1
|
Guisán-Ceinos S, R Rivero A, Romeo-Gella F, Simón-Fuente S, Gómez-Pastor S, Calvo N, Orrego AH, Guisán JM, Corral I, Sanz-Rodriguez F, Ribagorda M. Turn-on Fluorescent Biosensors for Imaging Hypoxia-like Conditions in Living Cells. J Am Chem Soc 2022; 144:8185-8193. [PMID: 35486830 PMCID: PMC9100661 DOI: 10.1021/jacs.2c01197] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
We present the synthesis,
photophysical properties, and biological
application of nontoxic 3-azo-conjugated BODIPY dyes as masked fluorescent
biosensors of hypoxia-like conditions. The synthetic methodology is
based on an operationally simple N=N bond-forming protocol,
followed by a Suzuki coupling, that allows for a direct access to
simple and underexplored 3-azo-substituted BODIPY. These dyes can
turn on their emission properties under both chemical and biological
reductive conditions, including bacterial and human azoreductases,
which trigger the azo bond cleavage, leading to fluorescent 3-amino-BODIPY.
We have also developed a practical enzymatic protocol, using an immobilized
bacterial azoreductase that allows for the evaluation of these azo-based
probes and can be used as a model for the less accessible and expensive
human reductase NQO1. Quantum mechanical calculations uncover the
restructuration of the topography of the S1 potential energy
surface following the reduction of the azo moiety and rationalize
the fluorescent quenching event through the mapping of an unprecedented
pathway. Fluorescent microscopy experiments show that these azos can
be used to visualize hypoxia-like conditions within living cells.
Collapse
Affiliation(s)
- Santiago Guisán-Ceinos
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Alexandra R Rivero
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Fernando Romeo-Gella
- Departamento de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Silvia Simón-Fuente
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Silvia Gómez-Pastor
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Natalia Calvo
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Alejandro H Orrego
- Departamento de Biocatálisis, Instituto de Catálisis y Petroquímica (CSIC), Campus UAM, 28049 Madrid, Spain
| | - José Manuel Guisán
- Departamento de Biocatálisis, Instituto de Catálisis y Petroquímica (CSIC), Campus UAM, 28049 Madrid, Spain
| | - Inés Corral
- Departamento de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Francisco Sanz-Rodriguez
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Maria Ribagorda
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| |
Collapse
|
2
|
Bai C, Klimkowski P, Jin C, Kuchlyan J, El-Sagheer AH, Brown T. A new phosphoramidite enables orthogonal double labelling to form combination oligonucleotide probes. Org Biomol Chem 2022; 20:8618-8622. [DOI: 10.1039/d2ob01899c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A novel phosphoramidite (AP-C3 dT) containing an alkyne and amine has been synthesized, enabling orthogonal labelling for combination oligonucleotides probes.
Collapse
Affiliation(s)
- Chunsen Bai
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Piotr Klimkowski
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Cheng Jin
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Jagannath Kuchlyan
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Afaf H. El-Sagheer
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| |
Collapse
|
3
|
LoopTag FRET Probe System for Multiplex qPCR Detection of Borrelia Species. Life (Basel) 2021; 11:life11111163. [PMID: 34833039 PMCID: PMC8624210 DOI: 10.3390/life11111163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/19/2022] Open
Abstract
Background: Laboratory diagnosis of Lyme borreliosis refers to some methods with known limitations. Molecular diagnostics using specific nucleic acid probes may overcome some of these limitations. Methods: We describe the novel reporter fluorescence real-time polymerase chain reaction (PCR) probe system LoopTag for detection of Borrelia species. Advantages of the LoopTag system include having cheap conventional fluorescence dyes, easy primer design, no restrictions for PCR product lengths, robustness, high sequence specificity, applicability for multiplex real-time PCRs, melting curve analysis (single nucleotide polymorphism analysis) over a large temperature range, high sensitivity, and easy adaptation of conventional PCRs. Results: Using the LoopTag probe system we were able to detect all nine tested European species belonging to the Borrelia burgdorferi (sensu lato) complex and differentiated them from relapsing fever Borrelia species. As few as 10 copies of Borrelia in one PCR reaction were detectable. Conclusion: We established a novel multiplex probe real-time PCR system, designated LoopTag, that is simple, robust, and incorporates melting curve analysis for the detection and in the differentiation of European species belonging to the Borrelia burgdorferi s.l. complex.
Collapse
|
4
|
Berry ME, Kearns H, Graham D, Faulds K. Surface enhanced Raman scattering for the multiplexed detection of pathogenic microorganisms: towards point-of-use applications. Analyst 2021; 146:6084-6101. [PMID: 34492668 PMCID: PMC8504440 DOI: 10.1039/d1an00865j] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/22/2021] [Accepted: 08/27/2021] [Indexed: 01/02/2023]
Abstract
Surface enhanced Raman scattering (SERS) is a technique that demonstrates a number of advantages for the rapid, specific and sensitive detection of pathogenic microorganisms. In this review, an overview of label-free and label-based SERS approaches, including microfluidics, nucleic acid detection and immunoassays, for the multiplexed detection of pathogenic bacteria and viruses from the last decade will be discussed, as well as their transition into promising point-of-use detection technologies in industrial and medical settings.
Collapse
Affiliation(s)
- Matthew E Berry
- Centre for Molecular Nanometrology, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, UK.
| | - Hayleigh Kearns
- Centre for Molecular Nanometrology, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, UK.
| | - Duncan Graham
- Centre for Molecular Nanometrology, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, UK.
| | - Karen Faulds
- Centre for Molecular Nanometrology, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, UK.
| |
Collapse
|
5
|
Luo X, Lai C, Lee Y, Kuo C, Chen I. Investigating metal‐enhanced fluorescence effect on fluorescein by gold nanotriangles and nanocubes using time‐resolved fluorescence spectroscopy. J CHIN CHEM SOC-TAIP 2021. [DOI: 10.1002/jccs.202100294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xue‐Feng Luo
- Department of Chemistry National Tsing Hua University Hsinchu Taiwan Republic of China
| | - Chien‐Chang Lai
- Department of Chemistry National Tsing Hua University Hsinchu Taiwan Republic of China
| | - Yin‐Yu Lee
- National Synchrotron Radiation Research Center Hsinchu Taiwan Republic of China
| | - Chun‐Hong Kuo
- Institute of Chemistry Academia Sinica Taipei Republic of China
| | - I‐Chia Chen
- Department of Chemistry National Tsing Hua University Hsinchu Taiwan Republic of China
| |
Collapse
|
6
|
Bucardo MS, Wu Y, Ludford PT, Li Y, Fin A, Tor Y. Real-Time Monitoring of Human Guanine Deaminase Activity by an Emissive Guanine Analog. ACS Chem Biol 2021; 16:1208-1214. [PMID: 34190533 DOI: 10.1021/acschembio.1c00232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Guanine deaminase (GDA) deaminates guanine to xanthine. Despite its significance, the study of human GDA remains limited compared to other metabolic deaminases. As a result, its substrate and inhibitor repertoire are limited, and effective real-time activity, inhibitory, and discovery assays are missing. Herein, we explore two emissive heterocyclic cores, based on thieno[3,4-d]pyrimidine (thN) and isothiazole[4,3-d]pyrimidine (tzN), as surrogate GDA substrates. We demonstrate that, unlike the thieno analog, thGN, the isothiazolo guanine surrogate, tzGN, does undergo effective enzymatic deamination by GDA and yields the spectroscopically distinct xanthine analog, tzXN. Further, we showcase the potential of this fluorescent nucleobase surrogate to provide a visible spectral window for a real-time study of GDA and its inhibition.
