51
|
Crawford AG, Liu Z, Mkhalid IAI, Thibault M, Schwarz N, Alcaraz G, Steffen A, Collings JC, Batsanov AS, Howard JAK, Marder TB. Synthesis of 2‐ and 2,7‐Functionalized Pyrene Derivatives: An Application of Selective CH Borylation. Chemistry 2012; 18:5022-35. [DOI: 10.1002/chem.201103774] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Indexed: 12/31/2022]
Affiliation(s)
- Andrew G. Crawford
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE (UK), Fax: (+44) 191‐384‐4737
| | - Zhiqiang Liu
- State Key Laboratory of Crystal Materials, Shandong University, 27 Shanda South Road, Jinan, 250100 (P. R. China)
| | | | - Marie‐Hélène Thibault
- Département de Chimie, Université Laval, 1045, avenue de la Médecine, Pavillon Alexandre‐Vachon, Québec, G1V 0A6 (Canada)
| | - Nicolle Schwarz
- Leibniz‐Institut für Katalyse e. V. an der Universität Rostock, Albert‐Einstein‐Strasse 29a, 18059 Rostock (Germany)
| | - Gilles Alcaraz
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, 31077 Toulouse, Cedex 04 (France)
| | - Andreas Steffen
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE (UK), Fax: (+44) 191‐384‐4737
| | - Jonathan C. Collings
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE (UK), Fax: (+44) 191‐384‐4737
| | - Andrei S. Batsanov
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE (UK), Fax: (+44) 191‐384‐4737
| | - Judith A. K. Howard
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE (UK), Fax: (+44) 191‐384‐4737
| | - Todd B. Marder
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE (UK), Fax: (+44) 191‐384‐4737
| |
Collapse
|
52
|
|
53
|
Kashida H, Asanuma H. Preparation of supramolecular chromophoric assemblies using a DNA duplex. Phys Chem Chem Phys 2012; 14:7196-204. [DOI: 10.1039/c2cp40520b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
54
|
Nakamura M, Fukuda M, Takada T, Yamana K. Highly ordered pyrene π-stacks on an RNA duplex display static excimer fluorescence. Org Biomol Chem 2012; 10:9620-6. [DOI: 10.1039/c2ob26773j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
55
|
Tanaka M, Kozakai R, Saito Y, Saito I. Stabilization of DNA duplex by 2-substituted adenine as a minor groove modifier. Bioorg Med Chem Lett 2011; 21:7021-4. [DOI: 10.1016/j.bmcl.2011.09.104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 09/24/2011] [Accepted: 09/27/2011] [Indexed: 01/07/2023]
|
56
|
Østergaard ME, Hrdlicka PJ. Pyrene-functionalized oligonucleotides and locked nucleic acids (LNAs): tools for fundamental research, diagnostics, and nanotechnology. Chem Soc Rev 2011; 40:5771-88. [PMID: 21487621 PMCID: PMC3644995 DOI: 10.1039/c1cs15014f] [Citation(s) in RCA: 202] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pyrene-functionalized oligonucleotides (PFOs) are increasingly explored as tools in fundamental research, diagnostics and nanotechnology. Their popularity is linked to the ability of pyrenes to function as polarity-sensitive and quenchable fluorophores, excimer-generating units, aromatic stacking moieties and nucleic acid duplex intercalators. These characteristics have enabled development of PFOs for detection of complementary DNA/RNA targets, discrimination of single nucleotide polymorphisms (SNPs), and generation of π-arrays on nucleic acid scaffolds. This critical review will highlight the physical properties and applications of PFOs that are likely to provide high degree of positional control of the chromophore in nucleic acid complexes. Particular emphasis will be placed on pyrene-functionalized Locked Nucleic Acids (LNAs) since these materials display interesting properties such as fluorescence quantum yields approaching unity and recognition of mixed-sequence double stranded DNA (144 references).
Collapse
|
57
|
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.
