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Affiliation(s)
- Yin Nah Teo
- Department of Chemistry, Stanford University, California 94305, United States
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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: 158] [Impact Index Per Article: 12.2] [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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Hainke S, Seitz O. Binaphthyl-DNA: stacking and fluorescence of a nonplanar aromatic base surrogate in DNA. Angew Chem Int Ed Engl 2010; 48:8250-3. [PMID: 19790219 DOI: 10.1002/anie.200903194] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sven Hainke
- Institut für Chemie der Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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Ueno Y, Komatsuzaki S, Takasu K, Kawai S, Kitamura Y, Kitade Y. Synthesis and Properties of Oligonucleotides Containing Novel Fluorescent Biaryl Units. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900567] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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5
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Hainke S, Seitz O. Binaphthyl-DNA: Stapelung und Fluoreszenz eines nichtplanaren aromatischen Basensurrogates in DNA. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903194] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Galievsky VA, Malinovskii VL, Stasheuski AS, Samain F, Zachariasse KA, Häner R, Chirvony VS. Photophysical characterization of oligopyrene modules for DNA-based nanosystems. Photochem Photobiol Sci 2009; 8:1448-54. [PMID: 19789815 DOI: 10.1039/b9pp00016j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photophysics of free pyrenedicarboxamide (Py-DCA) in solution as well as of single-stranded and double-stranded oligonucleotides (ss and ds ONs) containing 1-7 pyrene building blocks per strand were studied by steady-state and time-resolved fluorescence spectroscopy. It was found that the fluorescence quantum yield Phi(F) of free Py-DCA chromophore in solution is rather high (Phi(F) = 0.44). However, after incorporation of the chromophore into a ss ON the monomeric chromophore fluorescence is quenched more than 40-fold due to electron-transfer reactions with ON bases. An increase of the number n of neighboring pyrenes in an ON results in Phi(F) growth up to 0.25 at n = 6. Starting from n = 2, all fluorescence belongs mainly to excimer formed by pyrene chromophores. Sections composed of multiple pyrenes may be considered as robust functional entities that may serve as independent modules in DNA-based, functional nano-architectures.
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Affiliation(s)
- Victor A Galievsky
- B.I. Stepanov's Institute of Physics, National Academy of Sciences of Belarus, Nezavisimosti ave. 68, 220072, Minsk, Belarus
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Kashida H, Fujii T, Asanuma H. Threoninol as a scaffold of dyes (threoninol-nucleotide) and their stable interstrand clustering in duplexes. Org Biomol Chem 2008; 6:2892-9. [PMID: 18688481 DOI: 10.1039/b806406g] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Functional molecules such as dyes (Methyl Red, azobenzene, and Naphthyl Red) were tethered on D-threoninol as base surrogates (threoninol-nucleotide), which were consecutively incorporated at the center of natural oligodeoxyribonucleotides (ODNs). Hybridization of two ODNs involving threoninol-nucleotides allowed interstrand clustering of the dyes on D-threoninol and greatly stabilized the duplex. When two complementary ODNs, both of which had tethered Methyl Reds on consecutive D-threoninols, were hybridized, the melting temperature increased proportionally to the number of Methyl Reds, due to stacking interactions. Clustering of Methyl Reds induced both hypsochromicity and narrowing of the band, demonstrating that Methyl Reds were axially stacked relative to each other (H-aggregation). Since hybridization lowered the intensity of circular dichroism peaks at the pi-pi* transition region of Methyl Red (300-500 nm), clustered Methyl Reds were scarcely wound in the duplex. Alternate hetero dye clusters could also be prepared only by hybridization of two ODNs with different threoninol-nucleotides, such as Methyl Red-azobenzene and Methyl Red-Naphthyl Red combinations. A combination of Methyl Red and azobenzene induced bathochromic shift and broadening of the band at the Methyl Red region due to the disturbance of exciton interaction among Methyl Reds. But interestingly, the Methyl Red and Naphthyl Red combination induced merging of each absorption band to give a single sharp band, indicating that exciton interaction occurred among the different dyes. Thus, D-threoninol can be a versatile scaffold for introducing functional molecules into DNA for their ordered clustering.
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Affiliation(s)
- Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furocho, Chikusa, Nagoya, 464-8603, Japan
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Lin H, Morino K, Yashima E. Synthesis and chiroptical properties of a helical poly(phenylacetylene) bearing optically active pyrene pendants. Chirality 2008; 20:386-92. [PMID: 17724655 DOI: 10.1002/chir.20457] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A novel poly(phenylacetylene) derivative bearing optically active pyrene moieties as the pendant groups (poly-(R)-1) was prepared by the polymerization of the corresponding monomer (R)-1 in the presence of a rhodium catalyst, and its chiroptical property was investigated. Poly-(R)-1 exhibited an induced circular dichroism (ICD) in the polymer backbone region due to the predominantly one-handed helical conformation. The ICD pattern dramatically changed and was accompanied by inversion of the Cotton effect sign in response to a change in the temperature and solvent, indicating that poly-(R)-1 underwent a helix-helix transition in response to the external stimuli.
