Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Magic Numbers in DNA-Stabilized Fluorescent Silver Clusters Lead to Magic Colors.

ABSTRACT: DNA-stabilized silver clusters are remarkable for the selection of fluorescence color by the sequence of the stabilizing DNA oligomer. Yet despite a growing number of applications that exploit this property, no large-scale studies have probed origins of cluster color or whether certain colors occur more frequently than others. Here we employ a set of 684 randomly chosen 10-base oligomers to address these questions. Rather than a flat distribution, we find that specific color bands dominate. Cluster size data indicate that these "magic colors" originate from the existence of magic numbers for DNA-stabilized silver clusters, which differ from those of spheroidal gold clusters stabilized by small-molecule ligands. Elongated cluster structures, enforced by multiple base ligands along the DNA, can account for both magic number sizes and color variation around peak wavelength populations.

SUBMITTER: Copp SM

PROVIDER: S-EPMC3985885 | biostudies-other | 2014 Mar

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

Magic Numbers in DNA-Stabilized Fluorescent Silver Clusters Lead to Magic Colors.

Copp Stacy M SM Schultz Danielle D Swasey Steven S Pavlovich James J Debord Mark M Chiu Alexander A Olsson Kevin K Gwinn Elisabeth E

The journal of physical chemistry letters 20140227 6

DNA-stabilized silver clusters are remarkable for the selection of fluorescence color by the sequence of the stabilizing DNA oligomer. Yet despite a growing number of applications that exploit this property, no large-scale studies have probed origins of cluster color or whether certain colors occur more frequently than others. Here we employ a set of 684 randomly chosen 10-base oligomers to address these questions. Rather than a flat distribution, we find that specific color bands dominate. Clus ...[more]

PMID: 24803994

Similar Datasets

Measuring DNA hybridization using fluorescent DNA-stabilized silver clusters to investigate mismatch effects on therapeutic oligonucleotides.

Project description:BackgroundShort nucleic acid oligomers have found a wide range of applications in experimental physics, biology and medicine, and show potential for the treatment of acquired and genetic diseases. These applications rely heavily on the predictability of hybridization through Watson-Crick base pairing to allow positioning on a nanometer scale, as well as binding to the target transcripts, but also off-target binding to transcripts with partial homology. These effects are of particular importance in the development of therapeutic oligonucleotides, where off-target effects caused by the binding of mismatched sequences need to be avoided.ResultsWe employ a novel method of probing DNA hybridization using optically active DNA-stabilized silver clusters (Ag-DNA) to measure binding efficiencies through a change in fluorescence intensity. In this way we can determine their location-specific sensitivity to individual mismatches in the sequence. The results reveal a strong dependence of the hybridization on the location of the mismatch, whereby mismatches close to the edges and center show a relatively minor impact. In parallel, we propose a simple model for calculating the annealing ratios of mismatched DNA sequences, which supports our experimental results.ConclusionThe primary result shown in this work is a demonstration of a novel technique to measure DNA hybridization using fluorescent Ag-DNA. With this technique, we investigated the effect of mismatches on the hybridization efficiency, and found a significant dependence on the location of individual mismatches. These effects are strongly influenced by the length of the used oligonucleotides. The novel probe method based on fluorescent Ag-DNA functions as a reliable tool in measuring this behavior. As a secondary result, we formulated a simple model that is consistent with the experimental data.

| S-EPMC5887185 | biostudies-literature

Phosphorothioate DNA Stabilized Fluorescent Gold and Silver Nanoclusters.

Project description:Unmodified single-stranded DNA has recently gained popularity for the templated synthesis of fluorescent noble metal nanoclusters (NCs). Bright, stable, and biocompatible clusters have been developed primarily through optimization of DNA sequence. However, DNA backbone modifications have not yet been investigated. In this work, phosphorothioate (PS) DNAs are evaluated in the synthesis of Au and Ag nanoclusters, and are employed to successfully template a novel emitter using T15 DNA at neutral pH. Mechanistic studies indicate a distinct UV-dependent formation mechanism that does not occur through the previously reported thymine N3. The positions of PS substitution have been optimized. This is the first reported use of a T15 template at physiological pH for AgNCs.

| S-EPMC5312886 | biostudies-literature

Interplay between Perovskite Magic-Sized Clusters and Amino Lead Halide Molecular Clusters.