Collapse
Affiliation(s)
- Chalothorn Boonlua
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | | | | | | |
Collapse
|
58
|
Abstract
Research in nucleic acids has made major advances in the past decade in multiple fields of science and technology. Here we discuss some of the most important findings in DNA and RNA research in the fields of biology, chemistry, biotechnology, synthetic biology, nanostructures and optical materials, with emphasis on how chemistry has impacted, and is impacted by, these developments. Major challenges ahead include the development of new chemical strategies that allow synthetically modified nucleic acids to enter into, and function in, living systems.
Collapse
Affiliation(s)
- Omid Khakshoor
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA. Fax: +1 650 725 0259; Tel: +1 650 724 4741
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA. Fax: +1 650 725 0259; Tel: +1 650 724 4741
| |
Collapse
|
59
|
Burns JR, Zekonyte J, Siligardi G, Hussain R, Stulz E. Directed formation of DNA nanoarrays through orthogonal self-assembly. Molecules 2011; 16:4912-22. [PMID: 21677604 PMCID: PMC6264196 DOI: 10.3390/molecules16064912] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 05/31/2011] [Accepted: 06/10/2011] [Indexed: 01/12/2023] Open
Abstract
We describe the synthesis of terpyridine modified DNA strands which selectively form DNA nanotubes through orthogonal hydrogen bonding and metal complexation interactions. The short DNA strands are designed to self-assemble into long duplexes through a sticky-end approach. Addition of weakly binding metals such as Zn(II) and Ni(II) induces the formation of tubular arrays consisting of DNA bundles which are 50-200 nm wide and 2-50 nm high. TEM shows additional long distance ordering of the terpy-DNA complexes into fibers.
Collapse
Affiliation(s)
- Jonathan R. Burns
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Jurgita Zekonyte
- National Centre for Advanced Tribology, School of Engineering Sciences, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - Giuliano Siligardi
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Rohanah Hussain
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Eugen Stulz
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
- Author to whom correspondence should be addressed; ; Tel +44-2380-599369
| |
Collapse
|
60
|
Gujrati MD, Kumar NSS, Brown AS, Captain B, Wilson JN. Luminescent charge-transfer complexes: tuning emission in binary fluorophore mixtures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:6554-8. [PMID: 21548624 DOI: 10.1021/la2012809] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Charge-transfer (CT) complexes composed of a π-electron-poor naphthalene diimide (NDI) derivative combined with a series of π-electron-rich donors were investigated. Solutions of the CT complexes are nonemissive; however, solid-state complexes and aqueous suspensions display emission that is dependent on the energy of the HOMO of the electron donor. Crystallographic analysis of a pyrene-NDI complex reveals columnar packing and a high degree of frontier molecular orbital (FMO) overlap that likely contributes to the observed optical properties. The fluorescent CT particles are utilized as imaging agents; additional luminescent CT complexes may be realized by considering FMO energies and topologies.
Collapse
Affiliation(s)
- Maneesh D Gujrati
- Center for Supramolecular Science and Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33124, United States
| | | | | | | | | |
Collapse
|
61
|
Nadler A, Strohmeier J, Diederichsen U. 8-Vinyl-2'-deoxyguanosine as a fluorescent 2'-deoxyguanosine mimic for investigating DNA hybridization and topology. Angew Chem Int Ed Engl 2011; 50:5392-6. [PMID: 21542071 DOI: 10.1002/anie.201100078] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Indexed: 11/10/2022]
Affiliation(s)
- André Nadler
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany
| | | | | |
Collapse
|
62
|
Nadler A, Strohmeier J, Diederichsen U. 8-Vinyl-2′-desoxyguanosin als fluoreszierendes 2′-Desoxyguanosin- Analogon zur Untersuchung von DNA-Hybridisierung und Topologie. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100078] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
63
|
Dick B. Circular Dichroism of a Finite Number of Identical Chromophores in a Helical Arrangement. Chemphyschem 2011; 12:1578-87. [DOI: 10.1002/cphc.201000949] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2010] [Indexed: 11/11/2022]
|
64
|