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Affiliation(s)
- Hongzhen Lin
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
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Bouquin N, Malinovskii VL, Häner R. Highly efficient quenching of excimer fluorescence by perylene diimide in DNA. Chem Commun (Camb) 2008:1974-6. [DOI: 10.1039/b802193g] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Samain F, Malinovskii VL, Langenegger SM, Häner R. Spectroscopic properties of pyrene-containing DNA mimics. Bioorg Med Chem 2008; 16:27-33. [PMID: 17512737 DOI: 10.1016/j.bmc.2007.04.052] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Revised: 10/16/2006] [Accepted: 04/27/2007] [Indexed: 11/27/2022]
Abstract
DNA mimics containing non-nucleosidic pyrene building blocks are described. The modified oligomers form stable hybrids, although a slight reduction in hybrid stability is observed in comparison to the unmodified DNA duplex. The nature of the interaction between the pyrene residues in single and double stranded oligomers is analyzed spectroscopically. Intra- and interstrand stacking interactions of pyrenes are monitored by UV-absorbance as well as fluorescence spectroscopy. Excimer formation is observed in both single and double strands. In general, intrastrand excimers show fluorescence emission at shorter wavelengths (approx. 5-10 nm) than excimers formed by interstrand interactions. The existence of two different forms of excimers (intra- vs. interstrand) is also revealed in temperature dependent UV-absorbance spectra.
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Affiliation(s)
- Florent Samain
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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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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Nakamura M, Shimomura Y, Ohtoshi Y, Sasa K, Hayashi H, Nakano H, Yamana K. Pyrene aromatic arrays on RNA duplexes as helical templates. Org Biomol Chem 2007; 5:1945-51. [PMID: 17551644 DOI: 10.1039/b705933g] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA oligomers having multiple (2 to 4) pyrenylmethyl substituents at the 2'-O-sugar residues were synthesized. UV-melting studies showed that the pyrene-modified RNAs could form duplexes with complementary RNA sequences without loss of thermal stability. Absorption, fluorescence, and circular dichroism (CD) spectra revealed that the incorporated pyrenes projected toward the outside of A-form RNA duplexes and assembled in helical aromatic arrays along the minor grooves of the RNA duplexes. Results of computer simulations agreed with the assembled structures of the pyrenes. The helical pyrene arrays exhibited remarkably strong excimer fluorescence, which was dependent on the sequence contexts of RNA duplexes.
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Affiliation(s)
- Mitsunobu Nakamura
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Hyogo, Japan.
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Nagatoishi S, Nojima T, Juskowiak B, Takenaka S. A pyrene-labeled G-quadruplex oligonucleotide as a fluorescent probe for potassium ion detection in biological applications. Angew Chem Int Ed Engl 2006; 44:5067-70. [PMID: 16035025 DOI: 10.1002/anie.200501506] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Satoru Nagatoishi
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, Fukuoka 812-858, Japan
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Langenegger SM, Häner R. Selectivity in DNA interstrand-stacking. Bioorg Med Chem Lett 2006; 16:5062-5. [PMID: 16876406 DOI: 10.1016/j.bmcl.2006.07.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Revised: 07/11/2006] [Accepted: 07/12/2006] [Indexed: 10/24/2022]
Abstract
The synthesis and spectroscopic investigation of DNA hybrids containing non-nucleosidic pyrene and phenanthrene building blocks is reported. It was found that interstrand-stacking of the polyaromatic compounds in the DNA duplex takes place with a high degree of selectivity.
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Affiliation(s)
- Simon M Langenegger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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Wang Z, Yu Y, Zhang D, Zhu D. Thymine and adenine derivatives with pyrene, tetrathiafulvalene and nitronyl nitroxide units: Synthesis and formation of ensembles sensing thymine and adenine molecules. ACTA ACUST UNITED AC 2006. [DOI: 10.1007/s11434-006-2046-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Malinovskii VL, Häner R. Synthesis of Polysubstituted Pyrenes with Tuned Spectroscopic Properties for Two-Point Attachment. European J Org Chem 2006. [DOI: 10.1002/ejoc.200600256] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Nakamura M, Ohtoshi Y, Yamana K. Helical pyrene-array along the outside of duplex RNA. Chem Commun (Camb) 2005:5163-5. [PMID: 16228022 DOI: 10.1039/b507808c] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A helical pyrene-array was formed by incorporation of multiple pyrenes into the sugar residues of duplex RNA leading to strong excimer fluorescence.
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Affiliation(s)
- Mitsunobu Nakamura
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, 671-2201, Japan.
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Nagatoishi S, Nojima T, Juskowiak B, Takenaka S. A Pyrene-Labeled G-Quadruplex Oligonucleotide as a Fluorescent Probe for Potassium Ion Detection in Biological Applications. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501506] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Miyake Y, Ono A. Fluorescent sensor for redox environment: a redox controlled molecular device based on the reversible mercury mediated folded structure formation of oligothymidylate. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.02.049] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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