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Assembly of Biologically Functional Structures by Nucleic Acid Templating: Implementation of a Strategy to Overcome Inhibition by Template Excess. Molecules 2022; 27:molecules27206831. [PMID: 36296424 PMCID: PMC9610079 DOI: 10.3390/molecules27206831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/18/2022] Open
Abstract
Delivery of therapeutic molecules to pathogenic cells is often hampered by unintended toxicity to normal cells. In principle, this problem can be circumvented if the therapeutic effector molecule is split into two inactive components, and only assembled on or within the target cell itself. Such an in situ process can be realized by exploiting target-specific molecules as templates to direct proximity-enhanced assembly. Modified nucleic acids carrying inert precursor fragments can be designed to co-hybridize on a target-specific template nucleic acid, such that the enforced proximity accelerates assembly of a functional molecule for antibody recognition. We demonstrate the in vitro feasibility of this adaptation of nucleic acid-templated synthesis (NATS) using oligonucleotides bearing modified peptides (“haplomers”), for templated assembly of a mimotope recognized by the therapeutic antibody trastuzumab. Enforced proximity promotes mimotope assembly via traceless native chemical ligation. Nevertheless, titration of participating haplomers through template excess is a potential limitation of trimolecular NATS. In order to overcome this problem, we devised a strategy where haplomer hybridization can only occur in the presence of target, without being subject to titration effects. This generalizable NATS modification may find future applications in enabling directed targeting of pathological cells.
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2
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Fluorescence ratiometric DNA detection by peptide nucleic acid-pyrene binary probes. Bioorg Med Chem Lett 2022; 71:128838. [PMID: 35654301 DOI: 10.1016/j.bmcl.2022.128838] [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: 04/01/2022] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 11/23/2022]
Abstract
We developed a method for detecting DNA by excimer fluorescence from two peptide nucleic acids (PNAs) modified with a pyrene (Pyr). The two PNA-Pyr probes were prepared by solid-phase peptide synthesis, and we assessed fluorescence from the mixture of probes with DNA. From the results, excimer fluorescence derived from the two PNA-Pyr probes forming hybrids with the complementary DNA was observed, and the two probes showed the maximum excimer/monomer ratio when the probes and DNA were hybridized at a 1:1:1 ratio, indicating that the PNA-Pyr probes can detect target DNA. Furthermore, we adjusted the spatial arrangement between the two PNA-Pyr hybrids formed on the DNA to promote optimal excimer formation. As a result, optimal excimer formation was achieved by spacing the two nucleobases between the formed two hybrids and further inserting a hexamethylene linker (C6) between the PNA and Pyr of the PNA-Pyr probe on one side.
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3
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Fouad H, Yang G, El-Sayed AA, Mao G, Khalafallah D, Saad M, Ga'al H, Ibrahim E, Mo J. Green synthesis of AgNP-ligand complexes and their toxicological effects on Nilaparvata lugens. J Nanobiotechnology 2021; 19:318. [PMID: 34645452 PMCID: PMC8513204 DOI: 10.1186/s12951-021-01068-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Despite developments in nanotechnology for use in the pharmaceutical field, there is still a need for implementation of this technology in agrochemistry. In this study, silver nanoparticles (AgNPs) were successfully prepared by a facile and an eco-friendly route using two different ligands, 2'-amino-1,1':4',1″-terphenyl-3,3″,5,5″-tetracarboxylic acid (H4L) and 1,3,6,8-tetrakis (p-benzoic acid)-pyrene (TBAPy), as reducing agents. The physiochemical properties of the as-obtained AgNPs were characterized by scanning electron microscopy (SEM), energy-dispersive X-ray (EDX), X-ray diffraction (XRD) and transmission electron microscopy (TEM). The toxicity of H4L-AgNP and TBAPy-AgNP against the brown planthopper (BPH, Nilaparvata lugens) was also measured. RESULTS SEM and TEM analyses demonstrated the formation of quasi-spherical AgNP structures in the presence of H4L and TBAPy. Insecticidal assays showed that TBAPy is less effective against N. lugens, with a median lethal concentration (LC50) of 810 mg/L, while the toxicity of H4L increased and their LC50 reached 786 mg/L 168 h posttreatment at a high concentration of 2000 mg/L. H4L-AgNPs were also highly toxic at a low concentration of 20 mg/L, with LC50 = ~ 3.9 mg/L 168 h posttreatment, while TBAPy-AgNPs exhibited less toxicity at the same concentration, with LC50 = ~ 4.6 mg/L. CONCLUSIONS These results suggest that the synthesized AgNPs using the two ligands may be a safe and cheaper method compared with chemical insecticides for protection of rice plants from pests and has potential as an effective insecticide in the N. lugens pest management program.
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Affiliation(s)
- Hatem Fouad
- Ministry of Agriculture, Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Yuhangtang Road 866, Hangzhou, Zhejiang, 310058, People's Republic of China.
- Department of Field Crop Pests, Plant Protection Research Institute, Agricultural Research Centre 12622, Dokki, Cairo, Egypt.
| | - Guiying Yang
- Ministry of Agriculture, Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Yuhangtang Road 866, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Ahmed A El-Sayed
- Photochemistry Department, National Research Center, Dokki, Giza, Egypt
| | - Guofeng Mao
- Ministry of Agriculture, Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Yuhangtang Road 866, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Diab Khalafallah
- State Key Laboratory of Silicon Material, School of Materials Science and Engineering, Zhejiang University, Hangzhou, China
| | - Mahmoud Saad
- Department of Field Crop Pests, Plant Protection Research Institute, Agricultural Research Centre 12622, Dokki, Cairo, Egypt
| | - Hassan Ga'al
- Ministry of Agriculture, Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Yuhangtang Road 866, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Ezzeldin Ibrahim
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jianchu Mo
- Ministry of Agriculture, Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Yuhangtang Road 866, Hangzhou, Zhejiang, 310058, People's Republic of China.
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Novopashina DS, Semikolenova OA, Venyaminova AG. 5'-Monopyrene and 5'-Bispyrene 2'-O-methyl RNA Probes for Detection of RNA Mismatches. Methods Mol Biol 2020; 2063:45-56. [PMID: 31667762 DOI: 10.1007/978-1-0716-0138-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Progress in synthesis of novel fluorescent oligonucleotides has provided effective instruments for nucleic acid detection. Pyrene conjugated oligonucleotides have demonstrated their effectiveness as fluorescent hybridization probes. Here we describe the synthesis, isolation, and analysis of 5'-monopyrene and 5'-bispyrene conjugates of oligo(2'-O-methylribonucleotides) and their application as probes for fluorescent detection of mismatches in RNA targets.