Østergaard ME, Kumar P, Baral B, Guenther DC, Anderson BA, Ytreberg FM, Deobald L, Paszczynski AJ, Sharma PK, Hrdlicka PJ. C5-functionalized DNA, LNA, and α-L-LNA: positional control of polarity-sensitive fluorophores leads to improved SNP-typing. Chemistry 2011; 17:3157-65. [PMID: 21328492 DOI: 10.1002/chem.201002109] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 11/16/2010] [Indexed: 12/17/2022]
Abstract
Single nucleotide polymorphisms (SNPs) are important markers in disease genetics and pharmacogenomic studies. Oligodeoxyribonucleotides (ONs) modified with 5-[3-(1-pyrenecarboxamido)propynyl]-2'-deoxyuridine monomer X enable detection of SNPs at non-stringent conditions due to differential fluorescence emission of matched versus mismatched nucleic acid duplexes. Herein, the thermal denaturation and optical spectroscopic characteristics of monomer X are compared to the corresponding locked nucleic acid (LNA) and α-L-LNA monomers Y and Z. ONs modified with monomers Y or Z result in a) larger increases in fluorescence intensity upon hybridization to complementary DNA, b) formation of more brightly fluorescent duplexes due to markedly larger fluorescence emission quantum yields (Φ(F)=0.44-0.80) and pyrene extinction coefficients, and c) improved optical discrimination of SNPs in DNA targets. Optical spectroscopy studies suggest that the nucleobase moieties of monomers X-Z adopt anti and syn conformations upon hybridization with matched and mismatched targets, respectively. The polarity-sensitive 1-pyrenecarboxamido fluorophore is, thereby, either positioned in the polar major groove or in the hydrophobic duplex core close to quenching nucleobases. Calculations suggest that the bicyclic skeletons of LNA and α-L-LNA monomers Y and Z influence the glycosidic torsional angle profile leading to altered positional control and photophysical properties of the C5-fluorophore.
Collapse
Affiliation(s)
- Michael E Østergaard
- Department of Chemistry, University of Idaho, P.O. Box 442343, Moscow, ID 83844-2343, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
65
|
Brewer A, Siligardi G, Neylon C, Stulz E. Introducing structural flexibility into porphyrin-DNA zipper arrays. Org Biomol Chem 2010; 9:777-82. [PMID: 21103551 DOI: 10.1039/c0ob00535e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A more flexible nucleotide building block for the synthesis of new DNA based porphyrin-zipper arrays is described. Changing the rigid acetylene linker between the porphyrin substituent and the 2'-deoxyuridine to a more flexible propargyl amide containing linkage leads in part to an increased duplex stability. The CD spectra reveal different electronic interactions between the porphyrins depending on the type of linker used. Molecular modelling suggests large variation of the relative orientation of the porphyrins within the major groove of the DNA. The porphyrins can be metallated post-synthetically with different metals as shown with zinc, cobalt and copper. The spectroscopic features do not alter drastically upon metallation apart from the CD spectra, and the stability of the metal complex is highly dependent on the nature of the metal. As shown by CD spectroscopy, the zinc porphyrin is rapidly demetallated at high temperatures. Globular structure determination using SAXS indicates that a molecular assembly comprised of a two to four helical bundle dominates in solution at higher concentrations (≥50 μM) which is not observed by spectroscopy at lower concentrations (≤1 μM).
Collapse
Affiliation(s)
- Ashley Brewer
- School of Chemistry, University of Southampton, Highfield, Southampton, UK SO17 1BJ
| | | | | | | |
Collapse
|
66
|
Bandy TJ, Brewer A, Burns JR, Marth G, Nguyen T, Stulz E. DNA as supramolecular scaffold for functional molecules: progress in DNA nanotechnology. Chem Soc Rev 2010; 40:138-48. [PMID: 20694258 DOI: 10.1039/b820255a] [Citation(s) in RCA: 197] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Oligonucleotides have recently gained increased attraction as a supramolecular scaffold for the design and synthesis of functional molecules on the nanometre scale. This tutorial review focuses on the recent progress in this highly active field of research with an emphasis on covalent modifications of DNA; non-covalent interactions of DNA with molecules such as groove binders or intercalators are not part of this review. Both terminal and internal modifications are covered, and the various points of attachment (nucleobase, sugar moiety or phosphodiester backbone) are compared. Using selected examples of the recent literature, the diversity of the functionalities that have been incorporated into DNA strands is discussed.
