DNA as a template for synthesis of fluorescent gold nanoclusters

Water-soluble blue-emitting gold nanoclusters have been synthesized using dsDNA as a template without any additional reducing agent. The features of the formed nanoclusters have been revealed by fluorescence and electronic absorption spectroscopy as well as transmission electron microscopy. The prepared gold nanoclusters have been highly stable at physiological pH without any further modification.     

Spectroscopy of Ru(II) polypyridyl complexes used as intercalators in DNA: Towards a theoretical study of the light switch effect

The absorption spectroscopy of [Ru(phen)₂dppz]²⁺ and [Ru(tap)₂dppz]²⁺ (phen = 1,10-phenanthroline, tap = 1,4,5,8-tetraazaphenanthrene; dppz = dipyridophenazine) complexes used as molecular light switches by intercalation in DNA has been analysed by means of Time-Dependent Density Functional Theory (TD-DFT). The electronic ground state structures have been optimized at the DFT (B3LYP) level of theory. The absorption spectra are characterized by a high density of excited states between 500 nm and 250 nm. The absorption spectroscopy of [Ru (phen)₂dppz]²⁺ in vacuum is characterized by metal-to-ligand-charge-transfer (MLCT) transitions corresponding to charge transfer from Ru(II) either to the phen ligands or to the dppz ligand with a strong MLCT () absorption at 411 nm. In contrast, the main feature of the lowest part of the vacuum theoretical spectrum of [Ru(tap)₂dppz]²⁺ between 522 nm and 400 nm is the presence of various excited states such as MLCT (), ligand-to-ligand-charge-transfer LLCT () or intra-ligand IL () states. When taking into account solvent corrections within the polarizable continuum model (PCM) approach (H₂O, CH₃CN) the absorption spectrum of [Ru(tap)₂dppz]²⁺ is dominated by a strong absorption at 388 nm (CH₃CN) or 390 nm (H₂O) assigned to a ¹IL () corresponding to a charge transfer from the outside end of the dppz ligand to the site of coordination to Ru(II). These differences in the absorption spectra of the two Ru(II) complexes have dramatic effects on the mechanism of deactivation of these molecules after irradiation at about 400 nm. In particular, the electronic deficiency at the outside end of the dppz ligand created by absorption to the ¹IL state will favour electron transfer from the guanine to the Ru(II) complex when it is intercalated in DNA.     

Dynamic-light-scattering-based sequence-specific recognition of double-stranded DNA with oligonucleotide-functionalized gold nanoparticles

An ultrasensitive and simple dynamic-light-scattering (DLS) assay for the sequence-specific recognition of double-stranded DNA (dsDNA) was developed based on detection of the average diameter change of Au nanoparticle (AuNP) probes modified with oligonucleotides 5'-TTTCTCTTCCTT- CTCTTC-(T)(12)-SH-3' (Oligo 1) and 5'-TTCTTTCTTTTCTTTTTC-(T)(12)- SH-3' (Oligo 2). The target dsDNA was composed of two complementary oligonucleotides: 5'-AAAGAGAAGGAAGAGAAGAAGAAAGAAAAGAAAAAG-3' (Oligo 3) and 3'-TTTCTCTTCCTTCTCTTCTTCTTTCTTTTCTTTTTC-5' (Oligo 4). Hybridization of the two AuNPs-Oligo probes with the target dsDNA induced aggregation of the target dsDNA by forming triplex DNA, which accordingly increased the average diameter. This diameter change could then be detected by DLS. The average diameter was proportional to the target dsDNA concentration over the range from 593 fM to 40 pM, with a detection limit of 593 fM. Moreover, the assay had good sequence specificity for the target dsDNA.     

New potential DNA intercalators of the carbazole series from indole-2,3-quinodimethanes: Synthesis,crystal structure,and molecular modeling with a watson-crick mini-helix

Summary 1-Alkylpyrano[3,4-b]indol-3-ones3 react via a Diels-Alder step with an aryne or N-phenylmaleimide to furnish the new [b]annellated carbazoles4–10 in a one-pot process. In an analogous procedure, the in situ generated N-benzoylindole-2,3-quinodimethane (13) reacted with quinones to furnish the dioxocarbazoles14–16. Compounds4–8 and14–16 with a coplanar skeleton are members of a class of potential DNA intercalators, as has been shown for5 and8 by X-ray structural analysis. On the basis of the geometries determined by X-ray crystallography, the intercalative binding of these molecules with a Watson-Crick mini-helix was predicted by molecular modeling methods.

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Neue potentielle DNA-Interkalatoren der Carbazol-Reihe aus Indol-2,3-chinodimethanen: Synthese, Kristallstruktur und Molecular Modeling mit einer Watson-Crick Minihelix

Zusammenfassung 1-Alkylpyrano[3,4-b]indol-3-one3 reagieren über einen Diels-Alder-Schritt mit Arin oder N-Phenylmaleinimid zu [b]annellierten Carbazolen4–10 in einer Einstufenreaktion. In analoger Weise reagiert ein in situ erzeugtes N-Benzoylindol-2,3-chinodimethan13 mit Chinonen zu den Dioxocarbazolen14–16. Die Verbindungen4–8 und14–16 gehören infolge ihrer coplanaren Struktur zur Klasse potentieller DNA-Interkalatoren. Auf der Basis von Röntgenstrukturanalysen von5 und8 wird die interkalative Bindung mit einer Watson-Crick Minihelix durch Molecular Modeling vorhergesagt.