Project description:Recent progress has been made on the synthesis and characterization of metal halide perovskite magic-sized clusters (PMSCs) with ABX 3 composition (A = CH3NH3 + or Cs+, B = Pb2+, and X = Cl-, Br-, or I-). However, their mechanism of growth and structure is still not well understood. In our effort to understand their structure and growth, we discovered that a new species can be formed without the CH3NH3 + component, which we name as molecular clusters (MCs). Specifically, CH3NH3PbBr3 PMSCs, with a characteristic absorption peak at 424 nm, are synthesized using PbBr2 and CH3NH3Br as precursors and butylamine (BTYA) and valeric acid (VA) as ligands, while MCs, with an absorption peak at 402 nm, are synthesized using solely PbBr2 and BTYA, without CH3NH3Br. Interestingly, PMSCs are converted spontaneously overtime into MCs. An isosbestic point in their electronic absorption spectra indicates a direct interplay between the PMSCs and MCs. Therefore, we suggest that the MCs are precursors to the PMSCs. From spectroscopic and extended X-ray absorption fine structure (EXAFS) results, we propose some tentative structural models for the MCs. The discovery of the MCs is critical to understanding the growth of PMSCs as well as larger perovskite quantum dots (PQDs) or nanocrystals (PNCs).

| S-EPMC7877386 | biostudies-literature

Magic Numbers for the Photoelectron Anisotropy in Li-Doped Dimethyl Ether Clusters.

Project description:Photoelectron velocity map imaging of Li(CH3OCH3) n clusters (1 ≤ n ≤ 175) is used to search for magic numbers related to the photoelectron anisotropy. Comparison with density functional calculations reveals magic numbers at n = 4, 5, and 6, resulting from the symmetric charge distribution with high s-character of the highest occupied molecular orbital. Since each of these three cluster sizes correspond to the completion of a first coordination shell, they can be considered as "isomeric motifs of the first coordination shell". Differences in the photoelectron anisotropy, the vertical ionization energies and the enthalpies of vaporization between Li(CH3OCH3) n and Na(CH3OCH3) n can be rationalized in terms of differences in their solvation shells, atomic ionization energies, polarizabilities, metal-oxygen bonds, ligand-ligand interactions and by cooperative effects.

| S-EPMC6441944 | biostudies-literature

Base-Directed Formation of Fluorescent Silver Clusters.

Project description:Small silver clusters that form with short oligonucleotides are distinguished by their strong fluorescence. Previous work showed that red and blue/green emitting species form with the cytosine oligonucleotide dC12. To understand how the bases and base sequence influence cluster formation, the blue/green emitting clusters that form with the thymine-containing oligonucleotides dT12, dT4C4T4, and dC4T4C4 are discussed. With dT12 and dT4C4T4, variations in the solution pH establish that the clusters associate with the N3 of thymine. The small clusters are bound to the larger DNA template, as demonstrated by fluorescence anisotropy, circular dichroism, and fluorescence correlation spectroscopy (FCS) studies. For dT4C4T4, FCS studies showed that approximately 50% of the strands are labeled with the fluorescent clusters. Absorption spectra and the gas dependence of the fluorescence show that nonfluorescent clusters also form following the reduction of the silver cation - oligonucleotide conjugates. Fluorescent cluster formation is favored by oxygen, thus indicating that the DNA-bound clusters are partially oxidized. To elaborate the sequence dependence of cluster formation, dC4T4C4 was studied. Cluster formation depends on the oligonucleotide concentration, and higher concentrations favor a red emitting species. A blue/green emissive species dominates at lower concentrations of dC4T4C4, and it has spectroscopic, physical, and chemical properties that are similar to those of the clusters that form with dT12 and dT4C4T4. These results suggest that cytosine- and thymine-containing oligonucleotides stabilize a preferred emissive silver cluster.

| S-EPMC6178949 | biostudies-literature

Label-Free Fluorescent Detection of Trypsin Activity Based on DNA-Stabilized Silver Nanocluster-Peptide Conjugates.

Project description:Trypsin is important during the regulation of pancreatic exocrine function. The detection of trypsin activity is currently limited because of the need for the substrate to be labeled with a fluorescent tag. A label-free fluorescent method has been developed to monitor trypsin activity. The designed peptide probe consists of six arginine molecules and a cysteine terminus and can be conjugated to DNA-stabilized silver nanoclusters (DNA-AgNCs) by Ag-S bonding to enhance fluorescence. The peptide probe can also be adsorbed to the surface of graphene oxide (GO), thus resulting in the fluorescence quenching of DNA-AgNCs-peptide conjugate because of Förster resonance energy transfer. Once trypsin had degraded the peptide probe into amino acid residues, the DNA-AgNCs were released from the surface of GO, and the enhanced fluorescence of DNA-AgNCs was restored. Trypsin can be determined with a linear range of 0.0-50.0 ng/mL with a concentration as low as 1 ng/mL. This label-free method is simple and sensitive and has been successfully used for the determination of trypsin in serum. The method can also be modified to detect other proteases.

| S-EPMC5134428 | biostudies-literature

Switchable Dual-Emissive DNA-Stabilized Silver Nanoclusters.