Collapse
Affiliation(s)
- Thomas J Bandy
- University of Southampton, School of Chemistry, Highfield, Southampton SO17 1BJ, UK
| | | | | | | | | | | |
Collapse
|
67
|
Varghese R, Wagenknecht HA. Non-covalent Versus Covalent Control of Self-Assembly and Chirality of Nile Red-modified Nucleoside and DNA. Chemistry 2010; 16:9040-6. [DOI: 10.1002/chem.201001136] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
68
|
Teo YN, Kool ET. Polyfluorophore excimers and exciplexes as FRET donors in DNA. Bioconjug Chem 2010; 20:2371-80. [PMID: 19916519 DOI: 10.1021/bc9003926] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe studies aimed at testing whether oligomeric exciplex and excimer fluorophores conjugated to DNA have the potential to act as donors for energy transfer by the Forster mechanism. Oligodeoxyfluorosides (ODFs) are composed of stacked, electronically interacting fluorophores replacing the bases on a DNA scaffold. The monomer chromophores in the twenty tetramer-length ODFs studied here include pyrene (Y), benzopyrene (B), perylene (E), dimethylaminostilbene (D), and a nonfluorescent spacer (S); these are conjugated in varied combinations at the 3' end of a 14mer DNA probe sequence. In the absence of an acceptor chromophore, many of the ODF-DNAs show broad, unstructured long-wavelength emission peaks characteristic of excimer and exciplex excited states, similar to what has been observed for unconjugated ODFs. Although such delocalized excited states have been widely studied, we know of no prior report of their use in FRET. We tested the ability of the twenty ODFs to donate energy to Cy5 and TAMRA dyes conjugated to a complementary strand of DNA, with these acceptors oriented either at the near or far end of the ODF-conjugated probes. Results showed that a number of the ODF fluorophores exhibited relatively efficient energy transfer characteristic of the Forster mechanism, as judged by drops in donor emission quantum yield and fluorescence lifetime, accompanied by increases in intensity of acceptor emission bands. Excimer/exciplex bands in the donors were selectively quenched while shorter-wavelength monomer emission stayed relatively constant, consistent with the notion that the delocalized excited states, rather than individual fluorophores, are the donors. Interestingly, only specific sequences of ODFs were able to act as donors, while others did not, even though their emission wavelengths were similar. The new FRET donors possess large Stokes shifts, which can be beneficial for multiple applications. In addition, all ODFs can be excited at a single wavelength; thus, ODFs may be candidates as "universal FRET donors", thus allowing multicolor FRET of multiple species to be carried out with one excitation.
Collapse
Affiliation(s)
- Yin Nah Teo
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | |
Collapse
|
69
|
Kashida H, Sekiguchi K, Liang X, Asanuma H. Accumulation of Fluorophores into DNA Duplexes To Mimic the Properties of Quantum Dots. J Am Chem Soc 2010; 132:6223-30. [DOI: 10.1021/ja101007d] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan, and Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Koji Sekiguchi
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan, and Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Xingguo Liang
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan, and Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan, and Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| |
Collapse
|
70
|
Fukuda M, Nakamura M, Takada T, Yamana K. Syntheses and fluorescence of RNA conjugates having pyrene-modified adenosine and nitrobenzene-modified uridine base pairs. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.01.081] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
71
|
Kashida H, Takatsu T, Sekiguchi K, Asanuma H. An Efficient Fluorescence Resonance Energy Transfer (FRET) between Pyrene and Perylene Assembled in a DNA Duplex and Its Potential for Discriminating Single-Base Changes. Chemistry 2010; 16:2479-86. [DOI: 10.1002/chem.200902078] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
72
|
Abstract
Due to its self-assembling nature, DNA is undoubtedly an excellent molecule for the creation of various multidimensional nanostructures and the placement of functional molecules and materials. DNA molecules behave according to the programs of their sequences. Mixtures of numbers of DNA molecules can be placed precisely and organized into single structures to form nanoarchitectures. Once the appropriate sequences for the target nanostructure are established, the predesigned structure can be built up by self-assembly of the designed DNA strands. DNA nanotechnology has already reached the stage at which the organization of desired functional molecules and nanomaterials can be programmed on a defined DNA scaffold. In this review, we will focus on DNA nanotechnology and describe the potential of synthetic chemistry to contribute to the further development of DNA nanomaterials.
