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Tzeliou CE, Tzeli D. 3-Input AND Molecular Logic Gate with Enhanced Fluorescence Output: The Key Atom for the Accurate Prediction of the Spectra. J Chem Inf Model 2022; 62:6436-6448. [PMID: 35439413 DOI: 10.1021/acs.jcim.2c00257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The development of artificial receptors for sensing and recognition of species, as well as for advanced logic functions, is a significant challenge in the field of molecular information technology. Here, we study theoretically, via DFT/TD-DFT calculations, the photophysical properties of a 3-input AND molecular logic gate which presents an enhanced fluorescence spectrum. It was found that the geometry conformation at an N atom of the piperazine group is the key factor for the correct calculation of the absorption spectra of the calculated structures. Its geometry is between tetrahedral and planar, while changes in the corresponding CNCC dihedral angle of about 10 degrees can cause significant shifts of the main peak of the absorption spectra up to 100 nm. Moreover, the unusually enhanced fluorescence of a molecular logic gate (MLG) is explained. Finally, we conclude that molecular systems having N atoms, whose geometry is between planar and tetrahedral, can be ideal molecules as sensors and molecular logic gates. Our calculated absorption and emission spectra are in excellent agreement with available experimental data.
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Affiliation(s)
- Christina Eleftheria Tzeliou
- Laboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens 157 84, Greece
| | - Demeter Tzeli
- Laboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens 157 84, Greece.,Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 116 35, Greece
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2
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Usta HM, Forough M, Persil Çetinkol Ö. Coumarin 6H-fused fluorescent probe for highly sensitive detection of coralyne using oligonucleotide-modified silver nanoparticles. Anal Bioanal Chem 2022; 414:7299-7313. [PMID: 35976422 DOI: 10.1007/s00216-022-04282-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022]
Abstract
In this study, a novel, rapid, and sensitive fluorescence sensing platform was developed for the detection of coralyne (COR) by the conjugation of coumarin 6H (C6H) fluorescent dye with oligonucleotide-modified silver nanoparticles [(dT)32-AgNPs]. In the presence of COR, a remarkable and rapid decrease in the fluorescence signal of the probe with a quenching efficiency of around 62% was observed. The quenching response of the system towards COR was possibly due to the displacement of thymidine-rich deoxyoligonucleotides by COR on the surface of AgNPs. The complementary experiments with an adenine-rich single strand as well as with two different secondary structures (i.e., duplex and triplex) revealed a favorable sequence specificity of the sensing platform. The influence of key parameters including the incubation time and temperature was evaluated and optimized to achieve the highest performance. The linear range of 10-183 nM with a correlation coefficient of R = 0.9982 and a limit of detection of 5.24 nM were obtained under the optimized conditions. The selectivity of the proposed probe towards COR was revealed by the evaluation of its response to other small molecules that have molecular structures similar to COR. Finally, the successful applicability of the system was shown with the obtained average recoveries in the range of 87.28-104.52% in human urine samples.
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Affiliation(s)
- Hatice Müge Usta
- Department of Chemistry, Middle East Technical University, 06800, Çankaya, Ankara, Turkey
| | - Mehrdad Forough
- Department of Chemistry, Middle East Technical University, 06800, Çankaya, Ankara, Turkey
| | - Özgül Persil Çetinkol
- Department of Chemistry, Middle East Technical University, 06800, Çankaya, Ankara, Turkey.