Collapse
Affiliation(s)
- Marcela S. Bucardo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - You Wu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Paul T. Ludford
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Yao Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Andrea Fin
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| |
Collapse
|
7
|
Brylev VA, Lysenko IL, Kokin EA, Martynenko-Makaev YV, Ryazantsev DY, Shmanai VV, Korshun VA. Molecular Beacon DNA Probes with Fluorescein Bifluorophore. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021; 47:734-740. [PMID: 34149274 PMCID: PMC8193957 DOI: 10.1134/s1068162021030055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 10/26/2020] [Accepted: 10/31/2020] [Indexed: 11/25/2022]
Abstract
An azido-derivative of a fluorescein bifluorophore was obtained and used for the synthesis of “molecular beacon”-type oligonucleotide fluorogenic probes for RT-PCR. Eight probe variants were synthesized based on an optimized sequence: with one or two quencher residues at the 3'-end, with a single or bifluorophore fluorescein label attached to 5'-end using modifying phosphoramidites (short linker) or “click reaction” (long linker). Comparison of probes in RT-PCR showed that probes with a doubled quencher (single fluorescein on a short linker) and doubled dye on a short linker (single dye) are somewhat superior in sensitivity to a standard probe (single quencher, single dye on a short linker) by the value of ΔCt = 1–2.
Collapse
Affiliation(s)
- V A Brylev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - I L Lysenko
- Institute of Physical Organic Chemistry of NAS Belarus, 220072 Minsk, Belarus
| | - E A Kokin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | | | - D Y Ryazantsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - V V Shmanai
- Institute of Physical Organic Chemistry of NAS Belarus, 220072 Minsk, Belarus
| | - V A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia.,Department of Biology and Biotechnology, National Research University Higher School of Economics, 117312 Moscow, Russia.,Gause Institute of New Antibiotics, 119021 Moscow, Russia
| |
Collapse
|
8
|
Ramezani A. CtNorm: Real time PCR cycle of threshold (Ct) normalization algorithm. J Microbiol Methods 2021; 187:106267. [PMID: 34116107 DOI: 10.1016/j.mimet.2021.106267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/05/2021] [Accepted: 06/06/2021] [Indexed: 11/25/2022]
Abstract
In relative quantification with Real Time PCR (qRT-PCR,), accurate analysis requires equal amplification efficiency for both genes (Gene of interest and reference gene) and equal threshold values for all the samples. In this quantification method the expression level in treated samples will be calculated in comparison to the control group. We conducted the present study to design an algorithm for converting the data obtained from different runs containing identical standard samples into one run with the same amplification efficiency and threshold value. For this purpose, two formulas were designed; one to convert the amplification efficiency of the each run to 100%, and the other one for converting data from different runs into one run. Utilizing these two formulas, an algorithm was developed and named CtNorm. The online version of CtNorm algorithm is available at http://ctnorm.sums.ac.ir/. We used qRT-PCR technique to validate the accuracy of the designed algorithm for the normalization of four different human internal control genes. Normalizing the Ct values obtained from separate runs with the CtNorm algorithm has eliminated the differences and the average of the Ct values has become similar to the condition in which all the samples were amplified in a single run. The CtNorm algorithm could be utilized for equalizing the Ct values of several qRT-PCR runs with the same standard samples. The algorithm has also the ability to convert the amplification efficiency to 100% which is useful in absolute and relative quantification.
Collapse
Affiliation(s)
- Amin Ramezani
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Science, Shiraz, Iran; Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
| |
Collapse
|
9
|
Fantoni NZ, El-Sagheer AH, Brown T. A Hitchhiker's Guide to Click-Chemistry with Nucleic Acids. Chem Rev 2021; 121:7122-7154. [PMID: 33443411 DOI: 10.1021/acs.chemrev.0c00928] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Click chemistry is an immensely powerful technique for the fast and efficient covalent conjugation of molecular entities. Its broad scope has positively impacted on multiple scientific disciplines, and its implementation within the nucleic acid field has enabled researchers to generate a wide variety of tools with application in biology, biochemistry, and biotechnology. Azide-alkyne cycloadditions (AAC) are still the leading technology among click reactions due to the facile modification and incorporation of azide and alkyne groups within biological scaffolds. Application of AAC chemistry to nucleic acids allows labeling, ligation, and cyclization of oligonucleotides efficiently and cost-effectively relative to previously used chemical and enzymatic techniques. In this review, we provide a guide to inexperienced and knowledgeable researchers approaching the field of click chemistry with nucleic acids. We discuss in detail the chemistry, the available modified-nucleosides, and applications of AAC reactions in nucleic acid chemistry and provide a critical view of the advantages, limitations, and open-questions within the field.
Collapse
Affiliation(s)
- Nicolò Zuin Fantoni
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.,Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
| |
Collapse
|
10
|
Ikonnikova AY, Shershov VE, Moroz YV, Vasiliskov VA, Lapa SA, Miftakhov RA, Kuznetsova VE, Chudinov AV, Nasedkina TV. The Efficacy of Hybridization Analysis of DNA Labeled with Red and Near-Infrared Cyanine Dyes. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s000635092101005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
11
|
Gouda AS, Przypis Ł, Walczak K, Jørgensen PT, Wengel J. Carbazole modified oligonucleotides: synthesis, hybridization studies and fluorescence properties. Org Biomol Chem 2020; 18:6935-6948. [PMID: 32936176 DOI: 10.1039/d0ob01553a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Synthesis of the novel thiophenyl carbazole phosphoramidite DNA building block 5 was accomplished in four steps using a Suzuki-Miyaura cross-coupling reaction from the core carbazole and it was seamlessly accommodated into a 9-mer DNA-based oligonucleotide by incorporation at the flanking 5'-end in combination with a central insertion of an LNA-T nucleotide. The carbazole-containing oligonucleotide was combined in different duplex hybrids, which were characterized by thermal denaturation, circular dichroism and fluorescence studies. The carbazole monomer modulates the duplex stability in various ways. Thus, monomer Z increased the thermal stability of the 9-mer towards the complementary 9-mer/15-mer DNA duplex by 4.2 °C. Furthermore, indications of its intercalation into the duplex were obtained by modeling studies and robust decreases in fluorescence emission intensities upon duplex formation. In contrast, no clear intercalating tendency was corroborated for monomer Z within the DNA/RNA hybrid duplex as indicated by moderate quenching of the fluorescence and similar duplex thermal stabilities relative to the corresponding control duplex. The recognition efficiencies of the carbazole modified oligonucleotide toward single nucleotide mismatches were studied with two 15-mer model targets (DNA and RNA). For both systems, mismatches positioned at the juxtaposition of the carbazole monomer showed pronounced deceases in thermal denaturation temperature. Steady-state fluorescence emission studies of all mismatched duplexes with incorporation of Z monomer typically displayed efficient fluorescence quenching.
