of Ag than the neutral pterin. The characteristics of absorption and vibrational spectra of silver-pterin should be exploited during biosensor development.
Fluorescent beacons based on silver (Ag) clusters for DNA/RNA detection represent a new type of turn-on probe that fluoresces upon hybridization to target nucleobase sequences. Physical–chemical ...mechanisms of their fluorescence activation still remain poorly understood. We studied in detail the fluorescence activation of dark Ag clusters induced by interactions of Ag–DNA complexes with different DNA sequences. In all cases, the final result depends neither on the location of the precursors (dark clusters) nor on their spectral properties. The reaction of fluorescence activation is a process similar to the growth of fluorescent silver clusters on dsDNA matrices. In both cases, reactants are dark clusters and two adjacent DNA strands. The latter form a double-stranded template for cluster nucleation. We found the optimized structure of a green fluorescent Ag4 +2 cluster assembled on a C3/C3 DNA dimer in two different ssDNA pairs using QM modeling. The calculated absorption spectra match nicely the experimental ones, which proves the optimized structures. We conclude that apparent fluorescence activation in the studied systems results from reassembling Ag clusters on the new dsDNA template formed upon hybridization with the target. The suggested mechanism of “fluorescence activation” offers a way to design new light-up DNA probes. Two DNA strands making up the dsDNA template providing a high yield of bright Ag clusters can be used as the halves with the “stick” tails hybridizing with the base sequence of the target DNA. In this way, we have designed a light-up Ag cluster probe for β-actin mRNA.
We calculate geometry and electronic excitation spectra of silver clusters containing 1–6 atoms bound to single DNA bases and also to dC3 cytosine oligomer using density functional theory method. We ...show that planar shaped silver clusters complexed with the bases exhibit nearly forbidden the lowest transitions and weak fluorescence ability. Their calculated spectra do not appear to match experimentally observed fluorescence excitation spectra of silver clusters on DNA and other polymers. On the contrary, threadlike-shaped silver clusters reveal intense the lowest transition, energy of which depends on the chain bend. We show the equilibrium structures of Ag3 + cluster stabilized by oxygen atoms on phosphates and in the minor groove of dC3 oligomer. The calculated excitation spectrum of Ag3 + cluster in the minor groove appears to be close to the experimental spectrum of green emitting clusters on cytosine oligomers.
DNA as UV light-harvesting antenna Volkov, Ivan L; Reveguk, Zakhar V; Serdobintsev, Pavel Yu ...
Nucleic acids research,
04/2018, Letnik:
46, Številka:
7
Journal Article
Recenzirano
Odprti dostop
Abstract
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.
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.
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•Gold clusters can be synthesized directly in human serum.•Gold clusters on albumins and immunoglobulins differ in spectral properties.•Joint colorimetric and fluorescence assay ...allows quantification of serum proteins.
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.
The rapidly developing field of bionanotechnology requires detailed knowledge of the mechanisms of interaction between inorganic matter and biomolecules. Under conditions different from those in an ...aqueous solution, however, the chemistry of these systems is elusive and may differ dramatically from their interactions in vitro and in vivo. Here, we report for the first time a photoemission study of a metal silver–DNA interface, formed in vacuo, in comparison with DNA–Ag+ and fluorescent DNA–Ag complexes formed in solution. The high-resolution photoelectron spectra reveal that in vacuo silver atoms interact mainly with oxygen atoms of the phosphodiester bond and deoxyribose in DNA, in contrast to the behavior of silver ions, which interact preferentially with the nitrogen atoms of the bases. This offers new insight into the mechanism of DNA metallization, which is of importance in creating metal–bio interfaces for nanotechnology applications.
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