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Podder A, Lee HJ, Kim BH. Fluorescent Nucleic Acid Systems for Biosensors. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Arup Podder
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Ha Jung Lee
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
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2
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Fluorescent nucleobases as tools for studying DNA and RNA. Nat Chem 2017; 9:1043-1055. [PMID: 29064490 DOI: 10.1038/nchem.2859] [Citation(s) in RCA: 213] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/11/2017] [Indexed: 02/07/2023]
Abstract
Understanding the diversity of dynamic structures and functions of DNA and RNA in biology requires tools that can selectively and intimately probe these biomolecules. Synthetic fluorescent nucleobases that can be incorporated into nucleic acids alongside their natural counterparts have emerged as a powerful class of molecular reporters of location and environment. They are enabling new basic insights into DNA and RNA, and are facilitating a broad range of new technologies with chemical, biological and biomedical applications. In this Review, we will present a brief history of the development of fluorescent nucleobases and explore their utility as tools for addressing questions in biophysics, biochemistry and biology of nucleic acids. We provide chemical insights into the two main classes of these compounds: canonical and non-canonical nucleobases. A point-by-point discussion of the advantages and disadvantages of both types of fluorescent nucleobases is made, along with a perspective into the future challenges and outlook for this burgeoning field.
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Kölmel DK, Barandun LJ, Kool ET. Efficient synthesis of fluorescent alkynyl C-nucleosides via Sonogashira coupling for the preparation of DNA-based polyfluorophores. Org Biomol Chem 2016; 14:6407-12. [PMID: 27296353 PMCID: PMC4935563 DOI: 10.1039/c6ob01199c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A facile and general procedure for the preparation of alkynyl C-nucleosides with varied fluorophores is presented. Sonogashira coupling was used as a key reaction to conjugate the dyes to an easily accessible ethynyl functionalized deoxyribose derivative. The new C-nucleosides were used for the preparation of DNA-based polyfluorophores.
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Affiliation(s)
- Dominik K Kölmel
- Department of Chemistry, Stanford University, Stanford, California 94305, USA.
| | - Luzi J Barandun
- Department of Chemistry, Stanford University, Stanford, California 94305, USA.
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, California 94305, USA.
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Elmehriki AAH, Suchý M, Chicas KJ, Wojciechowski F, Hudson RHE. Synthesis and spectral characterization of environmentally responsive fluorescent deoxycytidine analogs. ARTIFICIAL DNA, PNA & XNA 2015; 5:e29174. [PMID: 25483932 DOI: 10.4161/adna.29174] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Herein, we describe the synthesis and spectroscopic properties of five novel pyrrolodeoxycytidine analogs, and the related 5-(1-pyrenylethynyl)-2'-deoxycytidine analog; as well as fluorescence characterization of 5-(p-methoxyphenylethynyl)-2'-deoxyuridine. Within this series of compounds, rigidification of the structure from 6-phenylpyrrolodeoxycytidine to 5,6-benzopyrroldeoxycytidine made remarkable improvement of the fluorescence quantum yield (Φ ~1, EtOH) and substantially increased the Stokes shift. Exchange of the phenyl group of 6-phenylpyrrolodeoxycytidine for other heterocycles (benzofuryl or indolyl) produced an increase in the extinction coefficient at the excitation wavelength while preserving high quantum yields. The steady-state fluorescence response to the environment was determined by sensitivity of Stokes shift to solvent polarity. The effect of solvent polarity on fluorescence emission intensity was concurrently examined and showed that 5,6-benzopyrrolodeoxycytidine is highly sensitive to the presence of water. On the other hand, the previously synthesized 5-(p-methoxyphenylethynyl)-2'-deoxyuridine was found to be sensitive to solvent viscosity indicating molecular rotor behavior.
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Affiliation(s)
- Adam A H Elmehriki
- a Department of Chemistry; The University of Western Ontario; London, ON Canada
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Kim KT, Heo W, Joo T, Kim BH. Photophysical and structural investigation of a PyA-modified adenine cluster: its potential use for fluorescent DNA probes exhibiting distinct emission color changes. Org Biomol Chem 2015; 13:8470-8. [DOI: 10.1039/c5ob01159k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A PyA-modified adenine cluster, exhibiting a large Stokes shift based on interstrand stacking interactions of adenines, was investigated and exploited as signaling parts of fluorescent DNA probes.
