Integration of G-quadruplex and DNA-templated Ag NCs for nonarithmetic information processing

Gao, Ruru; Yao, Tianming; Lv, Xiaoyan; Zhu, Yong; Zhang, Yi-Wei; Shi, Shuo

doi:10.1039/c7sc00361g

Cited by 50 publications

(29 citation statements)

References 72 publications

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“…Various techniques have been developed for the synthesis of stable, water‐soluble silver NCs by using dendrimers, polymers, polypeptides, thiols, DNA, thiolated DNA, and other ligands to stabilize silver ions . The influence of various thiolates on binding energy with silver NCs has been studied in details .…”

Section: Introductionmentioning

confidence: 99%

Predicting absorption spectra of silver‐ligand complexes

Buglak

Pomogaev

Kononov

2019

Int J of Quantum Chemistry

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The detailed structures of most of ligand-stabilized metal nanoclusters (NCs) remain unknown due to the absence of crystal structure data for them. In such a situation, quantum-chemical modeling is of particular interest. We compared the performance of different theoretical methods of geometry optimization and absorption spectra calculation for silver-thiolate complexes. We showed that the absorption spectra calculated with the ADC(2) method were consistent with the spectra obtained with CC2 method. Three DFT functionals (B3LYP, CAM-B3LYP, and M06-2X) failed to reproduce the CC2 absorption spectra of the silver-thiolate complexes. K E Y W O R D SADC(2), CAM-B3LYP, CC2, M062X, silver nanoclusters, silver-thiolate complexes, TDDFT | INTRODUCTIONLigand protected metal nanoclusters (NCs) have gained much attention in the last decade due to their unique physicochemical properties. These metal NCs typically measure less than 2 nm. [1,2] Electronic, chemical, and optical properties of NCs differ from both bulk and atomic scale materials. Optically active NCs may possess strong visible or near infrared luminescence, [3] which can be used in various applications, such as bioimaging, biosensing, and optical detection of biomolecules. [4] Among the great variety of NCs, gold (Au) NCs are the most extensively investigated due to their chemical stability. [5] However, fluorescent silver (Ag) clusters are the brightest, exhibiting high quantum yield and large absorption cross-section. [6] Various techniques have been developed for the synthesis of stable, water-soluble silver NCs by using dendrimers, [7] polymers, [8] polypeptides, [9,10] thiols, [11] DNA, [12,13] thiolated DNA, [14] and other ligands to stabilize silver ions. [15] The influence of various thiolates on binding energy with silver NCs has been studied in details. [16] The nature of the ligand seems to have a strong effect on fluorescent properties of noble metal NCs. [17] Noble metal NCs protected with thiolate ligands have been of interest because of their long-term stability, which allows one to use them as building blocks constructing assembled systems with novel and improved functions. [2] Silver-thiolate and silver-amino acid complexes are studied in many laboratories nowadays both theoretically and experimentally. [18][19][20] It is assumed that silver nanoclusters are stabilized by cysteine residues in protein matrices. [21,22] While the composition of the ligand-protected NCs can be analyzed using mass-spectroscopy technique, [23] their detailed structures remain unknown in many cases. In this respect, quantum-chemical modeling of silver-ligand complexes is of particular interest. [24][25][26][27][28][29][30][31][32] Gell and coworkers investigated thiolate-protected silver NCs that contained zero, two, or four confined electrons in the cluster core. [33] They found that the number of confined electrons determine the spectroscopic patterns. For systems with two or four confined electrons, strong absorption and fluorescence in the visible or even IR energ...

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Section: Introductionmentioning

confidence: 99%

Predicting absorption spectra of silver‐ligand complexes

Buglak

Pomogaev

Kononov

2019

Int J of Quantum Chemistry

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“…However,i ti sh ard to design G-quadruplexes with different subtypes in am ulti-output system,a nd only few investigations have attempted in this way. [101] As mentioned, imotifsh ave similar spatialp roperty as G-quadruplexes and have been involved in some logic systems. However,f ew multi-output circuits designed provide signals that are directly based on the structural conversion of i-motif till now,o wing to the lack of highly specific i-motif probes.…”

Section: Homogeneousand Label-free Signal Actuatorsmentioning

confidence: 97%

“…Yaoe tal. [101] then reported as eries of multi-output logic circuits by employing three label-free fluorescent probes. Among which, NMM and ThT can bind on certain G-quadruplexes formed by different sequences and AgNCs can be induced by C-rich domains.…”

Section: Selectingindividuals Ignal Transducersmentioning

confidence: 99%

“…Sequential logic units like accumulators, registers, and timers are widely used in modern computers and play fundamental roles in frequency division, timing, and arithmetic operations, but the only reported sequential logic units are a keypad-lock [111] and flip-flop. [101] Ta ke the simplest counter, which is used to count the stimulus pulses, as an example, a logic system must fulfil the following requirements:1 )multichannel compatibility;(2) transformations among different output channels triggered by the same stimulusw ithd ifferent amounts; 3) availability of chemical or biochemical pairs with opposite actions to the system.T hese requirements are so challenging to be satisfied simultaneously that the sequential functions are hard to realize only dependingo nD NA structural conversionsa nd reactions. Novel probes with multi-channel signals and pulse/time-dependent properties can satisfy partial requirements of the sequential logic and possibly endow new signal patterns on DNA systems.…”

Section: Probes With Multi-role and Multi-channelmentioning

confidence: 99%

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Recent Progress in Fluorescence Signal Design for DNA‐Based Logic Circuits