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3
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Zhang X, Zhang Q, Liu Y, Wei X. A DNAzyme-mediated logic gate system based on Ag(I)-cysteine. Analyst 2020; 145:6572-6578. [PMID: 32780055 DOI: 10.1039/d0an01315c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Ag+ plays an important role in DNA mismatch technology due to its affinity for cytosine in DNA. This article introduces a strategy to control the enzyme digesting reaction by utilizing the characteristics of C-Ag+-C mismatches, effectively regulating and controlling the activity of the E6 DNAzyme via changing the structure of its conservative domain. We designed a series of basic logic gates, a "Yes" Gate, an "Or" Gate and an "Inhibit" Gate. Cysteine (Cys) can combine with Ag+, reducing the concentration of Ag+ in solution, thus restraining the C-Ag+-C mismatch effect. Based on this principle, we regard Cys as a threshold, and designed a type of "Inhibit" Gate based on input quantity by changing the concentration of Ag+, thus generating different statues of logic output. On this basis, the E6 DNAzyme and Ag10c DNAzyme can be integrated into new systems with the function of logic operation circuit based on the control of Ag+ concentration in solution. This system could represent three different states of logical expression by controlling the quantity of Ag+ and Cys.
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Affiliation(s)
- Xun Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Xiaopeng Wei
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China.
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4
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Kikuchi N, Kolpashchikov DM. A universal split spinach aptamer (USSA) for nucleic acid analysis and DNA computation. Chem Commun (Camb) 2018; 53:4977-4980. [PMID: 28425510 DOI: 10.1039/c7cc01540b] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We demonstrate how a single universal spinach aptamer (USSA) probe can be used to detect multiple (potentially any) nucleic acid sequences. USSA can be used for cost-efficient and highly selective analysis of even folded DNA and RNA analytes, as well as for the readout of outputs of DNA logic circuits.
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Affiliation(s)
- Nanami Kikuchi
- Chemistry Department, University of Central Florida, Orlando, 32816, Florida, USA
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5
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A turn-on spiropyran derivative based reversible photo-driven colorimetric and fluorescent chemosensor for trivalent metal ions. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.10.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Choi JS, Kim S, Yoo D, Shin TH, Kim H, Gomes MD, Kim SH, Pines A, Cheon J. Distance-dependent magnetic resonance tuning as a versatile MRI sensing platform for biological targets. NATURE MATERIALS 2017; 16:537-542. [PMID: 28166216 DOI: 10.1038/nmat4846] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 12/12/2016] [Indexed: 06/06/2023]
Abstract
Nanoscale distance-dependent phenomena, such as Förster resonance energy transfer, are important interactions for use in sensing and imaging, but their versatility for bioimaging can be limited by undesirable photon interactions with the surrounding biological matrix, especially in in vivo systems. Here, we report a new type of magnetism-based nanoscale distance-dependent phenomenon that can quantitatively and reversibly sense and image intra-/intermolecular interactions of biologically important targets. We introduce distance-dependent magnetic resonance tuning (MRET), which occurs between a paramagnetic 'enhancer' and a superparamagnetic 'quencher', where the T1 magnetic resonance imaging (MRI) signal is tuned ON or OFF depending on the separation distance between the quencher and the enhancer. With MRET, we demonstrate the principle of an MRI-based ruler for nanometre-scale distance measurement and the successful detection of both molecular interactions (for example, cleavage, binding, folding and unfolding) and biological targets in in vitro and in vivo systems. MRET can serve as a novel sensing principle to augment the exploration of a wide range of biological systems.