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Affiliation(s)
- D S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia. .,Novosibirsk State University, Novosibirsk, Russia.
| | | | - A G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
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5
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Krasheninina OA, Lomzov AA, Fishman VS, Novopashina DS, Venyaminova AG. Rational design and studies of excimer forming novel dual probes to target RNA. Bioorg Med Chem 2017; 25:2244-2250. [PMID: 28279557 DOI: 10.1016/j.bmc.2017.02.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 01/31/2017] [Accepted: 02/22/2017] [Indexed: 11/18/2022]
Abstract
In this paper, we report structure-based rational design and physico-chemical and biological studies of novel pyrene excimer forming dual probes for visualization of intracellular RNAs. Herein, the probes based on 2'-O-methyl RNA with linkers of different structure and length between pyrene moiety and ribose are studied with respect to their hybridization and spectral properties. We found optimal linkers that provide more intense excimer emission (at ∼480nm) of RNA-bound probes; particularly, the length of the linker arm of the 3'-component of dual probes plays a key role in formation of pyrene excimer. Calculated molecular dynamics trajectories and probability distributions of pyrene-pyrene dimer formation upon hybridization of the dual probes with RNA target are in agreement with the obtained fluorescence spectroscopy data for the corresponding duplexes. Our study demonstrates the excellent binding properties of new dual probes to structured RNA and their feasibility for the visualization of intracellular RNA targets.
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Affiliation(s)
- O A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogov str., Novosibirsk 630090, Russia.
| | - A A Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogov str., Novosibirsk 630090, Russia
| | - V S Fishman
- Institute of Cytology and Genetics SB RAS, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - D S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogov str., Novosibirsk 630090, Russia
| | - A G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia
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Maekawa S, Sato R, Hirao K, Shigeta Y. Solvent effects on excited-state electron-transfer rate of pyrene-labeled deoxyuridine: A theoretical study. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2015.11.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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7
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Gerasimova YV, Kolpashchikov DM. Enzyme-assisted target recycling (EATR) for nucleic acid detection. Chem Soc Rev 2015; 43:6405-38. [PMID: 24901032 DOI: 10.1039/c4cs00083h] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fast, reliable and sensitive methods for nucleic acid detection are of growing practical interest with respect to molecular diagnostics of cancer, infectious and genetic diseases. Currently, PCR-based and other target amplification strategies are most extensively used in practice. At the same time, such assays have limitations that can be overcome by alternative approaches. There is a recent explosion in the design of methods that amplify the signal produced by a nucleic acid target, without changing its copy number. This review aims at systematization and critical analysis of the enzyme-assisted target recycling (EATR) signal amplification technique. The approach uses nucleases to recognize and cleave the probe-target complex. Cleavage reactions produce a detectable signal. The advantages of such techniques are potentially low sensitivity to contamination and lack of the requirement of a thermal cycler. Nucleases used for EATR include sequence-dependent restriction or nicking endonucleases or sequence independent exonuclease III, lambda exonuclease, RNase H, RNase HII, AP endonuclease, duplex-specific nuclease, DNase I, or T7 exonuclease. EATR-based assays are potentially useful for point-of-care diagnostics, single nucleotide polymorphisms genotyping and microRNA analysis. Specificity, limit of detection and the potential impact of EATR strategies on molecular diagnostics are discussed.
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Affiliation(s)
- Yulia V Gerasimova
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA.
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Vanga DG, Santra M, Keerthi A, Valiyaveettil S. Synthesis and photophysical properties of pyrene-based green fluorescent dyes: butterfly-shaped architectures. Org Biomol Chem 2014; 12:7914-8. [PMID: 25220392 DOI: 10.1039/c4ob01509f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A few pyrene-based fluorescent compounds were synthesized using Pd/Cu-catalyzed cross-coupling reaction. Photophysical properties of the π-conjugated pyrene derivatives were studied and the results indicate materials with high quantum efficiency and high extinction coefficient. No π stacking was observed in the crystal lattice. The molecules described here may be useful in developing sensors or imaging agents.
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Affiliation(s)
- Devendar Goud Vanga
- S5-05-02, Materials Research Laboratory, Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543.
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9
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Moriguchi T, Ichimura M, Kato M, Suzuki K, Takahashi Y, Shinozuka K. Development of the excimer probe responsible for DNA target bearing the silylated pyrenes at base moiety. Bioorg Med Chem Lett 2014; 24:4372-4375. [DOI: 10.1016/j.bmcl.2014.08.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/04/2014] [Accepted: 08/07/2014] [Indexed: 01/04/2023]
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10
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Manicardi A, Guidi L, Ghidini A, Corradini R. Pyrene-modified PNAs: Stacking interactions and selective excimer emission in PNA2DNA triplexes. Beilstein J Org Chem 2014; 10:1495-503. [PMID: 25161706 PMCID: PMC4142857 DOI: 10.3762/bjoc.10.154] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/03/2014] [Indexed: 12/17/2022] Open
Abstract
Pyrene derivatives can be incorporated into nucleic acid analogs in order to obtain switchable probes or supramolecular architectures. In this paper, peptide nucleic acids (PNAs) containing 1 to 3 1-pyreneacetic acid units (PNA1–6) with a sequence with prevalence of pyrimidine bases, complementary to cystic fibrosis W1282X point mutation were synthesized. These compounds showed sequence-selective switch-on of pyrene excimer emission in the presence of target DNA, due to PNA2DNA triplex formation, with stability depending on the number and positioning of the pyrene units along the chain. An increase in triplex stability and a very high mismatch-selectivity, derived from combined stacking and base-pairing interactions, were found for PNA2, bearing two distant pyrene units.
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Affiliation(s)
- Alex Manicardi
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy. ; Tel: +39 0521 905410
| | - Lucia Guidi
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy. ; Tel: +39 0521 905410
| | - Alice Ghidini
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy. ; Tel: +39 0521 905410 ; Present Address: Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Hälsovägen 7, 14183, Huddinge, Sweden
| | - Roberto Corradini
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy. ; Tel: +39 0521 905410
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11
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Maneelun N, Vilaivan T. Dual pyrene-labeled pyrrolidinyl peptide nucleic acid as an excimer-to-monomer switching probe for DNA sequence detection. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.10.096] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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12
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Abstract
Fluorescent silver nanoclusters (few atoms, quantum sized) have attracted much attention as promising substitutes for conventional fluorophores. Due to their unique environmental sensitivities, new fluorescent probes have been developed based on silver nanoclusters for the sensitive and specific detection of DNA. In this review we present the recent discoveries of activatable and color-switchable properties of DNA-templated silver nanoclusters and discuss the strategies to use these new properties in DNA sensing.