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Affiliation(s)
- Ki Tae Kim
- Department of Chemistry
- BK School of Molecular Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 790-784
- South Korea
| | - Wooseok Heo
- Department of Chemistry
- BK School of Molecular Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 790-784
- South Korea
| | - Taiha Joo
- Department of Chemistry
- BK School of Molecular Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 790-784
- South Korea
| | - Byeang Hyean Kim
- Department of Chemistry
- BK School of Molecular Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 790-784
- South Korea
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Tedeschi T, Tonelli A, Sforza S, Corradini R, Marchelli R. A pyrenyl-PNA probe for DNA and RNA recognition: Fluorescence and UV absorption studies. ARTIFICIAL DNA, PNA & XNA 2014; 1:83-89. [PMID: 21686243 DOI: 10.4161/adna.1.2.13899] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Revised: 10/08/2010] [Accepted: 10/09/2010] [Indexed: 11/19/2022]
Abstract
The design and the synthesis of a PNA oligomer containing a pyrenyl residue in the backbone were performed. PNA sequence was chosen complementary to a "G rich" target sequence involved in G-quadruplex formation. The pyrenyl unit replaced a nucleobase in the middle of the PNA through covalent linkage to the backbone by a carboxymethyl unit. A systematic study on the binding properties of this probe towards DNA and RNA complementary strands was carried out by UV and fluorescence spectroscopy. UV melting curves indicated that the PNA probe binds more tightly to RNA rather than to DNA. Thermodynamic data obtained by Van't Hoff fitting of the melting curves indicated that, in the case of RNA, a more favorable interaction occurs between the pyrenyl unit and the RNA nucleobases, leading to a very favorable enthalpic contribution.The fluorescence analysis showed specific quenching of the pyrene emission associated to the formation of the full-match PNA-DNA or PNA-RNA duplexes. Again, this behavior was more evident in the case of RNA, consistently with the stronger interaction of the pyrenyl unit with the complementary strand. In order to study the sequence specificity of the pyrenyl-PNA probe (pyr-PNA), recognition experiments on mismatched DNA and RNA sequences were also performed.
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Affiliation(s)
- Tullia Tedeschi
- Department of Organic and Industrial Chemistry; University of Parma; Parma, Italy
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7
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Kim MJ, Seo Y, Hwang GT. Synthesis and photophysical properties of 2′-deoxyguanosine derivatives labeled with fluorene and fluorenone units: toward excimer probes. RSC Adv 2014. [DOI: 10.1039/c3ra47383j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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8
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Nucleoside and oligonucleotide pyrene conjugates with 1,2,3-triazolyl or ethynyl linkers: synthesis, duplex stability, and fluorescence changes generated by the DNA-dye connector. Tetrahedron 2014. [DOI: 10.1016/j.tet.2013.11.048] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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9
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Sezi S, Wagenknecht HA. DNA-templated formation of fluorescent self-assembly of ethynyl pyrenes. Chem Commun (Camb) 2013; 49:9257-9. [DOI: 10.1039/c3cc44733b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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10
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Sezi S, Varghese R, Vilaivan T, Wagenknecht HA. Conformational Control of Dual Emission by Pyrrolidinyl PNA-DNA Hybrids. ChemistryOpen 2012; 1:173-6. [PMID: 24551507 PMCID: PMC3922446 DOI: 10.1002/open.201200016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Indexed: 01/09/2023] Open
Affiliation(s)
- Sabrina Sezi
- Institute for Organic Chemistry, Karlsruhe Institute of Technology Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany) E-mail:
| | - Reji Varghese
- Institute for Organic Chemistry, Karlsruhe Institute of Technology Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany) E-mail:
| | - Tirayut Vilaivan
- Department of Chemistry, Faculty of Science, Chulalongkorn University Phyathai Road, Pathumwan, Bangkok 10330 (Thailand) E-mail:
| | - Hans-Achim Wagenknecht
- Institute for Organic Chemistry, Karlsruhe Institute of Technology Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany) E-mail:
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11
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Barrois S, Wagenknecht HA. Diarylethene-modified nucleotides for switching optical properties in DNA. Beilstein J Org Chem 2012; 8:905-14. [PMID: 23015841 PMCID: PMC3388881 DOI: 10.3762/bjoc.8.103] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 05/09/2012] [Indexed: 01/03/2023] Open
Abstract
Diarylethenes were attached to the 5-position of 2’-deoxyuridine in order to yield three different photochromic nucleosides. All nucleosides were characterized with respect to their absorption and photochromic properties. Based on these results, the most promising photochromic DNA base modification was incorporated into representative oligonucleotides by using automated phosphoramidite chemistry. The switching of optical properties in DNA can be achieved selectively at 310 nm (forward) and 450 nm (backward); both wavelengths are outside the normal nucleic acid absorption range. Moreover, this nucleoside was proven to be photochemically stable and allows switching back and forth several times. These results open the way for the use of diarylethenes as photochromic compounds in DNA-based architectures.