Collapse
Affiliation(s)
- Alaa S Gouda
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | | | | | | | | |
Collapse
|
12
|
Kim YT, Moon J, Hong IS. Simultaneous Detection of Multiple Pathogenic Targets with Stem-Tagged Primer Sets. Chembiochem 2020; 21:1116-1120. [PMID: 31705704 DOI: 10.1002/cbic.201900668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Indexed: 11/07/2022]
Abstract
Simultaneous multiple gene detection is indispensable for the detection of various genes in a small sample obtained by an invasive method. A typical detection method is probe-based fluorescence melting curve analysis by means of real-time PCR. It is very limited because, for each target, a probe sequence with at least a different Tm must be designed. To overcome this limitation, we developed a simultaneous multiple gene detection method based on a giant amplicon molecular beacon. PCR was performed by attaching stem sequences with different Tm values to each primer set, and the melting Tm was measured by hybridizing the stem sequences at both ends of the amplified amplicon; this generated well-separated Tm signals. The important point here is that the stem sequence that produces the Tm signal is an arbitrarily selectable sequence unrelated to the target gene. Because it is arbitrarily selectable, the desired Tm can be freely adjusted. As a result, we succeeded in the simultaneous detection of four samples with the use of only one fluorophore. Theoretically, a combination of five fluorophores could detect more than 20 multiple genes simultaneously.
Collapse
Affiliation(s)
- Yong-Tae Kim
- Department of Chemistry, College of Natural Science, Kongju National University, 56, Gongjudaehak-ro, Gongju-si, Chungnam, 32588, Republic of Korea
| | - Junhye Moon
- Research Institute, Sejong Medical Co. Ltd., 11, Sinchon 2-ro, Paju-si, Gyeonggi-do, 10880, Republic of Korea
| | - In Seok Hong
- Department of Chemistry, College of Natural Science, Kongju National University, 56, Gongjudaehak-ro, Gongju-si, Chungnam, 32588, Republic of Korea
| |
Collapse
|
13
|
Hollett G, Roberts DS, Sewell M, Wensley E, Wagner J, Murray W, Krotz A, Toth B, Vijayakumar V, Sailor MJ. Quantum Ensembles of Silicon Nanoparticles: Discrimination of Static and Dynamic Photoluminescence Quenching Processes. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2019; 123:17976-17986. [PMID: 32489514 PMCID: PMC7266134 DOI: 10.1021/acs.jpcc.9b04334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Porous silicon photoluminescence is characterized by a broad emission band that displays unusually long (tens to hundreds of micro-seconds), wavelength-dependent emissive lifetimes. The photoluminescence is associated with quantum confinement of excitons in silicon nanocrystallites contained within the porous matrix, and the broad emission spectrum derives from the wide distribution of nanocrystallite sizes in the material. The longer emissive lifetimes in the ensemble of quantum-confined emitters correspond to the larger nanocrystallites, with their longer wavelengths of emission. The quenching of this photoluminescence by aromatic, redox-active molecules aminochrome (AMC), dopamine, adrenochrome, sodium anthraquinone-2-sulfonate, benzyl viologen dichloride, methyl viologen dichloride hydrate, and ethyl viologen dibromide is studied, and dynamic and static quenching mechanisms are distinguished by the emission lifetime analysis. Because of the dependence of the emission lifetime on emission wavelength from the silicon nanocrystallite ensemble, a pronounced blue shift is observed in the steady-state emission spectrum upon exposure to dynamic-type quenchers. Conversely, static-type quenching systems show uniform quenching across all emission wavelengths. Thus, the difference between static and dynamic quenching mechanisms is readily distinguished by ratiometric photoluminescence spectroscopy. The application of this concept to imaging of AMC, the oxidized form of the neurotransmitter dopamine that is of interest for its role in neurodegenerative diseases, is demonstrated. It is found that static electron acceptors result in no ratiometric contrast, while AMC shows a strong contrast, allowing ready visualization in a 2-D imaging experiment.
Collapse
Affiliation(s)
- Geoffrey Hollett
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
| | - David S. Roberts
- Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Mollie Sewell
- Bioengineering, North Carolina A&T State University, Greensboro, North Carolina 27412, United States
| | - Emma Wensley
- Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Julia Wagner
- Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - William Murray
- Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Alex Krotz
- Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Bryan Toth
- Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Vibha Vijayakumar
- Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Michael J. Sailor
- Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| |
Collapse
|
14
|
A Novel Bioelectronic Reporter System in Living Cells Tested with a Synthetic Biological Comparator. Sci Rep 2019; 9:7275. [PMID: 31086248 PMCID: PMC6513987 DOI: 10.1038/s41598-019-43771-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 05/01/2019] [Indexed: 12/19/2022] Open
Abstract
As the fields of biotechnology and synthetic biology expand, cheap and sensitive tools are needed to measure increasingly complicated genetic circuits. In order to bypass some drawbacks of optical fluorescent reporting systems, we have designed and created a co-culture microbial fuel cell (MFC) system for electronic reporting. This system leverages the syntrophic growth of Escheriachia. coli (E. coli) and an electrogenic bacterium Shewanella oneidensis MR-1 (S. oneidensis). The fermentative products of E. coli provide a carbon and electron source for S. oneidensis MR-1, which then reports on such activity electrically at the anode of the MFC. To further test the capability of electrical reporting of complicated synthetic circuits, a novel synthetic biological comparator was designed and tested with both fluorescent and electrical reporting systems. The results suggest that the electrical reporting system is a good alternative to commonly used optical fluorescent reporter systems since it is a non-toxic reporting system with a much wider dynamic range.
Collapse
|
15
|
Farzan VM, Kvach MV, Aparin IO, Kireev DE, Prikazchikova TA, Ustinov AV, Shmanai VV, Shipulin GA, Korshun VA, Zatsepin TS. Novel homo Yin-Yang probes improve sensitivity in RT-qPCR detection of low copy HIV RNA. Talanta 2019; 194:226-232. [DOI: 10.1016/j.talanta.2018.10.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 10/09/2018] [Accepted: 10/11/2018] [Indexed: 12/31/2022]
|
16
|
Güixens-Gallardo P, Zawada Z, Matyašovský J, Dziuba D, Pohl R, Kraus T, Hocek M. Brightly Fluorescent 2′-Deoxyribonucleoside Triphosphates Bearing Methylated Bodipy Fluorophore for in Cellulo Incorporation to DNA, Imaging, and Flow Cytometry. Bioconjug Chem 2018; 29:3906-3912. [DOI: 10.1021/acs.bioconjchem.8b00721] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Pedro Güixens-Gallardo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Zbigniew Zawada
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Ján Matyašovský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Dmytro Dziuba
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Tomáš Kraus
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| |
Collapse
|
17
|
Saito Y, Hudson RH. Base-modified fluorescent purine nucleosides and nucleotides for use in oligonucleotide probes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2018. [DOI: 10.1016/j.jphotochemrev.2018.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
18
|
Seio K, Kanamori T, Masaki Y. Synthesis of Fluorescent Nucleic Acids bearing Nucleobases Modified with Heteroaryl Group and Fluorophores. J SYN ORG CHEM JPN 2018. [DOI: 10.5059/yukigoseikyokaishi.76.792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology
| | | | | |
Collapse
|
19
|
Abstract
Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years.
Collapse
Affiliation(s)
- Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| |
Collapse
|
20
|
Maity D, Matković M, Li S, Ehlers M, Wu J, Piantanida I, Schmuck C. Peptide-Based Probes with an Artificial Anion-Binding Motif for Direct Fluorescence "Switch-On" Detection of Nucleic Acid in Cells. Chemistry 2017; 23:17356-17362. [PMID: 28967979 DOI: 10.1002/chem.201703813] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Indexed: 01/08/2023]
Abstract
This work reports two new peptide-based fluorescence probes (1 and 2) for the detection of ds-DNA at physiological pH. Probes 1 and 2 contain a fluorophore, either amino-naphthalimide or diethyl-aminocoumarin, respectively, and two identical peptide arms each equipped with a guanidiniocarbonylpyrrole (GCP) anion-binding motif. These probes show "switch-on" fluorescence response upon binding to ds-DNA, whereby they can differentiate between various types of polynucleotides. For instance, they exhibit more pronounced fluorescence response for AT-rich polynucleotides than GC-rich polynucleotides, and both give only negligible response to ds-RNA. The fluorimetric response of 1 is proportional to the AT-basepair content in DNA, whereas the fluorescence of 2 is sensitive to the secondary structure of the polynucleotide. Fluorescence experiments, thermal melting experiments and circular dichroism studies suggest that 1 interacts with ds-DNA in a combined intercalation and minor groove binding, whereas 2 interacts mainly with the outer surface of DNA/RNA. As 1 and 2 have a very low cytotoxicity, 1 can be applied for the imaging of nuclear DNA in cells.