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Affiliation(s)
- Judy M Obliosca
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
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13
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Dembska A, Rzepecka P, Juskowiak B. Spectroscopic characterization of i-motif forming c-myc derived sequences double-labeled with pyrene. J Fluoresc 2013; 23:807-12. [PMID: 23519528 PMCID: PMC3696180 DOI: 10.1007/s10895-013-1184-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 02/24/2013] [Indexed: 11/25/2022]
Abstract
In current studies we use the oligonucleotides based on c-myc sequence: CCC CAC CCT CCC CAC CCT CCC C (cmyc22) and CCC CAC CCT CCC CAC CCT CCC CA (cmyc22A) functionalized by pyrene moieties at both termini. Results of the circular dichroism (CD), UV absorption melting experiments, and steady-state fluorescence measurements of pyrene-modified i-motifs as well as their unlabeled precursors are presented and discussed here. The pyrene labels have a remarkable influence on i-motif stability which was deduced from CD spectra and confirmed by UV melting experiments. Both probes emit fluorescence band of pyrene monomer with intensity decreasing upon pH lowering.
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Affiliation(s)
- Anna Dembska
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614, Poznań, Poland.
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14
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Kashida H, Asanuma* H. Oligonucleotide Conjugates for Detection of Specific Nucleic Acid Sequences. DNA CONJUGATES AND SENSORS 2012. [DOI: 10.1039/9781849734936-00242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In this chapter, we summarise the designs of fluorophore-modified nucleic acids used as probes for the detection of target DNA/RNA. Recently, there has been an increasing demand for the sequence-specific detection of DNA and RNA in biology and biotechnology. Fluorescent probes based on nucleic acids are useful because of their simplicity and ease of handling. Here, we described three types of fluorescent probe: 1) linear probes, 2) binary probes, and 3) molecular beacons. Each can have one or more fluorophores. Mechanisms for the fluorescence responses of these probes are also discussed in detail. These fluorescent probes have been used in real-time polymerase chain reaction (PCR), genetic analyses, and messenger RNA (mRNA) imaging in living cells. Improvements in sensitivity, selectivity, and nuclease resistance of these probes will lead to more widespread applications in chemical biology, biotechnology, and medicine.
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Affiliation(s)
- Hiromu Kashida
- Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku, Nagoya 464-8603 Japan
| | - Hiroyuki Asanuma*
- Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku, Nagoya 464-8603 Japan
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15
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Affiliation(s)
- Yin Nah Teo
- Department of Chemistry, Stanford University, California 94305, United States
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16
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Kolpashchikov DM, Gerasimova YV, Khan MS. DNA nanotechnology for nucleic acid analysis: DX motif-based sensor. Chembiochem 2011; 12:2564-7. [PMID: 22006680 PMCID: PMC3221779 DOI: 10.1002/cbic.201100545] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Indexed: 11/09/2022]
Abstract
A light on the tiles: A sensor that fluoresces in the presence of specific nucleic acids was designed and characterized. The sensor uses a molecular beacon probe and three adaptor strands to form a five-stranded assembly, a DX-tile, with a specific analyte. This sensor is a highly selective and affordable tool for the real-time analysis of DNA and RNA.
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17
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Nguyen C, Grimes J, Gerasimova YV, Kolpashchikov DM. Molecular-beacon-based tricomponent probe for SNP analysis in folded nucleic acids. Chemistry 2011; 17:13052-8. [PMID: 21956816 PMCID: PMC3221966 DOI: 10.1002/chem.201101987] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Indexed: 01/13/2023]
Abstract
Hybridization probes are often inefficient in the analysis of single-stranded DNA or RNA that are folded in stable secondary structures. A molecular beacon (MB) probe is a short DNA hairpin with a fluorophore and a quencher attached to opposite sides of the oligonucleotide. The probe is widely used in real-time analysis of specific DNA and RNA sequences. This study demonstrates how a conventional MB probe can be used for the analysis of nucleic acids that form very stable (T(m) > 80 °C) hairpin structures. Here we demonstrate that the MB probe is not efficient in direct analysis of secondary structure-folded analytes, whereas a MB-based tricomponent probe is suitable for these purposes. The tricomponent probe takes advantage of two oligonucleotide adaptor strands f and m. Each adaptor strand contains a fragment complementary to the analyte and a fragment complementary to a MB probe. In the presence of a specific analyte, the two adaptor strands hybridize to the analyte and the MB probe, thus forming a quadripartite complex. DNA strand f binds to the analyte with high affinity and unwinds its secondary structure. Strand m forms a stable complex only with the fully complementary analyte. The MB probe fluorescently reports the formation of the quadripartite associate. It was demonstrated that the DNA analytes folded in hairpin structures with stems containing 5, 6, 7, 8, 9, 11, or 13 base pairs can be detected in real time with the limit of detection (LOD) lying in the nanomolar range. The stability of the stem region in the DNA analyte did not affect the LOD. Analytes containing single base substitutions in the stem or in the loop positions were discriminated from the fully complementary DNA at room temperature. The tricomponent probe promises to simplify nucleic acid analysis at ambient temperatures in such applications as in vivo RNA monitoring, detection of pathogens, and single nucleotide polymorphism (SNP) genotyping by DNA microarrays.
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Affiliation(s)
- Camha Nguyen
- Camha Nguyen, Jeffrey Grimes, Dr. Y. V. Gerasimova, Dr. D. M. Kolpashchikov Chemistry Department University of Central Florida 4000 Central Florida Blvd., Orlando, FL 32816, USA
| | - Jeffrey Grimes
- Camha Nguyen, Jeffrey Grimes, Dr. Y. V. Gerasimova, Dr. D. M. Kolpashchikov Chemistry Department University of Central Florida 4000 Central Florida Blvd., Orlando, FL 32816, USA
| | - Yulia V. Gerasimova
- Camha Nguyen, Jeffrey Grimes, Dr. Y. V. Gerasimova, Dr. D. M. Kolpashchikov Chemistry Department University of Central Florida 4000 Central Florida Blvd., Orlando, FL 32816, USA
| | - Dmitry M. Kolpashchikov
- Camha Nguyen, Jeffrey Grimes, Dr. Y. V. Gerasimova, Dr. D. M. Kolpashchikov Chemistry Department University of Central Florida 4000 Central Florida Blvd., Orlando, FL 32816, USA
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18
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Crawford AG, Dwyer AD, Liu Z, Steffen A, Beeby A, Pålsson LO, Tozer DJ, Marder TB. Experimental and Theoretical Studies of the Photophysical Properties of 2- and 2,7-Functionalized Pyrene Derivatives. J Am Chem Soc 2011; 133:13349-62. [DOI: 10.1021/ja2006862] [Citation(s) in RCA: 242] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andrew G. Crawford
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Austin D. Dwyer
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Zhiqiang Liu
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
- State Key Lab of Crystal Materials, Shandong University, 27 Shanda South Road, Jinan 250100, China
| | - Andreas Steffen
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Andrew Beeby
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Lars-Olof Pålsson
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - David J. Tozer
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Todd B. Marder
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
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Grimes J, Gerasimova YV, Kolpashchikov DM. Real-time SNP analysis in secondary-structure-folded nucleic acids. Angew Chem Int Ed Engl 2011; 49:8950-3. [PMID: 20963740 DOI: 10.1002/anie.201004475] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jeffrey Grimes
- Chemistry Department, University of Central Florida, 4000 Central Blvd, Orlando, FL 32816, USA
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20
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Juskowiak B. Nucleic acid-based fluorescent probes and their analytical potential. Anal Bioanal Chem 2011; 399:3157-76. [PMID: 21046088 PMCID: PMC3044240 DOI: 10.1007/s00216-010-4304-5] [Citation(s) in RCA: 161] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/04/2010] [Accepted: 10/05/2010] [Indexed: 12/21/2022]
Abstract
It is well known that nucleic acids play an essential role in living organisms because they store and transmit genetic information and use that information to direct the synthesis of proteins. However, less is known about the ability of nucleic acids to bind specific ligands and the application of oligonucleotides as molecular probes or biosensors. Oligonucleotide probes are single-stranded nucleic acid fragments that can be tailored to have high specificity and affinity for different targets including nucleic acids, proteins, small molecules, and ions. One can divide oligonucleotide-based probes into two main categories: hybridization probes that are based on the formation of complementary base-pairs, and aptamer probes that exploit selective recognition of nonnucleic acid analytes and may be compared with immunosensors. Design and construction of hybridization and aptamer probes are similar. Typically, oligonucleotide (DNA, RNA) with predefined base sequence and length is modified by covalent attachment of reporter groups (one or more fluorophores in fluorescence-based probes). The fluorescent labels act as transducers that transform biorecognition (hybridization, ligand binding) into a fluorescence signal. Fluorescent labels have several advantages, for example high sensitivity and multiple transduction approaches (fluorescence quenching or enhancement, fluorescence anisotropy, fluorescence lifetime, fluorescence resonance energy transfer (FRET), and excimer-monomer light switching). These multiple signaling options combined with the design flexibility of the recognition element (DNA, RNA, PNA, LNA) and various labeling strategies contribute to development of numerous selective and sensitive bioassays. This review covers fundamentals of the design and engineering of oligonucleotide probes, describes typical construction approaches, and discusses examples of probes used both in hybridization studies and in aptamer-based assays.