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Affiliation(s)
- Sebastian Barrois
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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12
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Cho JH, Shaughnessy KH. Aqueous‐Phase Sonogashira Alkynylation to Synthesize 5‐Substituted Pyrimidine and 8‐Substituted Purine Nucleosides. ACTA ACUST UNITED AC 2012; Chapter 1:Unit1.27. [DOI: 10.1002/0471142700.nc0127s49] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Joon Hyung Cho
- Department of Chemistry, The University of Alabama Tuscaloosa Alabama
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13
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Karlsen KK, Pasternak A, Jensen TB, Wengel J. Pyrene-Modified Unlocked Nucleic Acids: Synthesis, Thermodynamic Studies, and Fluorescent Properties. Chembiochem 2012; 13:590-601. [DOI: 10.1002/cbic.201100689] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Indexed: 01/09/2023]
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14
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Boonlua C, Vilaivan C, Wagenknecht HA, Vilaivan T. 5-(Pyren-1-yl)uracil as a base-discriminating fluorescent nucleobase in pyrrolidinyl peptide nucleic acids. Chem Asian J 2011; 6:3251-9. [PMID: 21976408 DOI: 10.1002/asia.201100490] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Indexed: 12/15/2022]
Abstract
A pyrene-labeled uridine (U(Py)) monomer for a pyrrolidinyl peptide nucleic acid with an alternating proline/2-aminocyclopentanecarboxylic acid backbone (acpcPNA) was synthesized and incorporated into the PNA. The U(Py) base in acpcPNA could specifically recognize the base A in its complementary DNA strand as determined by thermal denaturation (T(m)) experiments. The fluorescence of the U(Py)-containing single-stranded acpcPNA was very weak in aqueous buffer. In the presence of a complementary DNA target, the fluorescence was enhanced significantly (2.7-41.9 folds, depending on sequences). The fluorescence enhancement was specific to the pairing between U(Py) and dA, making the U(Py)-modified acpcPNA useful as a hybridization-responsive fluorescence probe for DNA-sequence determination.
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Affiliation(s)
- Chalothorn Boonlua
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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15
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Zhao Y, Guo JF, Ren AM, Feng JK. Theoretical study of one- and two-photon absorption properties of pyrene derivatives. Theor Chem Acc 2010. [DOI: 10.1007/s00214-010-0842-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Cho JH, Prickett CD, Shaughnessy KH. Efficient Sonogashira Coupling of Unprotected Halonucleosides in Aqueous Solvents Using Water-Soluble Palladium Catalysts. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000313] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev 2010; 110:2579-619. [PMID: 20205430 PMCID: PMC2868948 DOI: 10.1021/cr900301e] [Citation(s) in RCA: 658] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Renatus W. Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| | | | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
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18
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Jeong HS, Park M, Yi JW, Joo T, Kim BH. Structural diversity induced by pyrene intercalators in homogeneous oligodeoxyguanylates. MOLECULAR BIOSYSTEMS 2010; 6:951-3. [PMID: 20485740 DOI: 10.1039/b926677a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Homogeneous oligodeoxyguanylates incorporating small-molecule intercalator pyrene moieties in a 1,5 relationship form various structures of dimer, trimer, tetramer and internal hairpin form that are yellowish in color because of the intermolecular interactions between the pyrene units.