Collapse
Affiliation(s)
- Debabrata Maity
- Institute of Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
| | | | - Shang Li
- Key Lab for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, 200237, Shanghai, P. R. China
| | - Martin Ehlers
- Institute of Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
| | - Junchen Wu
- Key Lab for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, 200237, Shanghai, P. R. China
| | | | - Carsten Schmuck
- Institute of Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
| |
Collapse
|
21
|
Comparative Study of Novel Fluorescent Cyanine Nucleotides: Hybridization Analysis of Labeled PCR Products Using a Biochip. J Fluoresc 2017; 27:2001-2016. [PMID: 28752470 DOI: 10.1007/s10895-017-2139-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 07/18/2017] [Indexed: 01/08/2023]
Abstract
This study investigated the synthesis and substrate properties of Cy5-labeled dUTP derivatives with different substituents, linkers between the dye unit and pyrimidine heterocycle and fluorophore charges. Fluorescently labeled nucleoside triphosphates were studied as substrates using multiplex PCR with Taq and Vent (exo-) DNA polymerases, the typical representatives of the A and B polymerase families. The efficiency of nucleotide incorporation during PCR was assessed with a multi-parameter hybridization analysis using a diagnostic DNA microarray. The hybridization analysis indirectly estimates the incorporation efficiency of dye-labeled nucleotides in multiplex PCR. Our results demonstrated higher efficiencies of substrates with electrically neutral dyes than electropositive and electronegative Cy5 residues.
Collapse
|
22
|
Astakhova K, Golovin AV, Prokhorenko IA, Ustinov AV, Stepanova IA, Zatsepin TS, Korshun VA. Design of 2′-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection: The attachment manner matters. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.04.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
23
|
Pyrrolidinyl peptide nucleic acid terminally labeled with fluorophore and end-stacking quencher as a probe for highly specific DNA sequence discrimination. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.10.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
24
|
Molecular beacons with JOE dye: Influence of linker and 3′ couple quencher. Mol Cell Probes 2016; 30:285-290. [DOI: 10.1016/j.mcp.2016.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 10/05/2016] [Accepted: 10/05/2016] [Indexed: 11/23/2022]
|
25
|
Qiu J, Wilson A, El-Sagheer AH, Brown T. Combination probes with intercalating anchors and proximal fluorophores for DNA and RNA detection. Nucleic Acids Res 2016; 44:e138. [PMID: 27369379 PMCID: PMC5041472 DOI: 10.1093/nar/gkw579] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/16/2016] [Indexed: 12/20/2022] Open
Abstract
A new class of modified oligonucleotides (combination probes) has been designed and synthesised for use in genetic analysis and RNA detection. Their chemical structure combines an intercalating anchor with a reporter fluorophore on the same thymine nucleobase. The intercalator (thiazole orange or benzothiazole orange) provides an anchor, which upon hybridisation of the probe to its target becomes fluorescent and simultaneously stabilizes the duplex. The anchor is able to communicate via FRET to a proximal reporter dye (e.g. ROX, HEX, ATTO647N, FAM) whose fluorescence signal can be monitored on a range of analytical devices. Direct excitation of the reporter dye provides an alternative signalling mechanism. In both signalling modes, fluorescence in the unhybridised probe is switched off by collisional quenching between adjacent intercalator and reporter dyes. Single nucleotide polymorphisms in DNA and RNA targets are identified by differences in the duplex melting temperature, and the use of short hybridization probes, made possible by the stabilisation provided by the intercalator, enhances mismatch discrimination. Unlike other fluorogenic probe systems, placing the fluorophore and quencher on the same nucleobase facilitates the design of short probes containing multiple modifications. The ability to detect both DNA and RNA sequences suggests applications in cellular imaging and diagnostics.
Collapse
Affiliation(s)
- Jieqiong Qiu
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Adam Wilson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez, 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| |
Collapse
|
26
|
Synthesis of acridine-1,8-dione substituted (E)-5-(3-aminoallyl)-uridine-5′-triphosphate: a new potential fluorogenic molecular probe. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.03.089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
27
|
Samanta A, Medintz IL. Nanoparticles and DNA - a powerful and growing functional combination in bionanotechnology. NANOSCALE 2016; 8:9037-95. [PMID: 27080924 DOI: 10.1039/c5nr08465b] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Functionally integrating DNA and other nucleic acids with nanoparticles in all their different physicochemical forms has produced a rich variety of composite nanomaterials which, in many cases, display unique or augmented properties due to the synergistic activity of both components. These capabilities, in turn, are attracting greater attention from various research communities in search of new nanoscale tools for diverse applications that include (bio)sensing, labeling, targeted imaging, cellular delivery, diagnostics, therapeutics, theranostics, bioelectronics, and biocomputing to name just a few amongst many others. Here, we review this vibrant and growing research area from the perspective of the materials themselves and their unique capabilities. Inorganic nanocrystals such as quantum dots or those made from gold or other (noble) metals along with metal oxides and carbon allotropes are desired as participants in these hybrid materials since they can provide distinctive optical, physical, magnetic, and electrochemical properties. Beyond this, synthetic polymer-based and proteinaceous or viral nanoparticulate materials are also useful in the same role since they can provide a predefined and biocompatible cargo-carrying and targeting capability. The DNA component typically provides sequence-based addressability for probes along with, more recently, unique architectural properties that directly originate from the burgeoning structural DNA field. Additionally, DNA aptamers can also provide specific recognition capabilities against many diverse non-nucleic acid targets across a range of size scales from ions to full protein and cells. In addition to appending DNA to inorganic or polymeric nanoparticles, purely DNA-based nanoparticles have recently surfaced as an excellent assembly platform and have started finding application in areas like sensing, imaging and immunotherapy. We focus on selected and representative nanoparticle-DNA materials and highlight their myriad applications using examples from the literature. Overall, it is clear that this unique functional combination of nanomaterials has far more to offer than what we have seen to date and as new capabilities for each of these materials are developed, so, too, will new applications emerge.