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Affiliation(s)
- Bernard Juskowiak
- Faculty of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznan, Poland.
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Bichenkova EV, Lang Z, Yu X, Rogert C, Douglas KT. DNA-mounted self-assembly: New approaches for genomic analysis and SNP detection. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:1-23. [PMID: 21111076 DOI: 10.1016/j.bbagrm.2010.11.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 11/07/2010] [Accepted: 11/12/2010] [Indexed: 11/25/2022]
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Shanmugaraju S, Joshi SA, Mukherjee PS. Fluorescence and visual sensing of nitroaromatic explosives using electron rich discrete fluorophores. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1jm10406c] [Citation(s) in RCA: 200] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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23
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Todoroki K, Yoshida H, Hayama T, Itoyama M, Nohta H, Yamaguchi M. Highly sensitive and selective derivatization-LC method for biomolecules based on fluorescence interactions and fluorous separations. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 879:1325-37. [PMID: 21190905 DOI: 10.1016/j.jchromb.2010.11.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 11/29/2010] [Accepted: 11/29/2010] [Indexed: 11/29/2022]
Abstract
A fluorescence derivatization LC method is a powerful tool for the analysis with high sensitivity and selectivity of biological compounds. In this review, we introduce new types of fluorescence derivatization LC analysis methods. These are (1) detection-selective derivatization methods based on fluorescence interactions generated from fluorescently labeled analytes: excimer fluorescence derivatization and fluorescence resonance energy transfer (FRET) derivatization; (2) separation-selective derivatization methods using the fluorous separation technique: fluorous derivatization, F-trap fluorescence derivatization, and fluorous scavenging derivatization (FSD).
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Affiliation(s)
- Kenichiro Todoroki
- Faculty of Pharmaceutical Sciences, Fukuoka University, Nanakuma, Johnan, Fukuoka 814-0180, Japan
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Grimes J, Gerasimova YV, Kolpashchikov DM. Real-Time SNP Analysis in Secondary-Structure-Folded Nucleic Acids. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201004475] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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26
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Gerasimova YV, Hayson A, Ballantyne J, Kolpashchikov DM. A single molecular beacon probe is sufficient for the analysis of multiple nucleic acid sequences. Chembiochem 2010; 11:1762-8. [PMID: 20665615 PMCID: PMC2953724 DOI: 10.1002/cbic.201000287] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Indexed: 11/05/2022]
Abstract
Molecular beacon (MB) probes are dual-labeled hairpin-shaped oligodeoxyribonucleotides that are extensively used for real-time detection of specific RNA/DNA analytes. In the MB probe, the loop fragment is complementary to the analyte: therefore, a unique probe is required for the analysis of each new analyte sequence. The conjugation of an oligonucleotide with two dyes and subsequent purification procedures add to the cost of MB probes, thus reducing their application in multiplex formats. Here we demonstrate how one MB probe can be used for the analysis of an arbitrary nucleic acid. The approach takes advantage of two oligonucleotide adaptor strands, each of which contains a fragment complementary to the analyte and a fragment complementary to an MB probe. The presence of the analyte leads to association of MB probe and the two DNA strands in quadripartite complex. The MB probe fluorescently reports the formation of this complex. In this design, the MB does not bind the analyte directly; therefore, the MB sequence is independent of the analyte. In this study one universal MB probe was used to genotype three human polymorphic sites. This approach promises to reduce the cost of multiplex real-time assays and improve the accuracy of single-nucleotide polymorphism genotyping.
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Affiliation(s)
- Yulia V Gerasimova
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816, USA.
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Hernandez-Folgado L, Baretić D, Piantanida I, Marjanović M, Kralj M, Rehm T, Schmuck C. Guanidiniocarbonylpyrrole-aryl derivatives: structure tuning for spectrophotometric recognition of specific DNA and RNA sequences and for antiproliferative activity. Chemistry 2010; 16:3036-56. [PMID: 20119980 DOI: 10.1002/chem.200901999] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We present a systematic study of different guanidiniocarbonylpyrrole-aryl derivatives designed to interact with DNA or RNA both through intercalation of an aromatic moiety into the base stack of the nucleotide and through groove binding of a guanidiniocarbonylpyrrole cation. We varied 1) the size of the aromatic ring (benzene, naphthalene, pyrene and acridine), 2) the length and flexibility of the linker connecting the two binding groups, and 3) the total number of positive charges present at different pH values. The compounds and their interactions with DNA and RNA were studied by UV/Vis, fluorescence and CD spectroscopy. Antiproliferative activities against human tumour cell lines were also determined. Our studies show that efficient interaction with, for example, DNA requires a significantly large aromatic ring (pyrene) connected through a flexible linker to the pyrrole moiety. However, a positive charge, as in 12, is also needed. Compound 12 allows for base-pair-selective recognition of ds-DNA at physiological pH values. The antiproliferative activities of these compounds correlate with their binding affinities towards DNA, suggesting that their biological effects are most probably due to DNA binding.