     

纳米金-曙红Y体系荧光增强法检测异烟肼

基于异烟肼对纳米金-曙红Y体系的荧光增强作用,通过测定加入异烟肼前后体系荧光信号变化与异烟肼含量的关系,建立测定异烟肼的荧光分析方法.并探讨了实验机理,在优化的实验条件下,方法的线性范围为0.02～2.0 μg/mL,检出限为9 ng/mL.对异烟肼片中异烟肼含量进行了测定,测定值与标识值没有显著差异,加标回收率在96...     

Discovery of the DNA "genetic code" for abiological gold nanoparticle morphologies

DNA is in control: Different combinations of DNA nucleotides can control the shape and surface roughness of gold nanoparticles during their synthesis. These nanoparticles were synthesized in the presence of either homogenous oligonucleotides or mixed-base oligonucleotides using gold nanoprisms as seeds. The effect of the individual DNA bases and their combinations on shape control are shown in the figure.     

Ultrafast excited-state dynamics of DNA fluorescent intercalators: new insight into the fluorescence enhancement mechanism

The excited-state dynamics of the DNA bisintercalator YOYO-1 and of two derivatives has been investigated using ultrafast fluorescence up-conversion and time-correlated single photon counting. The free dyes in water exist in two forms: nonaggregated dyes and intramolecular H-type aggregates, the latter form being only very weakly fluorescent because of excitonic interaction. The excited-state dynamics of the nonaggregated dyes is dominated by a nonradiative decay with a time constant of the order of 5 ps associated with large amplitude motion around the monomethine bridge of the cyanine chromophores. The strong fluorescence enhancement observed upon binding of the dyes to DNA is due to both the inhibition of this nonradiative deactivation of the nonaggregated dyes and the dissociation of the aggregates and thus to the disruption of the excitonic interaction. However, the interaction between the two chromophoric moieties in DNA is sufficient to enable ultrafast hopping of the excitation energy as revealed by the decay of the fluorescence anisotropy. Finally, these dyes act as solvation probes since a dynamic fluorescence Stokes shift was observed both in bulk water and in DNA. Very similar time scales were found in bulk water and in DNA.     

Differentiating a diverse range of volatile organic compounds with polyfluorophore sensors built on a DNA scaffold

Oligodeoxyfluorosides (ODFs) are short DNA-like oligomers in which DNA bases are replaced with fluorophores. A preliminary study reported that some sequences of ODFs were able to respond to a few organic small molecules in the vapor phase, giving a change in fluorescence. Here, we follow up on this finding by investigating a larger range of volatile organic analytes, and a considerably larger set of sensors. A library of tetramer ODFs of 2401 different sequences was prepared by using combinatorial methods, and was screened in air for fluorescence responses to a set of ten different volatile organics, including multiple aromatic and aliphatic compounds, acids and bases, varied functional groups, and closely related structures. Nineteen responding sensors were selected and characterized. These sensors were cross-screened against all ten analytes, and responses were measured qualitatively (by changes in color and intensity) and quantitatively (by measuring ΔR, ΔG, and ΔB values averaged over five to six sensor beads; R=red, G=green, B=blue). The results show that sensor responses were diverse, with a single sensor responding differently to as many as eight of the ten analytes; multiple classes of responses were seen, including quenching, lighting-up, and varied shifts in wavelength. Responses were strong, with raw ΔR, ΔG, and ΔB values of as high as >200 on a 256-unit scale and unamplified changes in many cases apparent to the naked eye. Sensors were identified that could distinguish clearly between even very closely related compounds such as acrolein and acrylonitrile. Statistical methods were applied to select a small set of four sensors that, as a pattern response, could distinguish between all ten analytes with high confidence. Sequence analysis of the full set of sensors suggested that sequence/order of the monomer components, and not merely composition, was highly important in the responses.     

Bifunctional DNA Architectonics: Three‐Way Junctions with Sticky Perylene Bisimide Caps and a Central Metal Lock

A new type of a bifunctional DNA architecture based on a three way junction is developed that combines the structural motif of sticky perylene bisimide caps with a tris‐bipyridyl metal ion lock in the center part. A clear stabilizing effect was observed in the presence of Fe³⁺, Ni²⁺ and Zn²⁺ by the formation of corresponding bipyridyl complexes in the branching part of the DNA three way junctions. The dimerization of the 5′‐terminally attached perylene diimides (PDI) chromophores by hydrophobic interactions can be followed by significant changes in the UV/Vis absorption and steady‐state fluorescence. The PDI‐mediated DNA assembly occurs at temperatures below the melting temperature and is not influenced by the metal‐ion bipyridyl locks in the central part. The corresponding AFM images revealed the formation of higher‐ordered structures as the result of DNA assemblies mediated by the PDI interactions.     