Collapse
Affiliation(s)
- Masayuki Endo
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | | |
Collapse
|
73
|
Mammana A, Pescitelli G, Asakawa T, Jockusch S, Petrovic AG, Monaco RR, Purrello R, Turro NJ, Nakanishi K, Ellestad GA, Balaz M, Berova N. Role of environmental factors on the structure and spectroscopic response of 5'-DNA-porphyrin conjugates caused by changes in the porphyrin-porphyrin interactions. Chemistry 2010; 15:11853-66. [PMID: 19844929 DOI: 10.1002/chem.200902029] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We have explored the utility, strength, and limitation of through-space exciton-coupled circular dichroism in determination of the secondary structure of optically active chromophoric nanoarrays using the example of end-capped porphyrin- and metalloporphyrin-oligodeoxynucleotide conjugates. We put special emphasis on the explanation of the origin and significance of the distinctive multiple bands in the CD spectra (trisignate and tetrasignate CD bands). Such CD profiles are often observed in chiral aggregates or multichromophoric arrays but have never before been studied in detail. We found that variation of temperature and ionic strength has a profound effect on the geometry of the porphyrin-DNA conjugates and thus the nature of electronic interactions. At lower temperatures and in the absence of NaCl all three 5'-DNA-porphyrin conjugates display negative bisignate CD exciton couplets of variable intensity in the Soret region resulting from through-space interaction between the electric transition dipole moments of the two end-capped porphyrins. As the temperature is raised these exciton couplets are transformed into single positive bands originating from the porphyrin-single-strand DNA interactions. At higher ionic strengths and low temperatures, multisignate CD bands are observed in the porphyrin Soret region. These CD signature bands originate from a combination of intermolecular, end-to-end porphyrin-porphyrin stacking between duplexes and porphyrin-DNA interactions. The intermolecular aggregation was confirmed by fluorescence and absorption spectroscopy and resonance light scattering. DeVoe theoretical CD calculations, in conjunction with molecular dynamics simulations and Monte Carlo conformational searches, were used to mimic the observed bisignate exciton-coupled CD spectra as well as multiple CD bands. Calculations correctly predicted the sign and shape of the experimentally observed CD spectra. These studies reveal that the exciton-coupled circular dichroism is a very useful technique for the determination of the structure of optically active arrays.
Collapse
Affiliation(s)
- Angela Mammana
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
74
|
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
| | | |
Collapse
|
75
|
Affiliation(s)
- Thomas Rühl
- a School of Chemistry , University of Southampton , Highfield, Southampton, SO17 1EW, UK
| | - Eugen Stulz
- a School of Chemistry , University of Southampton , Highfield, Southampton, SO17 1EW, UK
| |
Collapse
|
76
|
Teo YN, Wilson JN, Kool ET. Polyfluorophore labels on DNA: dramatic sequence dependence of quenching. Chemistry 2010; 15:11551-8. [PMID: 19780115 DOI: 10.1002/chem.200901607] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We describe studies carried out in the DNA context to test how a common fluorescence quencher, dabcyl, interacts with oligodeoxynucleoside fluorophores (ODFs)--a system of stacked, electronically interacting fluorophores built on a DNA scaffold. We tested twenty different tetrameric ODF sequences containing varied combinations and orderings of pyrene (Y), benzopyrene (B), perylene (E), dimethylaminostilbene (D), and spacer (S) monomers conjugated to the 3' end of a DNA oligomer. Hybridization of this probe sequence to a dabcyl-labeled complementary strand resulted in strong quenching of fluorescence in 85% of the twenty ODF sequences. The high efficiency of quenching was also established by their large Stern-Volmer constants (K(SV)) of between 2.1 x 10(4) and 4.3 x 10(5) M(-1), measured with a free dabcyl quencher. Interestingly, quenching of ODFs displayed strong sequence dependence. This was particularly evident in anagrams of ODF sequences; for example, the sequence BYDS had a K(SV) that was approximately two orders of magnitude greater than that of BSDY, which has the same dye composition. Other anagrams, for example EDSY and ESYD, also displayed different responses upon quenching by dabcyl. Analysis of spectra showed that apparent excimer and exciplex emission bands were quenched with much greater efficiency compared to monomer emission bands by at least an order of magnitude. This suggests an important role played by delocalized excited states of the pi stack of fluorophores in the amplified quenching of fluorescence.