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Affiliation(s)
- Laura Hernandez-Folgado
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
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Morrison LE. Basic Principles of Fluorescence and Energy Transfer Applied to Real-Time PCR. Mol Biotechnol 2009; 44:168-76. [DOI: 10.1007/s12033-009-9225-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Gbaj A, Bichenkova E, Walsh L, Savage H, Sardarian A, Etchells L, Gulati A, Hawisa S, Douglas K. New concepts of fluorescent probes for specific detection of DNA sequences: bis-modified oligonucleotides in excimer and exciplex detection. Libyan J Med 2009; 4:152-9. [PMID: 21483539 PMCID: PMC3066750 DOI: 10.4176/090801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The detection of single base mismatches in DNA is important for diagnostics, treatment of genetic diseases, and identification of single nucleotide polymorphisms. Highly sensitive, specific assays are needed to investigate genetic samples from patients. The use of a simple fluorescent nucleoside analogue in detection of DNA sequence and point mutations by hybridisation in solution is described in this study. The 5′-bispyrene and 3′-naphthalene oligonucleotide probes form an exciplex on hybridisation to target in water and the 5′-bispyrene oligonucleotide alone is an adequate probe to determine concentration of target present. It was also indicated that this system has a potential to identify mismatches and insertions. The aim of this work was to investigate experimental structures and conditions that permit strong exciplex emission for nucleic acid detectors, and show how such exciplexes can register the presence of mismatches as required in SNP analysis. This study revealed that the hybridisation of 5′-bispyrenyl fluorophore to a DNA target results in formation of a fluorescent probe with high signal intensity change and specificity for detecting a complementary target in a homogeneous system. Detection of SNP mutations using this split-probe system is a highly specific, simple, and accessible method to meet the rigorous requirements of pharmacogenomic studies. Thus, it is possible for the system to act as SNP detectors and it shows promise for future applications in genetic testing.
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Affiliation(s)
- A Gbaj
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
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30
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Hu JY, Era M, Elsegood MRJ, Yamato T. Synthesis and Photophysical Properties of Pyrene-Based Light-Emitting Monomers: Highly Pure-Blue-Fluorescent, Cruciform-Shaped Architectures. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900806] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Thuong NT, Asseline U. Modification of the 5' terminus of oligonucleotides for attachment of reporter and conjugate groups. ACTA ACUST UNITED AC 2008; Chapter 4:Unit 4.2. [PMID: 18428849 DOI: 10.1002/0471142700.nc0402s00] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Reporter and conjugate groups can be added directly to the 5' terminus of oligonucleotides by appropriate modification. Conjugate groups can be used to increase the affinity of complementary strands, induce irreversible modification of target sequences, or enable sequences to recognize and permeate target cell membranes. This overview discusses the 5' modifications that can be used and strategies for the covalent attachment of ligands to the modified oligonucleotides. Step-by-step protocols for attachment of conjugate groups are given elsewhere in the series.
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Affiliation(s)
- N T Thuong
- Centre de Biophysique Moléculaire, CNRS, Orléans, France
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32
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Walsh L, Gbaj A, Etchells LL, Douglas KT, Bichenkova EV. SNP detection for cytochrome P450 alleles by target-assembled tandem oligonucleotide systems based on exciplexes. J Biomol Struct Dyn 2008; 25:629-40. [PMID: 18399696 DOI: 10.1080/07391102.2008.10507209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We report the first use of exciplex-based split-probes for detection of the wild type and *3 mutant alleles of human cytochrome P450 2C9. A tandem 8-mer split DNA oligonucleotide probe system was designed that allows detection of the complementary target DNA sequence. This exciplex-based fluorescence detector system operates by means of a contiguous hybridization of two oligonucleotide exciplex split-probes to a complementary target nucleic acid target. Each probe oligonucleotide is chemically modified at one of its termini by a potential exciplex-forming partner, each of which is fluorescently silent at the wavelength of detection. Under conditions that ensure correct three-dimensional assembly, the chemical moieties on suitable photoexcitation form an exciplex that fluoresces with a large Stokes shift (in this case 130 nm). Preliminary proof-of-concept studies used two 8-mer probe oligonucleotides, but in order to give better specificity for genomic applications, probe length was extended to give coverage of 24 bases. Eight pairs of tandem 12-mer oligonucleotide probes spanning the 2C9*3 region were designed and tested to find the best set of probes. Target sequences tested were in the form of (i) synthetic oligonucleotides, (ii) embedded in short PCR products (150 bp), or (iii) inserted into plasmid DNA (approximately 3 Kbp). The exciplex system was able to differentiate wild type and human cytochrome P450 2C9 *3 SNP (1075 A-->C) alleles, based on fluorescence emission spectra and DNA melting curves, indicating promise for future applications in genetic testing and molecular diagnostics.
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Affiliation(s)
- Lindsey Walsh
- Wolfson Center for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Manchester, M13 9PL, U.K
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33
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Conlon P, Yang CJ, Wu Y, Chen Y, Martinez K, Kim Y, Stevens N, Marti AA, Jockusch S, Turro NJ, Tan W. Pyrene excimer signaling molecular beacons for probing nucleic acids. J Am Chem Soc 2008; 130:336-42. [PMID: 18078339 PMCID: PMC2531189 DOI: 10.1021/ja076411y] [Citation(s) in RCA: 246] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular beacon DNA probes, containing 1-4 pyrene monomers on the 5' end and the quencher DABCYL on the 3' end, were engineered and employed for real-time probing of DNA sequences. In the absence of a target sequence, the multiple-pyrene labeled molecular beacons (MBs) assumed a stem-closed conformation resulting in quenching of the pyrene excimer fluorescence. In the presence of target, the beacons switched to a stem-open conformation, which separated the pyrene label from the quencher molecule and generated an excimer emission signal proportional to the target concentration. Steady-state fluorescence assays resulted in a subnanomolar limit of detection in buffer, whereas time-resolved signaling enabled low-nanomolar target detection in cell-growth media. It was found that the excimer emission intensity could be scaled by increasing the number of pyrene monomers conjugated to the 5' terminal. Each additional pyrene monomer resulted in substantial increases in the excimer emission intensities, quantum yields, and excited-state lifetimes of the hybridized MBs. The long fluorescence lifetime ( approximately 40 ns), large Stokes shift (130 nm), and tunable intensity of the excimer make this multiple-pyrene moiety a useful alternative to traditional fluorophore labeling in nucleic acid probes.