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Affiliation(s)
- Hyun Seok Jeong
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Korea
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19
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Beyer C, Wagenknecht HA. In situ azide formation and "click" reaction of nile red with DNA as an alternative postsynthetic route. Chem Commun (Camb) 2010; 46:2230-1. [PMID: 20234915 DOI: 10.1039/b924471a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oligonucleotides that contain a 5-iodo-2'-deoxyuridine in the sequence can be applied for a postsynthetic "click"-type modification with ethynyl-modified nile red as a fluorescent label by in situ formation of the intermediate azide.
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Affiliation(s)
- Christoph Beyer
- Institute for Organic Chemistry, University of Regensburg, 93040 Regensburg, Germany
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20
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Structural features of the adenosine conjugate in means of vibrational spectroscopy and DFT. Biophys Chem 2009; 142:17-26. [DOI: 10.1016/j.bpc.2009.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 02/19/2009] [Accepted: 02/19/2009] [Indexed: 11/18/2022]
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21
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Kim HM, Lee YO, Lim CS, Kim JS, Cho BR. Two-Photon Absorption Properties of Alkynyl-Conjugated Pyrene Derivatives. J Org Chem 2008; 73:5127-30. [PMID: 18547109 DOI: 10.1021/jo800363v] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hwan Myung Kim
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Yeon Ok Lee
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Chang Su Lim
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Jong Seung Kim
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Bong Rae Cho
- Department of Chemistry, Korea University, Seoul 136-701, Korea
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22
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Wanninger-Weiss C, Di Pasquale F, Ehrenschwender T, Marx A, Wagenknecht HA. Nucleotide insertion and bypass synthesis of pyrene- and BODIPY-modified oligonucleotides by DNA polymerases. Chem Commun (Camb) 2008:1443-5. [PMID: 18338050 DOI: 10.1039/b718002k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The chromophores pyrene and bordipyrromethenylbenzene directly linked to the 5-position of uridine are tolerated and recognized as thymine derivatives by DNA polymerases in primer extension experiments.
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23
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Wanninger-Weiss C, Valis L, Wagenknecht HA. Pyrene-modified guanosine as fluorescent probe for DNA modulated by charge transfer. Bioorg Med Chem 2008; 16:100-6. [PMID: 17509886 DOI: 10.1016/j.bmc.2007.04.064] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Accepted: 04/27/2007] [Indexed: 11/24/2022]
Abstract
8-(Pyren-1-yl)-2'-deoxyguanosine (Py-G) was incorporated synthetically as a modified DNA base and optical probe into oligonucleotides. A variety of Py-G-modified DNA duplexes have been investigated by methods of optical spectroscopy. The DNA duplex hybridization can be observed by both fluorescence and absorption spectroscopy since the Py-G group exhibits altered properties in single strands versus double strands for both spectroscopy methods. The fluorescence enhancement upon DNA hybridization can be improved significantly by the presence of 7-deazaguanin as an additional modification and charge acceptor three bases away from the Py-G modification site. Moreover, Py-G in DNA can be applied as a photoinducable donor for charge transfer processes when indol is present as an artificial DNA base and charge acceptor. Correctly base-paired duplexes can be discriminated from mismatched ones by comparison of their fluorescence quenching.
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Affiliation(s)
- Claudia Wanninger-Weiss
- University of Regensburg, Institute for Organic Chemistry, Universitätstr. 31, D-93053 Regensburg, Germany
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24
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Wanninger-Weiß C, Wagenknecht HA. Synthesis of 5-(2-Pyrenyl)-2′-deoxyuridine as a DNA Modification for Electron-Transfer Studies: The Critical Role of the Position of the Chromophore Attachment. European J Org Chem 2008. [DOI: 10.1002/ejoc.200700818] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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25
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Wagenknecht HA. Fluorescent DNA base modifications and substitutes: multiple fluorophore labeling and the DETEQ concept. Ann N Y Acad Sci 2007; 1130:122-30. [PMID: 18096856 DOI: 10.1196/annals.1430.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
There is an increasing need for fluorescent nucleic acid probes that are able to sense genetic variations without the application of enzymes. The incorporation of organic fluorophores either as DNA base modifications or as DNA base substitutions represents a powerful and versatile method for such new fluorescent DNA assays. Multiple labeling of oligonucleotides using several adjacent chromophore-modified DNA bases yields fluorescence enhancement and modulation that are sensitive to single-base mismatches in the complementary oligonucleotide. Charge transfer processes that cause fluorescence quenching are DNA-base mediated and occur over several base pairs distance. Our "DETEQ" setup, consisting of a fluorescence DNA base substitution and the charge acceptor as a second modification two base pairs away, allows the homogeneous detection of single-base mutations simply by fluorescence readout. This could lead to new DNA microarrays which are based on charge transfer processes and can be analyzed by commonly used fluorescence readout techniques.