Collapse
Affiliation(s)
- Yin Nah Teo
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
| | | | | |
Collapse
|
77
|
Schwartz E, Le Gac S, Cornelissen JJLM, Nolte RJM, Rowan AE. Macromolecular multi-chromophoric scaffolding. Chem Soc Rev 2010; 39:1576-99. [DOI: 10.1039/b922160c] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
78
|
Varghese R, Wagenknecht HA. Red-white-blue emission switching molecular beacons: ratiometric multicolour DNA hybridization probes. Org Biomol Chem 2009; 8:526-8. [PMID: 20090965 DOI: 10.1039/b918381g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular beacons with two fluorophores derived from ethynyl pyrene and ethynyl nile red exhibit red emission in the hairpin that changes to blue through white upon binding to the target sequence with a dramatic shift of approximately 225 nm.
Collapse
Affiliation(s)
- Reji Varghese
- Univeristy of Regensburg, Institute for Organic Chemistry, Universitätsstr. 31, D-93053 Regensburg, Germany
| | | |
Collapse
|
79
|
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]
|
80
|
|
81
|
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.
Collapse
Affiliation(s)
- Victor A Galievsky
- B.I. Stepanov's Institute of Physics, National Academy of Sciences of Belarus, Nezavisimosti ave. 68, 220072, Minsk, Belarus
| | | | | | | | | | | | | |
Collapse
|
82
|
Synthesis of novel bispyrene diamines and their application as ratiometric fluorescent probes for detection of DNA. Biosens Bioelectron 2009; 24:3442-7. [DOI: 10.1016/j.bios.2009.04.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Revised: 04/11/2009] [Accepted: 04/14/2009] [Indexed: 11/23/2022]
|
83
|
Borsenberger V, Kukwikila M, Howorka S. Synthesis and enzymatic incorporation of modified deoxyuridine triphosphates. Org Biomol Chem 2009; 7:3826-35. [PMID: 19707689 DOI: 10.1039/b906956a] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe the synthesis of 2'-deoxyuridine-5'-triphosphate derivatives bearing linkers of varying length, bulk and flexibility, at position 5 of the pyrimidine base. Nucleotide analogues with terminal functional groups are of interest due to their application potential for the functional labelling of DNA strands. In the course of the synthesis of the nucleotide analogues, the methodology for the Yoshikawa phosphorylation procedure was optimised, resulting in an approach which reduces the amount of side-products and is compatible with labile functional groups attached to the base. The effect of linker composition on the enzymatic incorporation into DNA was systematically investigated using two different DNA polymerases. Deep Vent(R) exo(-) from the B-polymerase family accepted most nucleotide analogues as substrates, while Taq from the A-family was slightly less proficient. Both polymerases had difficulties incorporating 5-(3-amino-prop-1-ynyl)-2'-deoxyuridine triphosphate. A molecular model of the active site of the polymerase was used to rationalise why this nucleotide was not accepted as a substrate.