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Affiliation(s)
- Patrick Conlon
- Center for Research at Bio/NanoInterface, Department of Chemistry and Shands Cancer Center,University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611-7200. 352-846-2410
| | - Chaoyong James Yang
- Center for Research at Bio/NanoInterface, Department of Chemistry and Shands Cancer Center,University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611-7200. 352-846-2410
| | - Yanrong Wu
- Center for Research at Bio/NanoInterface, Department of Chemistry and Shands Cancer Center,University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611-7200. 352-846-2410
| | - Yan Chen
- Center for Research at Bio/NanoInterface, Department of Chemistry and Shands Cancer Center,University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611-7200. 352-846-2410
| | - Karen Martinez
- Center for Research at Bio/NanoInterface, Department of Chemistry and Shands Cancer Center,University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611-7200. 352-846-2410
| | - Youngmi Kim
- Center for Research at Bio/NanoInterface, Department of Chemistry and Shands Cancer Center,University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611-7200. 352-846-2410
| | - Nathan Stevens
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Angel A. Marti
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Steffen Jockusch
- Department of Chemistry, Columbia University, New York, NY 10027
| | | | - Weihong Tan
- Center for Research at Bio/NanoInterface, Department of Chemistry and Shands Cancer Center,University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611-7200. 352-846-2410
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Kadirvel M, Arsic B, Freeman S, Bichenkova EV. Exciplex and excimer molecular probes: detection of conformational flip in a myo-inositol chair. Org Biomol Chem 2008; 6:1966-72. [DOI: 10.1039/b800710a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
Fluorescence is highly sensitive to environment, and the distance separating fluorophores and quencher molecules can provide the basis for effective homogeneous nucleic acid hybridization assays. Molecular interactions leading to fluorescence quenching include collisions, ground state and excited state complex formation, and long-range dipole-coupled energy transfer. These processes are well understood and equations are provided for estimating the effects of each process on fluorescence intensity. Estimates for the fluorescein-tetramethylrhodamine donor-acceptor pair reveal the relative contributions of dipole-coupled energy transfer, collisional quenching, and static quenching in several common assay formats, and illustrate that the degree of quenching is dependent upon the hybridization complex formed and the manner of label attachment.
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36
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Gbaj A, Bichenkova E, Walsh L, Savage H, Sardarian A, Etchells L, Gulati A, Hawisa S, Douglas K. New Concepts of Fluorescent Probes for Specific Detection of DNA Sequences: Bis-Modified Oligonucleotides in Excimer and Exciplex Detection. Libyan J Med 2008. [DOI: 10.3402/ljm.v4i4.4841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A. Gbaj
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
- National Centre for Medical Research, Zawia-Libya
| | - E.V. Bichenkova
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
| | - L. Walsh
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
| | - H.E. Savage
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
| | - A.R. Sardarian
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
- Present address; Department of Chemistry, Shiraz University, Shiraz, Iran and
| | - L.L. Etchells
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
| | - A. Gulati
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
| | - S. Hawisa
- National Centre for Medical Research, Zawia-Libya
| | - K.T. Douglas
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
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Umemoto T, Hrdlicka PJ, Babu BR, Wengel J. Sensitive SNP Dual-Probe Assays Based on Pyrene-Functionalized 2′-Amino-LNA: Lessons To Be Learned. Chembiochem 2007; 8:2240-8. [DOI: 10.1002/cbic.200700408] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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38
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Astakhova IV, Malakhov AD, Stepanova IA, Ustinov AV, Bondarev SL, Paramonov AS, Korshun VA. 1-Phenylethynylpyrene (1-PEPy) as Refined Excimer Forming Alternative to Pyrene: Case of DNA Major Groove Excimer. Bioconjug Chem 2007; 18:1972-80. [PMID: 17896811 DOI: 10.1021/bc700280h] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
1-Phenylethynylpyrene fluorochrome was studied as meta- and para-derivatives of arabino-uridine-2'-carbamates in ss and dsDNA. 1-PEPy showed red-shifted emission and increased fluorescence quantum yield compared to pyrene. Although 1-PEPy has very short excited lifetime (<2.5 ns), it is able to form inter- and intrastrand excimers on DNA, probably resulting from spatial preorganization of two dye molecules.
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Affiliation(s)
- Irina V Astakhova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
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Martí AA, Jockusch S, Stevens N, Ju J, Turro NJ. Fluorescent hybridization probes for sensitive and selective DNA and RNA detection. Acc Chem Res 2007; 40:402-9. [PMID: 17458926 DOI: 10.1021/ar600013q] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We outline the different approaches taken by our group in the design of fluorescent hybridization sensors. Molecular beacons (MBs) and binary probes (BPs) using two dyes (2d-MB and 2d-BP, respectively) have been synthesized; these sensors serve as switches in emission upon binding to target biomolecules, such as DNA. These sensors allow for ratiometric fluorescence detection of polynucleotides (PNs) by visualization of the probes when bound to a target PN. Additionally, three-dye MBs (3d-MB) and BPs (3d-BP) have been developed, where an energy-transfer cascade is employed to decrease the overlap between the fluorophore emission spectra, resulting in a low direct excitation of the acceptor fluorophore. Pyrene-based MB (Py-MB) and BP (Py-BP), which possess the advantage of long fluorescence lifetimes, have also been synthesized. Time-resolved fluorescence spectra (TRES) can be used to discriminate between short-lived background fluorescence and long-lived fluorescence of the pyrene probes. This technique was demonstrated by time-resolving the signal of a Py-BP from the background fluorescence in Aplysia californica cell extracts.
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Affiliation(s)
- Angel A Martí
- Department of Chemistry, Columbia University, New York, NY 10027, USA
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40
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Bichenkova EV, Gbaj A, Walsh L, Savage HE, Rogert C, Sardarian AR, Etchells LL, Douglas KT. Detection of nucleic acids in situ: novel oligonucleotide analogues for target-assembled DNA-mounted exciplexes. Org Biomol Chem 2007; 5:1039-51. [PMID: 17377657 DOI: 10.1039/b700293a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This research describes the effects of structural variation and medium effects for the novel split-oligonucleotide (tandem) probe systems for exciplex-based fluorescence detection of DNA. In this approach the detection system is split at a molecular level into signal-silent components, which must be assembled correctly into a specific 3-dimensional structure to ensure close proximity of the exciplex partners and the consequent exciplex fluorescence emission on excitation. The model system consists of two 8-mer oligonucleotides, complementary to adjacent sites of a 16-mer DNA target. Each probe oligonucleotide is equipped with functions able to form an exciplex on correct, contiguous hybridization. This study investigates the influence of a number of structural aspects (i.e. chemical structure and composition of exciplex partners, length and structure of linker groups, locations of exciplex partner attachment, as well as effects of media) on the performance of DNA-mounted exciplex systems. The extremely rigorous structural demands for exciplex formation and emission required careful structural design of linkers and partners for exciplex formation, which are here described. Certain organic solvents (especially trifluoroethanol) specifically favour emission of the DNA-mounted exciplexes, probably the net result of the particular duplex structure and specific solvation of the exciplex partners. The exciplexes formed emitted at approximately 480 nm with large Stokes shifts ( approximately 130-140 nm). Comparative studies with pyrene excimer systems were also carried out.
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Affiliation(s)
- Elena V Bichenkova
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Manchester, UK.