Project description:We investigated an ss-DNA sequence that can stabilize a red- and a green-emissive silver nanocluster (DNA-AgNC). These two emitters can convert between each other in a reversible way. The change from red- to green-emitting DNA-AgNCs can be triggered by the addition of H2O2, while the opposite conversion can be achieved by the addition of NaBH4. Besides demonstrating the switching between red- and green-emissive DNA-AgNCs and determining the recoverability, we fully characterized the photophysical properties, such as steady-state emission, quantum yield, fluorescence lifetime, and anisotropy of the two emissive species. Understanding the mechanism behind the remarkable conversion between the two emitters could lead to the development of a new range of DNA-AgNC-based ratiometric sensors.

| S-EPMC6693819 | biostudies-literature

Chloride Ligands on DNA-Stabilized Silver Nanoclusters.

Project description:DNA-stabilized silver nanoclusters (AgN-DNAs) are known to have one or two DNA oligomer ligands per nanocluster. Here, we present the first evidence that AgN-DNA species can possess additional chloride ligands that lead to increased stability in biologically relevant concentrations of chloride. Mass spectrometry of five chromatographically isolated near-infrared (NIR)-emissive AgN-DNA species with previously reported X-ray crystal structures determines their molecular formulas to be (DNA)2[Ag16Cl2]8+. Chloride ligands can be exchanged for bromides, which red-shift the optical spectra of these emitters. Density functional theory (DFT) calculations of the 6-electron nanocluster show that the two newly identified chloride ligands were previously assigned as low-occupancy silvers by X-ray crystallography. DFT also confirms the stability of chloride in the crystallographic structure, yields qualitative agreement between computed and measured UV-vis absorption spectra, and provides interpretation of the 35Cl-nuclear magnetic resonance spectrum of (DNA)2[Ag16Cl2]8+. A reanalysis of the X-ray crystal structure confirms that the two previously assigned low-occupancy silvers are, in fact, chlorides, yielding (DNA)2[Ag16Cl2]8+. Using the unusual stability of (DNA)2[Ag16Cl2]8+ in biologically relevant saline solutions as a possible indicator of other chloride-containing AgN-DNAs, we identified an additional AgN-DNA with a chloride ligand by high-throughput screening. Inclusion of chlorides on AgN-DNAs presents a promising new route to expand the diversity of AgN-DNA structure-property relationships and to imbue these emitters with favorable stability for biophotonics applications.

| S-EPMC10197127 | biostudies-literature

Silver-induced reconstruction of an adeninate-based metal-organic framework for encapsulation of luminescent adenine-stabilized silver clusters.

Project description:Bright luminescent silver-adenine species were successfully stabilized in the pores of the MOF-69A (zinc biphenyldicarboxylate) metal-organic framework, starting from the intrinsically blue luminescent bio-MOF-1 (zinc adeninate 4,4'-biphenyldicarboxylate). Bio-MOF-1 is transformed to the MOF-69A framework by selectively leaching structural adenine linkers from the original framework using silver nitrate solutions in aqueous ethanol. Simultaneously, bright blue-green luminescent silver-adenine clusters are formed inside the pores of the recrystallized MOF-69A matrix in high local concentrations. The structural transition and concurrent changes in optical properties were characterized using a range of structural, physicochemical and spectroscopic techniques (steady-state and time-resolved luminescence, quantum yield determination, fluorescence microscopy). The presented results open new avenues for exploring the use of MOFs containing luminescent silver clusters for solid-state lighting and sensor applications.

| S-EPMC5361144 | biostudies-literature

DNA-Directed Fluorescence Switching of Silver Clusters.

Project description:Silver clusters with ?30 atoms are molecules with diverse electronic spectra and wide-ranging emission intensities. Specific cluster chromophores form within DNA strands, and we consider a DNA scaffold that transforms a pair of silver clusters. This ~20-nucleotide strand has two components, a cluster domain (S1) that stabilizes silver clusters and a recognition site (S2) that hybridizes with complementary oligonucleotides (S2C). The single-stranded S1-S2 exclusively develops clusters with violet absorption and low emission. This conjugate hybridizes with S2C to form S1-S2:S2C, and the violet chromophore transforms to a fluorescent counterpart with ?ex ? 490 nm/?em ? 550 nm and with ~100-fold stronger emission. Our studies focus on both the S1 sequence and structure that direct this violet ? blue-green cluster transformation. From the sequence perspective, C4X sequences with X = adenine, thymine, and/or guanine favor the blue-green cluster, and the specificity of the binding site depends on three factors: the number of C4X repeats, the identity of the X nucleobase, and the number of contiguous cytosines. A systematic series of oligonucleotides identified the optimal S1 sequence C4AC4T and discerned distinct roles for the adenine, thymine, and cytosines. From the structure perspective, two factors guide the conformation of the C4AC4T sequence: hybridization with the S2C complement and coordination by the cluster adduct. Spectroscopic and chromatographic studies show that the single-stranded C4AC4T is folded by its blue-green cluster adduct. We propose a structural model in which the two C4X motifs within C4AC4T are cross-linked by the encapsulated cluster. These studies suggest that the structures of the DNA host and the cluster adduct are interdependent.

| S-EPMC6136663 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data