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Trifonov A, Raytchev M, Buchvarov I, Rist M, Barbaric J, Wagenknecht HA, Fiebig T. Ultrafast energy transfer and structural dynamics in DNA. J Phys Chem B 2007; 109:19490-5. [PMID: 16853518 DOI: 10.1021/jp052108c] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultrafast structural dynamics concomitant to excitation energy transfer in DNA has been studied using a pair of pyrene-labeled DNA bases. The temporal evolution of the femtosecond pump-probe spectra reveals the existence of two electronic coupling pathways, through-base stack and through-space, which lead to excitation energy transfer and excimer formation even when the labeled DNA bases are separated by one AT base pair. The electronic coupling which mediates through-base stack energy transfer is so strong that a new absorption band arises in the excited-state absorption spectrum within 300 fs. From the analysis of time-dependent spectral shifts due to through-space excimer formation, the local structural dynamics and flexibility of DNA are characterized on the picosecond and nanosecond time scale.
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Affiliation(s)
- A Trifonov
- Eugene F. Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA
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28
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29
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The spectroscopy, dynamics, and electronic structure of pyrenyl–dU nucleosides: P+/dU− charge transfer state photophysics. Tetrahedron 2007. [DOI: 10.1016/j.tet.2006.11.095] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Tainaka K, Tanaka K, Ikeda S, Nishiza KI, Unzai T, Fujiwara Y, Saito I, Okamoto A. PRODAN-conjugated DNA: synthesis and photochemical properties. J Am Chem Soc 2007; 129:4776-84. [PMID: 17378568 DOI: 10.1021/ja069156a] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A solvatochromic fluorophore, PRODAN, has been used as a microenvironment-sensitive reporter. Based on the chemistry of PRODAN, we designed and synthesized four novel fluorescent nucleosides, PDNX (X = U, C, A, and G), to which a PRODAN fluorophore was attached at pyrimidine C5 or purine C8. The fluorescent nucleosides sensitively varied the Stokes shift values depending on the orientational polarizability of the solvent. The PDNX incorporated into DNA also changed the Stokes shift values depending on the DNA structure. In particular, the excitation spectrum of the PDNX-containing duplex shifted to a longer wavelength and gave a smaller Stokes shift value when the base opposite PDNX could form a Watson-Crick base pair with PDNX. A lower energy excitation of PDNX-containing DNA resulted in a strong fluorescence emission selective to the Watson-Crick pairing base. This unique photochemical character was applicable to the efficient typing of single-nucleotide polymorphisms of genes.
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Affiliation(s)
- Kazuki Tainaka
- Frontier Research System, RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama 351-1098, Japan
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31
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32
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Interaction of Pt(II) and Pd(II) complexes of terpyridine with 1-methylazoles: A combined experimental and density functional study. Inorganica Chim Acta 2007. [DOI: 10.1016/j.ica.2006.07.031] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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33
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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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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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35
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Valis L, Mayer-Enthart E, Wagenknecht HA. 8-(Pyren-1-yl)-2′-deoxyguanosine as an optical probe for DNA hybridization and for charge transfer with small peptides. Bioorg Med Chem Lett 2006; 16:3184-7. [PMID: 16621544 DOI: 10.1016/j.bmcl.2006.03.063] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2006] [Revised: 03/14/2006] [Accepted: 03/16/2006] [Indexed: 11/28/2022]
Abstract
8-(Pyren-1-yl)-2'-deoxyguanosine (Py-G) was incorporated synthetically as an optical probe into oligonucleotides. The Py-G group in DNA does not discriminate between any of the four natural nucleosides as a counterbase and exhibits altered optical properties in single strands versus double strands. Thus, the duplex hybridization of Py-G-modified DNA can be observed by both fluorescence and absorption spectroscopy. Moreover, Py-G in DNA can be applied as photoinducable donor for charge transfer processes with small peptides.