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41
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Prokhorenko IA, Malakhov AD, Kozlova AA, Momynaliev K, Govorun VM, Korshun VA. Phenylethynylpyrene-labeled oligonucleotide probes for excimer fluorescence SNP analysis of 23S rRNA gene in clarithromycin-resistant Helicobacter pylori strains. Mutat Res 2006; 599:144-51. [PMID: 16597449 DOI: 10.1016/j.mrfmmm.2006.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2005] [Revised: 02/14/2006] [Accepted: 02/15/2006] [Indexed: 05/08/2023]
Abstract
The use of phenylethynylpyrene excimer forming pair in the design of specific fluorescent probes for determination of A2144G (A2143G and/or A2143C) mutations in 23S rRNA gene of Helicobacter pylori is described. Analysis of fluorescence spectra of model duplexes revealed optimal positions of fluorophore residues in the probe sequences for maximum efficiency of SNP detection. Application of excimer forming probes for analysis of DNA samples isolated from natural bacterial strains of H. pylori was demonstrated.
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Affiliation(s)
- Igor A Prokhorenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
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42
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Lartia R, Asseline U. New cyanine-oligonucleotide conjugates: relationships between chemical structures and properties. Chemistry 2006; 12:2270-81. [PMID: 16419140 DOI: 10.1002/chem.200500908] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Because the influence of the chemical structure of monomethine cyanine-oligo-2'-deoxyribonucleotide (ODN) conjugates on their binding and fluorescence properties has remained largely undetermined, we synthesized and studied a wide range of conjugates with various structural patterns. Different cyanine dyes such as thiocyanine, quinocyanine, and thiazole orange isomers were obtained. In the case of unsymmetrical cyanines, the linker was attached to either the quinoline or the benzothiazole nucleus. The influence of the ODN counterpart was evaluated by linking the cyanines to the 5'-end or to an internucleotidic phosphate. In the first case, the influence of neighboring nucleic bases was studied, whereas in the second, the stereochemical configuration at the phosphorus atom bearing the cyanine was investigated. We report here on relationships between the structures of the dyes and conjugates and some of their properties, such as the stability and fluorescence changes observed on their hybridization with the target sequence. This study provides useful information towards the design of ODN-cyanine conjugates.
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Affiliation(s)
- Rémy Lartia
- Centre de Biophysique Moléculaire, CNRS UPR 4301 affiliated with the University of Orléans and with INSERM, Rue Charles Sadron, 45071 Orleans Cedex 02, France
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Martí AA, Li X, Jockusch S, Li Z, Raveendra B, Kalachikov S, Russo JJ, Morozova I, Puthanveettil SV, Ju J, Turro NJ. Pyrene binary probes for unambiguous detection of mRNA using time-resolved fluorescence spectroscopy. Nucleic Acids Res 2006; 34:3161-8. [PMID: 16769776 PMCID: PMC1477857 DOI: 10.1093/nar/gkl406] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2005] [Revised: 03/01/2006] [Accepted: 04/27/2006] [Indexed: 12/28/2022] Open
Abstract
We report here the design, synthesis and application of pyrene binary oligonucleotide probes for selective detection of cellular mRNA. The detection strategy is based on the formation of a fluorescent excimer when two pyrene groups are brought into close proximity upon hybridization of the probes with the target mRNA. The pyrene excimer has a long fluorescence lifetime (>40 ns) compared with that of cellular extracts (approximately 7 ns), allowing selective detection of the excimer using time-resolved emission spectra (TRES). Optimized probes were used to target a specific region of sensorin mRNA yielding a strong excimer emission peak at 485 nm in the presence of the target and no excimer emission in the absence of the target in buffer solution. While direct fluorescence measurement of neuronal extracts showed a strong fluorescent background, obscuring the detection of the excimer signal, time-resolved emission measurements indicated that the emission decay of the cellular extracts is approximately 8 times faster than that of the pyrene excimer probes. Thus, using TRES of the pyrene probes, we are able to selectively detect mRNA in the presence of cellular extracts, demonstrating the potential for application of pyrene excimer probes for imaging mRNAs in cellular environments that have background fluorescence.
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Affiliation(s)
- Angel A. Martí
- Department of Chemistry, Columbia UniversityNew York, NY 10027, USA
| | - Xiaoxu Li
- Columbia Genome Center, Columbia University College of Physicians and SurgeonsNew York, NY 10032, USA
| | - Steffen Jockusch
- Department of Chemistry, Columbia UniversityNew York, NY 10027, USA
| | - Zengmin Li
- Department of Chemical Engineering, Columbia UniversityNew York, NY 10027, USA
- Columbia Genome Center, Columbia University College of Physicians and SurgeonsNew York, NY 10032, USA
| | - Bindu Raveendra
- Columbia Genome Center, Columbia University College of Physicians and SurgeonsNew York, NY 10032, USA
| | - Sergey Kalachikov
- Columbia Genome Center, Columbia University College of Physicians and SurgeonsNew York, NY 10032, USA
| | - James J. Russo
- Columbia Genome Center, Columbia University College of Physicians and SurgeonsNew York, NY 10032, USA
| | - Irina Morozova
- Columbia Genome Center, Columbia University College of Physicians and SurgeonsNew York, NY 10032, USA
| | | | - Jingyue Ju
- Department of Chemical Engineering, Columbia UniversityNew York, NY 10027, USA
- Columbia Genome Center, Columbia University College of Physicians and SurgeonsNew York, NY 10032, USA
| | - Nicholas J. Turro
- Department of Chemistry, Columbia UniversityNew York, NY 10027, USA
- Department of Chemical Engineering, Columbia UniversityNew York, NY 10027, USA
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Bichenkova EV, Sardarian AR, Wilton AN, Bonnet P, Bryce RA, Douglas KT. Exciplex fluorescence emission from simple organic intramolecular constructs in non-polar and highly polar media as model systems for DNA-assembled exciplex detectors. Org Biomol Chem 2006; 4:367-78. [PMID: 16391780 DOI: 10.1039/b511707k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Organic intramolecular exciplexes, N-(4-dimethylaminobenzyl)-N-(1-pyrenemethyl)amine (1) and N'-4-dimethylaminonaphthyl-N-(1-pyrenemethyl)amine (2), were used as model systems to reveal major factors affecting their exciplex fluorescence, and thus lay the basis for developing emissive target-assembled exciplexes for DNA-mounted systems in solution. These models with an aromatic pyrenyl hydrocarbon moiety as an electron acceptor appropriately connected to an aromatic dimethylamino electron donor component (N,N-dimethylaminophenyl or N,N-dimethylaminonaphthyl) showed strong intramolecular exciplex emission in both non-polar and highly polar solvents. The effect of dielectric constant on the maximum wavelength for exciplex emission was studied, and emission was observed for 1 and 2 over the full range of solvent from non-polar hydrocarbons up to N-methylformamide with a dielectric constant of 182. Quantum yields were determined for these intramolecular exciplexes in a range of solvents relative to that for Hoechst 33,258. Conformational analysis of 1 was performed both computationally and via qualitative 2D NMR using (1)H-NOESY experiments. The results obtained indicated the contribution of pre-folded conformation(s) to the ground state of 1 conducive to exciplex emission. This research provides the initial background for design of self-assembled, DNA-mounted exciplexes and underpins further development of exciplex-based hybridisation bioassays.