Collapse
Affiliation(s)
- Anirban Samanta
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA. and College of Science, George Mason University, Fairfax, Virginia 22030, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
| |
Collapse
|
28
|
Ren X, El-Sagheer AH, Brown T. Efficient enzymatic synthesis and dual-colour fluorescent labelling of DNA probes using long chain azido-dUTP and BCN dyes. Nucleic Acids Res 2016; 44:e79. [PMID: 26819406 PMCID: PMC4856977 DOI: 10.1093/nar/gkw028] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/11/2016] [Indexed: 12/12/2022] Open
Abstract
A sterically undemanding azide analogue of dTTP (AHP dUTP) with an alkyl chain and ethynyl attachment to the nucleobase was designed and incorporated into DNA by primer extension, reverse transcription and polymerase chain reaction (PCR). An azide-modified 523 bp PCR amplicon with all 335 thymidines replaced by AHP dU was shown to be a perfect copy of the template from which it was amplified. Replacement of thymidine with AHP dU increases duplex stability, accounting in part for the high incorporation efficiency of the azide-modified triphosphate. Single-stranded azide-labelled DNA was conveniently prepared from PCR products by λ-exonuclease digestion and streptavidin magnetic bead isolation. Efficient fluorescent labelling of single and double-stranded DNA was carried out using dyes functionalized with bicyclo[6.1.0]non-4-yne (BCN) via the strain-promoted alkyne-azide cycloaddition (SPAAC) reaction. This revealed that the degree of labelling must be carefully controlled to achieve optimum fluorescence and avoid fluorescence quenching. Dual-coloured probes were obtained in a single tube fluorescent labelling reaction; and varying the ratios of the two dyes provides a simple method to prepare DNA probes with unique fluorescent signatures. AHP dUTP is a versatile clickable nucleotide with potentially wide applications in biology and nanotechnology including single molecule studies and synthesis of modified aptamer libraries via SELEX.
Collapse
Affiliation(s)
- Xiaomei Ren
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
| |
Collapse
|
29
|
Aparin IO, Farzan VM, Veselova OA, Chistov AA, Podkolzin AT, Ustinov AV, Shipulin GA, Formanovsky AA, Korshun VA, Zatsepin TS. 1-Phenylethynylpyrene (PEPy) as a novel blue-emitting dye for qPCR assay. Analyst 2016; 141:1331-8. [PMID: 26738806 DOI: 10.1039/c5an01767j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
An alkyl azide derivative of 1-phenylethynylpyrene (PEPy) dye was prepared and used in the functionalization of oligonucleotides via click chemistry. Spectral and photo-physical properties of the PEPy-modified oligonucleotides as a single strand, and in perfect or mismatched duplexes, have been studied. A series of PEPy-Dabcyl fluorogenic TaqMan probes were synthesized and tested in qPCR. PEPy proved to be a superior substitute for AMCA as a short wavelength fluorescent dye for qPCR probes. PEPy probes were shown to significantly reduce Cq (a fractional PCR cycle used for quantification) vs. AMCA labeled probes, thus improving on the reliability of detection. Moreover, a larger increase of fluorescence during amplification was observed in the case of PEPy probes that makes this dye very suitable for an end-point PCR technique. This study broadens the panel of fluorescent dyes suitable for the use in probes for quantitative real-time PCR.
Collapse
Affiliation(s)
- Ilya O Aparin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
De Coen LM, Heugebaert TSA, García D, Stevens CV. Synthetic Entries to and Biological Activity of Pyrrolopyrimidines. Chem Rev 2015; 116:80-139. [DOI: 10.1021/acs.chemrev.5b00483] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Laurens M. De Coen
- Department of Sustainable
Organic Chemistry and Technology, Ghent University, Coupure links
653, B-9000 Ghent, Belgium
| | - Thomas S. A. Heugebaert
- Department of Sustainable
Organic Chemistry and Technology, Ghent University, Coupure links
653, B-9000 Ghent, Belgium
| | - Daniel García
- Department of Sustainable
Organic Chemistry and Technology, Ghent University, Coupure links
653, B-9000 Ghent, Belgium
| | - Christian V. Stevens
- Department of Sustainable
Organic Chemistry and Technology, Ghent University, Coupure links
653, B-9000 Ghent, Belgium
| |
Collapse
|
31
|
A pH Sensitive High-Throughput Assay for miRNA Binding of a Peptide-Aminoglycoside (PA) Library. PLoS One 2015; 10:e0144251. [PMID: 26656788 PMCID: PMC4699463 DOI: 10.1371/journal.pone.0144251] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/16/2015] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRNA) are small RNAs that have a regulatory role in gene expression. Because of this regulatory role, miRNAs have become a new target for therapeutic compounds. Here, we outline an approach to target specific miRNAs using a high throughput capable assay and a 215 compound peptidic-aminosugar (PA) library. Aminosugars have been shown in a number of recent reports as important lead compounds that bind miRNA. In order to screen for compounds that bind miRNA, we have developed a high throughput displacement assay using a fluorescein-neomycin conjugated molecule (F-neo) as a probe for competitive miRNA binding compounds. We have applied the F-neo assay to four different miRNA constructs and the assay is applicable to most miRNAs, at various stages of processing. The results of the screen were validated by the determination of the IC50 for a select group of compounds from the library. For example, we identified eight compounds that bind to hsa-miR 504 with higher affinity than the parent neomycin. From the F-neo displacement assay we found that the number of binding sites differs for each miRNA, and the binding sites appear to differ both physically and chemically, with different affinity of the compounds resulting from the size of the molecule as well as the chemical structure. Additionally, the affinity of the compounds was dependent on the identity and position of the amino acid position of conjugation and the affinity of the compounds relative to other compounds in the library was miRNA dependent with the introduction of a second amino acid.
Collapse
|
32
|
Li P, He H, Wang Z, Feng M, Jin H, Wu Y, Zhang L, Zhang L, Tang X. Sensitive Detection of Single-Nucleotide Mutation in the BRAF Mutation Site (V600E) of Human Melanoma Using Phosphate-Pyrene-Labeled DNA Probes. Anal Chem 2015; 88:883-9. [PMID: 26652624 DOI: 10.1021/acs.analchem.5b03523] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A series of novel nucleotide phosphoramidites were rationally designed and synthesized and were then site-specifically incorporated in DNA oligonucleotide probes with pyrene-modified phosphate. These oligodeoxynucleotide (ODN) probes almost have no inherent fluorescence emission with pyrene modification at 3' phosphate of corresponding nucleotides as a result of the photoinduced electron-transfer quenching effect of nucleobases (thymidine ∼ cytidine > guanosine ≫ adenosine). However, strong fluorescence emission was observed only with the perfectly matched duplex for the probes with pyrene modified at 3' phosphate of thymidine and cytidine. These rationally designed ODN probes successfully worked as "turn on" fluorescence oligonucleotide sensors for single-nucleotide polymorphism (SNP) and were used for detecting a single BRAF mutation site (V600E) of human melanoma.
Collapse
Affiliation(s)
- Pengfei Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Hongyan He
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Zhixuan Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Mengke Feng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Yun Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China.,State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University , Nanjing, Jiangsu 210093, People's Republic of China.,Center for Noncoding RNA Medicine, Peking University Health Center , Beijing 100191, People's Republic of China
| |
Collapse
|
33
|
Şen E, Meral K, Atılgan S. From Dark to Light to Fluorescence Resonance Energy Transfer (FRET): Polarity-Sensitive Aggregation-Induced Emission (AIE)-Active Tetraphenylethene-Fused BODIPY Dyes with a Very Large Pseudo-Stokes Shift. Chemistry 2015; 22:736-45. [PMID: 26617068 DOI: 10.1002/chem.201503457] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 11/03/2015] [Indexed: 11/12/2022]
Abstract
The work presented herein is devoted to the fabrication of large Stokes shift dyes in both organic and aqueous media by combining dark resonance energy transfer (DRET) and fluorescence resonance energy transfer (FRET) in one donor-acceptor system. In this respect, a series of donor-acceptor architectures of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) dyes substituted by one, two, or three tetraphenylethene (TPE) luminogens were designed and synthesised. The photophysical properties of these three chromophore systems were studied to provide insight into the nature of donor-acceptor interactions in both THF and aqueous media. Because the generation of emissive TPE donor(s) is strongly polarity dependent, due to its aggregation-induced emission (AIE) feature, one might expect the formation of appreciable fluorescence emission intensity with a very large pseudo-Stokes shift in aqueous media when considering FRET process. Interestingly, similar results were also recorded in THF for the chromophore systems, although the TPE fragment(s) of the dyes are non-emissive. The explanation for this photophysical behaviour lies in the DRET. This is the first report on combining two energy-transfer processes, namely, FRET and DRET, in one polarity-sensitive donor-acceptor pair system. The accuracy of the dark-emissive donor property of the TPE luminogen is also presented for the first time as a new feature for AIE phenomena.