Visual scanometric detection of DNA through silver enhancement regulated by gold-nanoparticle aggregation with a molecular beacon as the trigger

A convenient and label-free scanometric approach for DNA assay was designed by integrating a metal-ion-mediated conformational molecular beacon (MB) and silver-signal amplification regulated by gold-nanoparticle (AuNP) aggregation. The strategy was based on displacing the interaction between the target DNA sequence and a competitor Hg(2+) ion with a link DNA sequence. In the absence of the target DNA sequence, a link DNA sequence interacted with the Hg(2+) ions, thus forming an inactive cyclic conformation of the MB. This result led to the poor aggregation of polyadenosine-functionalized AuNPs (A-AuNP). In the presence of a target DNA sequence with a stronger affinity than that of the competitor, hybridization between the link DNA and target DNA sequences turned on the trigger. The polythymidine end of the resulting linear duplex structure could react with A-AuNP, thus leading to a cross-linking aggregation. This aggregation weakened AuNP-catalyzed silver enhancement on a spot substrate. Further, by using scanometric detection, the concentration of the target DNA sequence could be conveniently read out within a linear range from 1.0 to 30 nM. Interestingly, in the same amount of Hg(2+) ions, one-base mismatched DNA showed only 22% of the relative gray-scale intensity for the target DNA sequence at the same concentration, thus indicating good specificity. The designed approach, with the help of the ion-mediated conformational MB, was simple, cost effective, adaptable, and convenient and provided significant potential applications in clinical analysis.     

基于未修饰纳米金及无标记单链DNA的Pb~(2+)比色测定

根据纳米金对ss DNA和G-四联体结构的DNA的不同吸附能力,设计了一种简单的Pb2+比色传感器。富含G的无标记ss DNA可以通过静电作用吸附于Au NPs表面,保护Au NPs在高盐浓度溶液中仍呈分散态;当Pb2+存在时,DNA与Pb2+结合形成Pb2+-G-四联体结构,使得Au NPs失去DNA的保护而发生聚集,溶液颜色由红色变成蓝色,最大吸收峰发生红移。通过优化条件,得到溶液吸光度比值(A630/A520)与Pb2+浓度在0.1~10μmol/L范围内呈良好的线性关系,检出限可达50 nmol/L。其他金属离子对Pb2+的检测几乎无干扰。该方法灵敏度高,选择性好,且无需复杂的Au NPs表面修饰过程及DNA标记,制备和操作简便、成本低、响应快(1 min),非常适合于现场实时应用。     

Fluorescent hydrophobic zippers inside duplex DNA: interstrand stacking of perylene-3,4:9,10-tetracarboxylic acid bisimides as artificial DNA base dyes

Perylene-3,4:9,10-tetracarboxylic acid bisimides (PBs) were incorporated synthetically into oligonucleotides by using automated DNA building-block chemistry. The 2'-deoxyribofuranoside of the natural nucleosides was replaced by (S)-aminopropan-2,3-diol as an acyclic linker between the phosphodiester bridges that is tethered to one of the imide nitrogen atoms of the PB dye. The S configuration of this linker was chosen to mimic the stereochemical situation at the 3'-position of the natural 2'-deoxyribofuranosides. By using this strategy, up to six PB dyes were incorporated in the middle of 18-mer DNA duplexes by using interstrand alternating sequences of PBs with thymines or an abasic site analogue. Both PB dimers and PB hexamers as artificial base substitutions inside the duplexes yield characteristic excimer-type fluorescence. The stacking properties of the PB chromophores are modulated by the presence or absence of thymines opposite the PB modification site in the counterstrand. The interstrand PB dimers can be regarded as hydrophobically interacting base pairs, which display a characteristic fluorescence readout signal. Hence, for the PB hexamers, we proposed a zipperlike recognition motif that is formed inside duplex DNA. The PB zipper shows characteristic excimer-type emission as a fluorescence readout signal for the pairing interaction.     

纳米金在DNA生物传感器和基因芯片研究中的应用

综述了近年来纳米金在DNA生物传感器及基因芯片中的研究、应用和发展,并对其在生物科技方面的发展趋势进行了展望。参考文献31篇。     

Positively Charged Compact Quantum Dot–DNA Complexes for Detection of Nucleic Acids

Selective DNA detection: The fluorescence, from stable cationic QDs, is quenched by 90% on complexation with modified DNA molecules. The QD–DNA probe is capable of detecting pathogenic DNA fragments at concentrations as low as 200 nM in solution and shows selective fluorescence recovery in the presence of target DNA (see spectrum c in figure) vs noncomplementary DNA (spectrum d).

     

DNA polyfluorophores for real-time multicolor tracking of dynamic biological systems

Dye-ing to live: Spectral limitations of common organic dyes make it difficult or impossible to visualize and follow multiple biological components in rapidly moving systems. The development of a multispectral set of improved DNA-scaffolded fluorophores is described. Their use in multicolor cellular imaging (see scheme) and in tracking of biological motions on the subsecond timescale is demonstrated.