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Affiliation(s)
- Elena V Bichenkova
- Wolfson Centre for Structure-Based Rational Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Manchester, UKM13 9PL.
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Aly Y, Wamberg M, Pedersen E. Intercalating Nucleic Acids with Insertion of 5-[(Pyren-1-yl)methylidene]hydantoin-Substituted Butane-1,2-diol. Helv Chim Acta 2005. [DOI: 10.1002/hlca.200590253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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46
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Synthesis, Absorption, and Fluorescence-Emission Properties of 1,3,6,8-Tetraethynylpyrene and Its Derivatives. European J Org Chem 2005. [DOI: 10.1002/ejoc.200500222] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Bichenkova EV, Savage HE, Sardarian AR, Douglas KT. Target-assembled tandem oligonucleotide systems based on exciplexes for detecting DNA mismatches and single nucleotide polymorphisms. Biochem Biophys Res Commun 2005; 332:956-64. [PMID: 15913549 DOI: 10.1016/j.bbrc.2005.05.048] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2005] [Accepted: 05/10/2005] [Indexed: 11/15/2022]
Abstract
We report the first exciplex-based split-probe system for DNA detection. The detector is split at a molecular level into signal-silent components which, before a signal is generated, must be assembled correctly into a particular three-dimensional arrangement. The model system comprises of two 8-mer oligonucleotides, complementary to neighbouring sites of a 16-mer DNA target, each equipped with moieties able to form an exciplex on correct, contiguous hybridization. The exciplex emits at approximately 480 nm with a large Stokes shift (135 nm). The extremely rigorous structural demands for exciplex formation and emission were achieved by careful structural design and by the discovery that high levels of certain organic solvents (especially trifluoroethanol) specifically favour emission of the DNA-mounted exciplex, probably the net result of the particular duplex structure and specific solvation of the exciplex partners. Inserts and mismatches can be effectively detected by this exciplex construct giving potential for single nucleotide polymorphism detection.
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Affiliation(s)
- Elena V Bichenkova
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Manchester M13 9PL, UK
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48
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Bichenkova EV, Sardarian A, Savage HE, Rogert C, Douglas KT. An exciplex-based, target-assembled fluorescence system with inherently low background to probe for specific nucleic acid sequences. Assay Drug Dev Technol 2005; 3:39-46. [PMID: 15798394 DOI: 10.1089/adt.2005.3.39] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A novel detection technique, called ExciProbes, has been developed to proof-of-principle level for DNA oligonucleotides. The new approach is based on the use of two short oligonucleotides complementary to a target nucleic acid sequence. Each short-probe oligonucleotide bears the separated parts of a new class of fluorescence detector, an exciplex. These isolated parts of the detector have no inherent signal at the detection wavelength. They are designed to detect biotarget by being assembled by the target itself to give a new molecular entity (the exciplex), with a characteristic fluorescence and very large Stokes shift (typically >150 nm). The technique is not related to fluorescence resonance energy transfer, and can potentially resolve to 1 base pair. ExciProbes can detect single or double mutations in a short sequence of DNA, and can be combined with temperature-filtering to provide allelic discrimination of single nucleotide polymorphism analysis. Compared to other fluorophore systems that have large backgrounds (typically >60%), ExciProbes show backgrounds of <1% under comparable conditions, and can be used with DNA, RNA, or synthetic nucleic acids such as locked nucleic acid.
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Affiliation(s)
- Elena V Bichenkova
- Wolfson Centre for Structure-Based Rational Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Manchester, UK.
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Bichenkova EV, Yu X, Bhadra P, Heissigerova H, Pope SJA, Coe BJ, Faulkner S, Douglas KT. DNA Mismatch Detection by Resonance Energy Transfer between Ruthenium(II) and Osmium(II) Tris(2,2‘-bipyridyl) Chromophores. Inorg Chem 2005; 44:4112-4. [PMID: 15934730 DOI: 10.1021/ic050586w] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Octahedral tris-chelate complexes [M(II)(bpy)(3)](2+) (M = Ru or Os, bpy = 2,2'-bipyridyl), covalently attached to the 3'- and 5'-phosphates of two oligonucleotides, are juxtaposed when hybridized contiguously to a fully complementary DNA target. Visible metal-to-ligand charge-transfer (MLCT) excitation of the [Ru(II)(bpy)(3)](2+) unit leads to resonance energy transfer to the MLCT state of the [Os(II)(bpy)(3)](2+) moiety, with the energy transfer efficiency depending on the degree of hybridization. The extent of attenuation of the intense red luminescence from the Ru(II) chromophore hence allows highly sensitive structural probing of the assembly and constitutes a novel approach to DNA sensing which is capable of detecting mutations.
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Affiliation(s)
- Elena V Bichenkova
- Wolfson Centre for Rational Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, and School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK
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Malicka J, Gryczynski I, Gryczynski Z, Lakowicz JR. DNA hybridization using surface plasmon-coupled emission. Anal Chem 2004; 75:6629-33. [PMID: 14640738 PMCID: PMC2763914 DOI: 10.1021/ac034881e] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe a new approach to measuring DNA hybridization using surface plasmon-coupled emission (SPCE). Excited fluorophores are known to couple with surface oscillations of electrons in thin metal films, typically 50 nm thick silver on a glass prism. These surface plasmons then radiate into the glass at a sharply defined angle determined by the emission wavelength and the optical properties of the glass and metal. This radiation has the same spectral profile as the emission spectrum of the fluorophores. We studied the emission due to Cy3-labeled DNA oligomers bound to complementary unlabeled oligomers which were themselves bound to the metal surface. Hybridization resulted in SPCE due to Cy3-DNA into the prism. Directional SPCE was observed whether the sample was illuminated from the sample side or through the glass substrate at the surface plasmon angle for the excitation wavelength. A large fraction of the total potential emission is coupled to the surface plasmons resulting in improved sensitivity. When illuminated through the prism at the surface plasmon angle, the sensitivity is increased due to the enhanced intensity of the resonance evanescent field. It is known that SPCE depends on proximity to the silver surface. As a result, changes in emission intensity are observed due to fluorophore localization even if hybridization does not affect the quantum yield of the fluorophore. The use of SPCE resulted in suppression of interfering emission from a noncomplementary Cy5-DNA oligomers due to weaker coupling of the more distant fluorophores with the surface plasmons. We expect SPCE to have numerous applications to nucleic acid analysis and for the measurement of bioaffinity reactions.
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Affiliation(s)
- Joanna Malicka
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland at Baltimore, 725 West Lombard Street, Baltimore, Maryland 21201, USA
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