Collapse
Affiliation(s)
- Esra Şen
- Department of Chemistry, Suleyman Demirel University, 32000, Isparta (Turkey)
| | - Kadem Meral
- Department of Chemistry, Ataturk University, 25240, Erzurum (Turkey)
| | - Serdar Atılgan
- Department of Chemistry, Suleyman Demirel University, 32000, Isparta (Turkey).
| |
Collapse
|
34
|
Kore AR, Yang B, Thiyagarajan SS, Srinivasan B. Synthesis and Substrate Evaluation of (E)-5-[(3-Selenophene-2-Carboxamido)Prop-1-en-1-yl]-Uridine-5'-O-Triphosphate for RNA Polymerase. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:866-76. [PMID: 26430834 DOI: 10.1080/15257770.2015.1081941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Design, synthesis and T7 RNA polymerase substrate evaluation of (E)-5-[(3-selenophene-2-carboxamido)prop-1-en-1-yl]-uridine-5'-O-triphosphate is reported. The title compound is shown to be a good substrate for RNA polymerase by RNA labeling through in vitro transcription. pTRI-plasmid DNA with β-actin gene sequence (∼300 base pairs) with T7 promoter was used as a template for the in vitro transcription. Transcribed product is characterized for incorporation by gel assay and for integrity, full length and size by bioanalyzer. The title compound will be very useful in biophysical techniques to obtain information on dynamics and recognition properties in real time as well as 3D structure of nucleic acids.
Collapse
Affiliation(s)
- Anilkumar R Kore
- a Life Sciences Solutions Group, Thermo Fisher Scientific , Austin , TX , USA
| | - Bo Yang
- a Life Sciences Solutions Group, Thermo Fisher Scientific , Austin , TX , USA
| | | | | |
Collapse
|
35
|
Aso T, Saito K, Suzuki A, Saito Y. Synthesis and photophysical properties of pyrene-labeled 3-deaza-2'-deoxyadenosines comprising a non-π-conjugated linker: fluorescence quenching-based oligodeoxynucleotide probes for thymine identification. Org Biomol Chem 2015; 13:10540-7. [PMID: 26338764 DOI: 10.1039/c5ob01605c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pyrene-labeled 3-deaza-2'-deoxyadenosine comprising a non-π-conjugated linker (py3z)A (1) was synthesized and its photophysical properties were investigated. Oligodeoxynucleotide (ODN) probes containing (py3z)A (1) exhibited remarkable fluorescence quenching only when the opposite base of the complementary strand was the perfectly matched thymine. Such fluorescence quenching-based ODN probes exhibited excellent on-off switching properties, making them useful tools for single nucleotide polymorphism (SNP) genotyping and for the identification of target genes and structural studies of nucleic acids.
Collapse
Affiliation(s)
- Tatsuya Aso
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan.
| | | | | | | |
Collapse
|
36
|
Zayas J, Annoual M, Das JK, Felty Q, Gonzalez WG, Miksovska J, Sharifai N, Chiba A, Wnuk SF. Strain Promoted Click Chemistry of 2- or 8-Azidopurine and 5-Azidopyrimidine Nucleosides and 8-Azidoadenosine Triphosphate with Cyclooctynes. Application to Living Cell Fluorescent Imaging. Bioconjug Chem 2015; 26:1519-32. [PMID: 26086070 DOI: 10.1021/acs.bioconjchem.5b00300] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Strain-promoted click chemistry of nucleosides and nucleotides with an azido group directly attached to the purine and pyrimidine rings with various cyclooctynes in aqueous solution at ambient temperature resulted in efficient formation (3 min to 3 h) of fluorescent, light-up, triazole products. The 2- and 8-azidoadenine nucleosides reacted with fused cyclopropyl cyclooctyne, dibenzylcyclooctyne, or monofluorocyclooctyne to produce click products functionalized with hydroxyl, amino, N-hydroxysuccinimide, or biotin moieties. The 5-azidouridine and 5-azido-2'-deoxyuridine were similarly converted to the analogous triazole products in quantitative yields in less than 5 min. The 8-azido-ATP quantitatively afforded the triazole product with fused cyclopropyl cyclooctyne in aqueous acetonitrile (3 h). The novel triazole adducts at the 2- or 8-position of adenine or 5-position of uracil rings induce fluorescence properties which were used for direct imaging in MCF-7 cancer cells without the need for traditional fluorogenic reporters. FLIM of the triazole click adducts demonstrated their potential utility for dynamic measuring and tracking of signaling events inside single living cancer cells.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Nima Sharifai
- §Department of Biology, University of Miami, Coral Gables, Florida 33146, United States
| | - Akira Chiba
- §Department of Biology, University of Miami, Coral Gables, Florida 33146, United States
| | | |
Collapse
|
37
|
Ding S, Cargill AA, Das SR, Medintz IL, Claussen JC. Biosensing with Förster Resonance Energy Transfer Coupling between Fluorophores and Nanocarbon Allotropes. SENSORS 2015; 15:14766-87. [PMID: 26110411 PMCID: PMC4507682 DOI: 10.3390/s150614766] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/01/2015] [Accepted: 06/05/2015] [Indexed: 01/10/2023]
Abstract
Nanocarbon allotropes (NCAs), including zero-dimensional carbon dots (CDs), one-dimensional carbon nanotubes (CNTs) and two-dimensional graphene, exhibit exceptional material properties, such as unique electrical/thermal conductivity, biocompatibility and high quenching efficiency, that make them well suited for both electrical/electrochemical and optical sensors/biosensors alike. In particular, these material properties have been exploited to significantly enhance the transduction of biorecognition events in fluorescence-based biosensing involving Förster resonant energy transfer (FRET). This review analyzes current advances in sensors and biosensors that utilize graphene, CNTs or CDs as the platform in optical sensors and biosensors. Widely utilized synthesis/fabrication techniques, intrinsic material properties and current research examples of such nanocarbon, FRET-based sensors/biosensors are illustrated. The future outlook and challenges for the research field are also detailed.
Collapse
Affiliation(s)
- Shaowei Ding
- Department of Mechanical Engineering, Iowa State University, 2104 Black Engineering, Ames, IA 50011, USA.
| | - Allison A Cargill
- Department of Mechanical Engineering, Iowa State University, 2104 Black Engineering, Ames, IA 50011, USA.
| | - Suprem R Das
- Department of Mechanical Engineering, Iowa State University, 2104 Black Engineering, Ames, IA 50011, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science & Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA.
| | - Jonathan C Claussen
- Department of Mechanical Engineering, Iowa State University, 2104 Black Engineering, Ames, IA 50011, USA.
| |
Collapse
|
38
|
Saito Y, Suzuki A, Yamauchi T, Saito I. Design and synthesis of 7-naphthyl-8-aza-7-deaza-2′-deoxyadenosines as environmentally sensitive fluorescent nucleosides. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2014.10.116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
39
|
Vasilyeva SV, Kuznetsova AS, Khalyavina JG, Glazunova VA, Shtil AA, Gornostaev LM, Silnikov VN. Novel fluorescent pyrimidine nucleosides containing 2,1,3-benzoxadiazole and naphtho-[1,2,3-CD] Indole-6 (2H)-one fragments. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 33:615-25. [PMID: 25105452 DOI: 10.1080/15257770.2014.913064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A series of novel fluorescent pyrimidine nucleosides containing 2,1,3-benzoxadiazole or naphtho[1,2,3-cd]indole-6 (2h)-one fragments was designed and synthesized. Introduction of fluorescent fragments into the position 5 of the uridine or cytidine heterocycle was carried out in two ways: by Sonogashira Coupling Reaction and CuI-catalyzed cycloaddition ("click" reaction). The obtained nucleoside derivatives became fluorescent due to the inserted fragments. The excitation wavelength (440-450 nm) was outside the absorption band of many biomolecules and significantly differed from the emission wavelength (560-600 nm). In addition, the intended nucleoside analogs were shown to kill cultured human tumor cells at submicromolar concentrations.