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Affiliation(s)
- Jin-Sil Choi
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Yonsei-IBS Institute, Yonsei University, Seoul 03722, Republic of Korea
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Soojin Kim
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Yonsei-IBS Institute, Yonsei University, Seoul 03722, Republic of Korea
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Dongwon Yoo
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Yonsei-IBS Institute, Yonsei University, Seoul 03722, Republic of Korea
| | - Tae-Hyun Shin
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Yonsei-IBS Institute, Yonsei University, Seoul 03722, Republic of Korea
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Hoyoung Kim
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Yonsei-IBS Institute, Yonsei University, Seoul 03722, Republic of Korea
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Muller D Gomes
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Sun Hee Kim
- Western Seoul Center, Korea Basic Science Institute, Seoul 03760, Republic of Korea
| | - Alexander Pines
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jinwoo Cheon
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Yonsei-IBS Institute, Yonsei University, Seoul 03722, Republic of Korea
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
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Pangannaya S, Kaur A, Mohan M, Raval K, Chand DK, Trivedi DR. Synthesis and spectral investigation of colorimetric receptors for the dual detection of copper and acetate ions: application in molecular logic gates. Supramol Chem 2017. [DOI: 10.1080/10610278.2017.1298764] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Srikala Pangannaya
- Supramolecular Chemistry Laboratory, National Institute of Technology Karnataka (NITK), Surathkal, India
| | - Arshiya Kaur
- Department of Chemistry, Indian Institute of Technology Madras (IITM), Chennai, India
| | - Makesh Mohan
- Department of Physics, National Institute of Technology Karnataka (NITK), Surathkal, India
| | - Keyur Raval
- Department of Chemical Engineering, National Institute of Technology Karnataka (NITK), Surathkal, India
| | - Dillip Kumar Chand
- Department of Chemistry, Indian Institute of Technology Madras (IITM), Chennai, India
| | - Darshak R. Trivedi
- Supramolecular Chemistry Laboratory, National Institute of Technology Karnataka (NITK), Surathkal, India
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Kaur P, Singh R, Kaur V, Talwar D. A chromogenic “off–on” azomethine sensor possessing ONNNO receptor site for iron species and its application in the fabrication of INHIBIT type molecular logic gate. Polyhedron 2016. [DOI: 10.1016/j.poly.2016.03.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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9
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Sabhachandani P, Cohen N, Sarkar S, Konry T. Microsphere-based immunoassay integrated with a microfluidic network to perform logic operations. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1518-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Huang H, Shi S, Zheng X, Yao T. Sensitive detection for coralyne and mercury ions based on homo-A/T DNA by exonuclease signal amplification. Biosens Bioelectron 2015; 71:439-444. [PMID: 25950941 DOI: 10.1016/j.bios.2015.04.076] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/13/2015] [Accepted: 04/23/2015] [Indexed: 12/27/2022]
Abstract
Based on specific homo-A/T DNA binding properties, a strategy for coralyne and mercury ions detection was realised by exonuclease-aided signal amplification. Coralyne could specifically bind homo-A DNA and protect it from the hydrolysis of exonuclease I. The coralyne-protected DNA was subsequently used as a trigger strand to hydrolyze DNA2 in exonuclease-aided signal amplification process. Thiazole orange was used to quantify the remainder DNA2. Under the optimal condition, the fluorescence intensity was linearly proportional to the concentration of coralyne in the range of 0.2-100 nM with a limit of detection (LOD) of 0.31 nM, which presented the lowest LOD for coralyne among all reported. With homo-T and Hg(2+) taking the place of homo-A DNA and coralyne, respectively, the system could also be used for Hg(2+) detection. The experiments in real samples also showed good results. This method was label-free, low-cost, easy-operating and highly repeatable for the detection of coralyne and mercury ions. It could also be extended to detect various analytes, such as other metal ions, proteins and small molecules by using appropriate aptamers.
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Affiliation(s)
- Hailiang Huang
- Department of Chemistry, and Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| | - Shuo Shi
- Department of Chemistry, and Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China.
| | - Xuyue Zheng
- Department of Chemistry, and Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| | - Tianming Yao
- Department of Chemistry, and Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China.
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11
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Gerasimova YV, Kolpashchikov DM. Divide and control: split design of multi-input DNA logic gates. Chem Commun (Camb) 2014; 51:870-2. [PMID: 25513764 DOI: 10.1039/c4cc08241a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Logic gates made of DNA have received significant attention as biocompatible building blocks for molecular circuits. The majority of DNA logic gates, however, are controlled by the minimum number of inputs: one, two or three. Here we report a strategy to design a multi-input logic gate by splitting a DNA construct.
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Affiliation(s)
- Yulia V Gerasimova
- Chemistry Department, University of Central Florida, Orlando, FL 32816, USA
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