Yang

Song

et al. 2019

Chemistry A European J

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DNA‐based logic circuits, encoding algorithms in DNA and processing information, are pushing the frontiers of molecular computers forward, owing to DNA′s advantages of stability, accessibility, manipulability, and especially inherent biological significance and potential medical application. In recent years, numerous logic functions, from arithmetic to nonarithmetic, have been realized based on DNA. However, DNA can barely provide a detectable signal by itself, so that the DNA‐based circuits depend on extrinsic signal actuators. The signal strategy of carrying out a response is becoming one of the design focuses in DNA‐based logic circuit construction. Although work on sequence and structure design for DNA‐based circuits has been well reviewed, the strategy on signal production lacks comprehensive summary. In this review, we focused on the latest designs of fluorescent output for DNA‐based logic circuits. Several basic strategies are summarized and a few designs for developing multi‐output systems are provided. Finally, some current difficulties and possible opportunities were also discussed.

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“…DNA‐templated silver nanoclusters (AgNCs) with excellent fluorescence properties have attracted wide research interests in the field of fabrication of logic devices, [ 20–24 ] due to remarkable merits, such as low cost, tunable emission wavelength, ease of preparation, and convenience of utilization in DNA reaction circuits, and noncovalent (so called label‐free) and distinctive logic systems could be designed. [ 21,22,25,26 ] Recently, a concept of “DNA Janus Logic Pair”, also named as “Contrary Logic Pair”, was proposed, [ 18,27 ] in which two contrary logic gates (positive and negative gates) were obtained via the same one‐time reaction, resulting in significant improvement of computing efficiency. However, systematic complexity remains as a constraining factor for effective implementation and integration of DNA‐based logic systems.…”

Section: Figurementioning

confidence: 99%

Illuminating Diverse Concomitant DNA Logic Gates and Concatenated Circuits with Hairpin DNA‐Templated Silver Nanoclusters as Universal Dual‐Output Generators

Zhou

Fan

et al. 2020

Advanced Materials

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issues which should be taken seriously. Plenty of logic devices with multi-output signals are implemented by the aid of covalently labeled reporters (e.g., dye or redox), which cause time wastage and high cost. [10][11][12][13][14][15][16][17] In order to generate more than one output signal, it is ineluctable to introduce many other types of substances (e.g., different dyes and unstable hydrogen peroxide), [18,19] which increase complexity of a logic platform and are much detrimental to the repeatability and assembly of different logic systems. In addition, sequence redesign is required for construction of different logic gates, which leads to high cost and low efficiency. Hence, to explore a simple and noncovalent logic platform in a cost-effective manner is urgently demanded.Aimed at surmounting these drawbacks, new DNA-based logic systems should be considered. DNA-templated silver nanoclusters (AgNCs) with excellent fluorescence properties have attracted wide research interests in the field of fabrication of logic devices, [20][21][22][23][24] due to remarkable merits, such as low cost, tunable emission wavelength, ease of preparation, and convenience of utilization in DNA reaction circuits, and noncovalent (so called label-free) and distinctive logic systems could be designed. [21,22,25,26] Recently, a concept of "DNA Janus Logic Pair", also named as "Contrary Logic Pair", was proposed, [18,27] in which two contrary logic gates (positive and negative gates) were obtained via the same one-time reaction, resulting in significant improvement of computing efficiency. However, systematic complexity remains as a constraining factor for effective implementation and integration of DNA-based logic systems. In this study, diverse concomitant contrary logic gates (CCLGs), such as INHIBIT (INH)^IMPLICATION (IMP), XOR^XNOR and MAJORITY (MAJ)^MINORITY (MIN) ("^" stands for "concomitant and contrary"), and extended concatenated logic circuits (e.g., 4-input MAJ||MIN-INH||IMP, "||" stands for "parallel") with specific functions (e.g., parity generator (Pg) and checker (Pc)) were constructed, by utilization of one novel type of hairpin DNA-templated AgNCs (H-AgNCs) as the universal dualfluorescence signal transducer, and based on the mechanism of DNA hybridization and toehold-mediated strand displacement (TSD). Each pair of CCLGs was achieved via the same DNA (YES^NOT, OR^NOR, INHIBIT^IMPLICATION, XOR^XNOR, and MAJORITY^MINORITY) and extended concatenated logic circuits are presented and some of them perform specific functions, such as parity generators and checkers. The introduction of H-AgNCs as noncovalent signal reporters avoids tedious and high-cost labeling procedures. Of note, the concomitant feature of CCLGs attributed to the dual-emitter AgNCs conduces to reducing the time and cost to devise multiple logic gates. As compared to previous ones, this design eliminates numerous substances (e.g., organic dyes) and unstable components (hydrogen peroxide), which not only decreases the complexity of logic performs and impr...

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Integration of G-quadruplex and DNA-templated Ag NCs for nonarithmetic information processing

Abstract: We constructed a series of label-free and multi-output logic circuits using G-quadruplex and DNA-templated Ag NCs.

Cited by 50 publications

References 72 publications

Predicting absorption spectra of silver‐ligand complexes

Predicting absorption spectra of silver‐ligand complexes

Recent Progress in Fluorescence Signal Design for DNA‐Based Logic Circuits

Illuminating Diverse Concomitant DNA Logic Gates and Concatenated Circuits with Hairpin DNA‐Templated Silver Nanoclusters as Universal Dual‐Output Generators

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