Collapse
Affiliation(s)
- Svetlana V Vasilyeva
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , Russia
| | | | | | | | | | | | | |
Collapse
|
40
|
|
41
|
Pawar MG, Nuthanakanti A, Srivatsan SG. Heavy atom containing fluorescent ribonucleoside analog probe for the fluorescence detection of RNA-ligand binding. Bioconjug Chem 2014; 24:1367-77. [PMID: 23841942 DOI: 10.1021/bc400194g] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Although numerous biophysical tools have provided effective systems to study nucleic acids, our current knowledge on how RNA structure complements its function is limited. Therefore, development of robust tools to study the structure–function relationship of RNA is highly desired. Toward this endeavor, we have developed a new ribonucleoside analog, based on a (selenophen-2-yl)pyrimidine core, which could serve as a fluorescence probe to study the function of RNA in real time and as an anomalous scattering label (selenium atom) for the phase determination in X-ray crystallography. The fluorescent selenophene-modified uridine analog is minimally perturbing and exhibits probe-like properties such as sensitivity to microenvironment and conformation changes. Utilizing these properties and amicability of the corresponding ribonucleotide analog to enzymatic incorporation, we have synthesized a fluorescent bacterial ribosomal decoding site (A-site) RNA construct and have developed a fluorescence binding assay to effectively monitor the binding of aminoglycoside antibiotics to the A-site. Our results demonstrate that this simple approach of building a dual probe could provide new avenues to study the structure–function relationship of not only nucleic acids, but also other biomacromolecules.
Collapse
|
42
|
Lee YJ, Kim D, Lee K, Chun JY. Single-channel multiplexing without melting curve analysis in real-time PCR. Sci Rep 2014; 4:7439. [PMID: 25501038 PMCID: PMC4262828 DOI: 10.1038/srep07439] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 11/21/2014] [Indexed: 01/08/2023] Open
Abstract
Multiplex real-time PCR with quantification of targets in a single fluorescence channel has been the demand in biotechnology industry. Here, we develop a novel analytical real-time PCR technique to detect multiple targets in a single fluorescence channel without melting curve analysis. In this technique, we show the intensity of the fluorescence signals of two discrete Tm targets is different at certain temperatures called detection temperatures, by which a high Tm target can be detected regardless of a low Tm target. We then identify the low Tm target by utilizing a change of the fluorescence signals between two different detection temperatures. Furthermore, it enables us to determine quantification of each target in a single channel, possibly facilitating convenient patient care for drug treatment in clinics.
Collapse
Affiliation(s)
- Young-Jo Lee
- Seegene, Inc., Taewon Bldg., 91 Ogeum-ro, Songpa-Gu, Seoul 138-828, South Korea
| | - Daeyoung Kim
- Seegene, Inc., Taewon Bldg., 91 Ogeum-ro, Songpa-Gu, Seoul 138-828, South Korea
| | - Kihoon Lee
- Seegene, Inc., Taewon Bldg., 91 Ogeum-ro, Songpa-Gu, Seoul 138-828, South Korea
| | - Jong-Yoon Chun
- Seegene, Inc., Taewon Bldg., 91 Ogeum-ro, Songpa-Gu, Seoul 138-828, South Korea
| |
Collapse
|
43
|
Kanamori T, Ohzeki H, Masaki Y, Ohkubo A, Takahashi M, Tsuda K, Ito T, Shirouzu M, Kuwasako K, Muto Y, Sekine M, Seio K. Controlling the fluorescence of benzofuran-modified uracil residues in oligonucleotides by triple-helix formation. Chembiochem 2014; 16:167-76. [PMID: 25469677 DOI: 10.1002/cbic.201402346] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Indexed: 12/16/2022]
Abstract
We developed fluorescent turn-on probes containing a fluorescent nucleoside, 5-(benzofuran-2-yl)deoxyuridine (dU(BF)) or 5-(3-methylbenzofuran-2-yl)deoxyuridine (dU(MBF)), for the detection of single-stranded DNA or RNA by utilizing DNA triplex formation. Fluorescence measurements revealed that the probe containing dU(MBF) achieved superior fluorescence enhancement than that containing dU(BF). NMR and fluorescence analyses indicated that the fluorescence intensity increased upon triplex formation partly as a consequence of a conformational change at the bond between the 3-methylbenzofuran and uracil rings. In addition, it is suggested that the microenvironment around the 3-methylbenzofuran ring contributed to the fluorescence enhancement. Further, we developed a method for detecting RNA by rolling circular amplification in combination with triplex-induced fluorescence enhancement of the oligonucleotide probe containing dU(MBF).
Collapse
Affiliation(s)
- Takashi Kanamori
- Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501 (Japan)
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Dziuba D, Pohl R, Hocek M. Bodipy-labeled nucleoside triphosphates for polymerase synthesis of fluorescent DNA. Bioconjug Chem 2014; 25:1984-95. [PMID: 25290695 DOI: 10.1021/bc5003554] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
New fluorescent nucleosides and nucleoside triphosphate (dNTPs) analogs bearing the F-Bodipy fluorophore linked through a short, flexible nonconjugate tether were synthesized. The Bodipy-labeled dNTPs were substrates for several DNA polymerases which incorporated them into DNA in primer extension, nicking enzyme amplification reaction, and polymerase chain reaction. The fluorescence of F-Bodipy is not quenched upon incorporation in DNA and can be detected both in solutions and on gels.
Collapse
Affiliation(s)
- Dmytro Dziuba
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center , Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | | | | |
Collapse
|
45
|
Narayanaswamy N, Kumar M, Das S, Sharma R, Samanta PK, Pati SK, Dhar SK, Kundu TK, Govindaraju T. A thiazole coumarin (TC) turn-on fluorescence probe for AT-base pair detection and multipurpose applications in different biological systems. Sci Rep 2014; 4:6476. [PMID: 25252596 PMCID: PMC4174567 DOI: 10.1038/srep06476] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 08/27/2014] [Indexed: 11/09/2022] Open
Abstract
Sequence-specific recognition of DNA by small turn-on fluorescence probes is a promising tool for bioimaging, bioanalytical and biomedical applications. Here, the authors report a novel cell-permeable and red fluorescent hemicyanine-based thiazole coumarin (TC) probe for DNA recognition, nuclear staining and cell cycle analysis. TC exhibited strong fluorescence enhancement in the presence of DNA containing AT-base pairs, but did not fluoresce with GC sequences, single-stranded DNA, RNA and proteins. The fluorescence staining of HeLa S3 and HEK 293 cells by TC followed by DNase and RNase digestion studies depicted the selective staining of DNA in the nucleus over the cytoplasmic region. Fluorescence-activated cell sorting (FACS) analysis by flow cytometry demonstrated the potential application of TC in cell cycle analysis in HEK 293 cells. Metaphase chromosome and malaria parasite DNA imaging studies further confirmed the in vivo diagnostic and therapeutic applications of probe TC. Probe TC may find multiple applications in fluorescence spectroscopy, diagnostics, bioimaging and molecular and cell biology.