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Affiliation(s)
- Linda Valis
- University of Regensburg, Institute for Organic Chemistry, D-93040 Regensburg, Germany
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Mayer-Enthart E, Wagenknecht HA. Structure-Sensitive and Self-Assembled Helical Pyrene Array Based on DNA Architecture. Angew Chem Int Ed Engl 2006; 45:3372-5. [PMID: 16619327 DOI: 10.1002/anie.200504210] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Elke Mayer-Enthart
- Institute for Organic Chemistry, University of Regensburg, 93040 Regensburg, Germany
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Mayer-Enthart E, Wagenknecht HA. Strukturempfindlicher und selbstassoziierter helicaler Pyrenstapel auf Basis der DNA-Architektur. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200504210] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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39
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Skorobogatyi MV, Malakhov AD, Pchelintseva AA, Turban AA, Bondarev SL, Korshun VA. Fluorescent 5-Alkynyl-2′-Deoxyuridines: High Emission Efficiency of a Conjugated Perylene Nucleoside in a DNA Duplex. Chembiochem 2006; 7:810-6. [PMID: 16572492 DOI: 10.1002/cbic.200600040] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Four fluorescent 5-alkynyl-2'-deoxyuridines were studied in DNA oligonucleotides and their duplexes. The fluorescence response to hybridization differs dramatically for nucleosides containing a perylene fluorochrome either conjugated or not conjugated to the nucleobase. The conjugated nucleoside, 5-(perylen-3-ylethynyl)-2'-deoxyuridine, shows enhanced long-wavelength emission in the DNA duplex, in contrast to the blue fluorescence of perylene on a flexible linker (in 5-[(perylen-3-yl)methoxyprop-1-ynyl]-2'-deoxyuridine), which is quenched upon duplex formation.
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Affiliation(s)
- Mikhail V Skorobogatyi
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
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Maeda H, Maeda T, Mizuno K, Fujimoto K, Shimizu H, Inouye M. Alkynylpyrenes as Improved Pyrene-Based Biomolecular Probes with the Advantages of High Fluorescence Quantum Yields and Long Absorption/Emission Wavelengths. Chemistry 2006; 12:824-31. [PMID: 16267869 DOI: 10.1002/chem.200500638] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The photochemical properties of various alkynylpyrene derivatives have been investigated in detail with a view to developing a new class of pyrene-based biomolecular probes. The absorption maxima of the alkynylpyrenes were seen to be shifted to longer wavelengths compared with those of the unsubstituted parent pyrene. Fluorescence quantum yields of the alkynylpyrenes dramatically increased up to 0.99 in ethanol, and only slight quenching of the fluorescence occurred even under aerated conditions. The alkynylpyrenes have been successfully introduced into representative biomolecules such as peptides, proteins, and DNAs. The detectabilities of the labeled biomolecules were significantly improved, with the unique photochemical characteristics of the pyrene nucleus being maintained.
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Affiliation(s)
- Hajime Maeda
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University, Japan
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41
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Barbaric J, Wagenknecht HA. DNA as a supramolecular scaffold for the helical arrangement of a stack of 1-ethynylpyrene chromophores. Org Biomol Chem 2006; 4:2088-90. [PMID: 16729121 DOI: 10.1039/b605251g] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A highly organized helical pi-stacked arrangement of 1-ethynylpyrene moieties along the major groove of duplex DNA can only be achieved if more than three chromophores have been synthetically incorporated adjacent to each other.
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Affiliation(s)
- Janez Barbaric
- University of Regensburg, Institute for Organic Chemistry, D-93040 Regensburg, Germany
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Wagenknecht HA. Electron transfer processes in DNA: mechanisms, biological relevance and applications in DNA analytics. Nat Prod Rep 2006; 23:973-1006. [PMID: 17119642 DOI: 10.1039/b504754b] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In principle, DNA-mediated charge transfer processes can be categorized as oxidative hole transfer and reductive electron transfer. With respect to the routes of DNA damage most of the past research has been focused on the investigation of oxidative hole transfer or transport. On the other hand, the transport or transfer of excess electrons has a large potential for biomedical applications, mainly for DNA chip technology.
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Affiliation(s)
- Hans-Achim Wagenknecht
- University of Regensburg, Institute for Organic Chemistry, D-93040, Regensburg, Germany.
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