Collapse
Affiliation(s)
- Nagarjun Narayanaswamy
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, Karnataka, India
| | - Manoj Kumar
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, Karnataka, India
| | - Sadhan Das
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, Karnataka, India
| | - Rahul Sharma
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Pralok K Samanta
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064, India
| | - Swapan K Pati
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064, India
| | - Suman K Dhar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, Karnataka, India
| | - T Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, Karnataka, India
| |
Collapse
|
46
|
Suzuki A, Yanaba T, Saito I, Saito Y. Molecular design of an environmentally sensitive fluorescent nucleoside, 3-deaza-2'-deoxyadenosine derivative: distinguishing thymine by probing the DNA minor groove. Chembiochem 2014; 15:1638-44. [PMID: 25044623 DOI: 10.1002/cbic.201402078] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Indexed: 12/14/2022]
Abstract
An environmentally sensitive fluorescent nucleoside containing a 3-deazaadenine skeleton has been developed, and its photophysical properties were investigated. Newly developed C3-naphthylethynylated 3-deaza-2'-deoxyadenosine ((3nz) A, 1) exhibited dual fluorescence emission from an intramolecular charge-transfer state and a locally excited state, depending upon molecular coplanarity. DNA probes containing 1 clearly discriminated a perfectly matched thymine base on the complementary strand by a distinct change in emission wavelength.
Collapse
Affiliation(s)
- Azusa Suzuki
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642 (Japan)
| | | | | | | |
Collapse
|
47
|
Xie S, Chai Y, Yuan Y, Bai L, Yuan R. A novel electrochemical aptasensor for highly sensitive detection of thrombin based on the autonomous assembly of hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme nanowires. Anal Chim Acta 2014; 832:51-7. [PMID: 24890694 DOI: 10.1016/j.aca.2014.04.065] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 04/28/2014] [Accepted: 04/30/2014] [Indexed: 11/26/2022]
Abstract
In this work, a new signal amplified strategy was constructed based on isothermal exponential amplification reaction (EXPAR) and hybridization chain reaction (HCR) generating the hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme (HRP-mimicking DNAzyme) nanowires as signal output component for the sensitive detection of thrombin (TB). We employed EXPAR's ultra-high amplification efficiency to produce a large amount of two hairpin helper DNAs within a minutes. And then the resultant two hairpin helper DNAs could autonomously assemble the hemin/G-quadruplex HRP-mimicking DNAzymes nanowires as the redox-active reporter units on the electrode surface via hybridization chain reaction (HCR). The hemin/G-quadruplex structures simultaneously served as electron transfer medium and electrocatalyst to amplify the signal in the presence of H2O2. Specifically, only when the EXPAR reaction process has occurred, the HCR could be achieved and the hemin/G-quadruplex complexes could be formed on the surface of an electrode to give a detectable signal. The proposed strategy combines the amplification power of the EXPAR, HCR, and the inherent high sensitivity of the electrochemical detection. With such design, the proposed assay showed a good linear relationship within the range of 0.1 pM-50 nM with a detection limit of 33 fM (defined as S/N=3) for TB.
Collapse
Affiliation(s)
- Shunbi Xie
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Yali Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Lijuan Bai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| |
Collapse
|
48
|
Denn B, Karmakar S, Guenther DC, Hrdlicka PJ. Sandwich assay for mixed-sequence recognition of double-stranded DNA: invader-based detection of targets specific to foodborne pathogens. Chem Commun (Camb) 2014; 49:9851-3. [PMID: 24036937 DOI: 10.1039/c3cc45705b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A 96-well plate sandwich assay based on Invader capture/signalling probes is used to recognize 28-mer mixed-sequence dsDNA targets specific to Salmonella enterica, Campylobacter jejuni, Escherichia coli. Targets are detected down to 20-55 pM concentration with excellent binding specificity.
Collapse
Affiliation(s)
- Benjamin Denn
- Department of Chemistry, University of Idaho, 875 Perimeter Drive MS 2343, Moscow, ID 83844-2343, USA.
| | | | | | | |
Collapse
|
49
|
Lefoix M, Mathis G, Kleinmann T, Truffert JC, Asseline U. Pyrazolo[1,5-a]-1,3,5-triazine C-nucleoside as deoxyadenosine analogue: synthesis, pairing, and resistance to hydrolysis. J Org Chem 2014; 79:3221-7. [PMID: 24649913 DOI: 10.1021/jo5000253] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The synthesis of a pyrazolo[1,5-a]-1,3,5-triazine C-nucleoside (dA(PT)), designed to form two hydrogen bonds with a complementary dT residue, is reported. Oligonucleotides including this dA nucleoside analogue possess base-pairing properties similar to those of the parent oligonucleotide. This dA nucleoside analogue is more resistant to acid-catalyzed hydrolysis than dA.
Collapse
Affiliation(s)
- Myriam Lefoix
- NucleoSyn. Pépinières d'entreprises - Centre Innovation 16, Rue Léonard de Vinci 45074 Orléans Cedex 2, France
| | | | | | | | | |
Collapse
|
50
|
Shu Y, Pi F, Sharma A, Rajabi M, Haque F, Shu D, Leggas M, Evers BM, Guo P. Stable RNA nanoparticles as potential new generation drugs for cancer therapy. Adv Drug Deliv Rev 2014; 66:74-89. [PMID: 24270010 DOI: 10.1016/j.addr.2013.11.006] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 10/11/2013] [Accepted: 11/13/2013] [Indexed: 12/13/2022]
Abstract
Human genome sequencing revealed that only ~1.5% of the DNA sequence coded for proteins. More and more evidence has uncovered that a substantial part of the 98.5% so-called "junk" DNAs actually code for noncoding RNAs. Two milestones, chemical drugs and protein drugs, have already appeared in the history of drug development, and it is expected that the third milestone in drug development will be RNA drugs or drugs that target RNA. This review focuses on the development of RNA therapeutics for potential cancer treatment by applying RNA nanotechnology. A therapeutic RNA nanoparticle is unique in that its scaffold, ligand, and therapeutic component can all be composed of RNA. The special physicochemical properties lend to the delivery of siRNA, miRNA, ribozymes, or riboswitches; imaging using fluogenenic RNA; and targeting using RNA aptamers. With recent advances in solving the chemical, enzymatic, and thermodynamic stability issues, RNA nanoparticles have been found to be advantageous for in vivo applications due to their uniform nano-scale size, precise stoichiometry, polyvalent nature, low immunogenicity, low toxicity, and target specificity. In vivo animal studies have revealed that RNA nanoparticles can specifically target tumors with favorable pharmacokinetic and pharmacodynamic parameters without unwanted accumulation in normal organs. This review summarizes the key studies that have led to the detailed understanding of RNA nanoparticle formation as well as chemical and thermodynamic stability issue. The methods for RNA nanoparticle construction, and the current challenges in the clinical application of RNA nanotechnology, such as endosome trapping and production costs, are also discussed.
Collapse
Affiliation(s)
- Yi Shu
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Fengmei Pi
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Ashwani Sharma
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Mehdi Rajabi
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Farzin Haque
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Dan Shu
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Markos Leggas
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - B Mark Evers
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Peixuan Guo
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA.
| |
Collapse
|