Collapse
Affiliation(s)
- Vinciane Borsenberger
- University College London, Department of Chemistry, 20 Gordon Street, London, UKWC1H OAJ
| | | | | |
Collapse
|
84
|
Wang G, Bobkov GV, Mikhailov SN, Schepers G, Van Aerschot A, Rozenski J, Van der Auweraer M, Herdewijn P, De Feyter S. Detection of RNA hybridization by pyrene-labeled probes. Chembiochem 2009; 10:1175-85. [PMID: 19373795 DOI: 10.1002/cbic.200900031] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Powerful pyrene probes: Two kinds of pyrene-labeled oligonucleotides (HNA- and RNA-skeleton probes) were explored. The enhanced fluorescence intensity in the monomer region and the disappearance of aggregate/excimer emission in duplexes has been successfully used to detect the hybridization of oligonucleotides. By covalently attaching pyrene chromophores with different linkers onto altritol nucleotides or ribonucleotides, and by varying the number of these pyrene modified altritol nucleotides and ribonucleotides in HNA (hexitol nucleic acid) and RNA, respectively, we have explored the general applicability of pyrene absorbance and especially fluorescence as a probe to monitor RNA hybridization. The results reveal that the backbone of the probes, the number of pyrene units attached and the nature of the tether can all substantially affect the absorbance and fluorescence properties of the probes both in single strand and double strand form. Moreover, the strength of hybridization is also affected. The disappearance of pyrene aggregate/excimer emission and simultaneous increase in monomer emission intensity of the multipyrene-labeled probes has been successfully used to monitor the hybridization of oligonucleotides, including a hairpin structure. Differences in optical response between the HNA- and RNA-skeleton probes upon hybridization indicate that the interaction of pyrene with the nucleobases in both types of duplexes is different.
Collapse
Affiliation(s)
- Guojie Wang
- Department of Chemistry, Division of Molecular and Nanomaterials, Laboratory of Photochemistry and Spectroscopy, Katholieke Universiteit Leuven, Celestijnenlaan 200 F, 3001 Leuven, Belgium
| | | | | | | | | | | | | | | | | |
Collapse
|
85
|
Fluorescence quenching properties of multiple pyrene-modified RNAs. Bioorg Med Chem 2009; 17:4996-5000. [DOI: 10.1016/j.bmc.2009.05.074] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Revised: 05/28/2009] [Accepted: 05/29/2009] [Indexed: 11/21/2022]
|
86
|
Abstract
The self-organization of oligopyrene foldamers is described. Bi- and tri-segmental oligomers composed of nucleotides and non-nucleosidic, achiral pyrene monomers form double-stranded helical structures, as shown by absorbance, fluorescence, and CD spectroscopy. The mixed nature of alternating aromatic and phosphate groups ensures water solubility which, in turn, favors folding of the aromatic units. Pyrene molecules also assemble though interstrand stacking interactions. Structural organization of the pyrene units is an intrinsic property of the oligoaryl part and takes place independently from the sequence of the attached DNA. Chirality transfer from DNA to the pyrene segment leads to formation of a double helix, in which neighboring pyrene units are, in the present case, twisted in a right-handed manner. Pyrene helicity is most pronounced in a bi-segmental chimera, in which a DNA stem is present only at one end of the pyrene section.
Collapse
Affiliation(s)
- Robert Häner
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
| | | | | |
Collapse
|
87
|
Teo YN, Wilson JN, Kool ET. Polyfluorophores on a DNA backbone: a multicolor set of labels excited at one wavelength. J Am Chem Soc 2009; 131:3923-33. [PMID: 19254023 DOI: 10.1021/ja805502k] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We recently described the assembly of fluorescent deoxyriboside monomers ("fluorosides") into DNA-like phosphodiester oligomers (oligodeoxyfluorosides or ODFs) in which hydrocarbon and heterocyclic aromatic fluorophores interact both physically and electronically. Here we report the identification of a multicolor set of water-soluble ODF dyes that display emission colors across the visible spectrum, and all of which can be simultaneously excited by long-wavelength UV light at 340-380 nm. Multispectral dye candidates were chosen from a library of 4096 tetramer ODFs constructed on PEG-polystyrene beads using a simple long-pass filter to observe all visible colors at the same time. We resynthesized and characterized a set of 23 ODFs containing one to four individual chromophores and included 2-3 spacer monomers to increase aqueous solubility and minimize aggregation. Emission maxima of this set range from 376 to 633 nm, yielding apparent colors from violet to red, all of which can be visualized directly. The spectra of virtually all ODFs in this set varied considerably from the simple combination of monomer components, revealing extensive electronic interactions between the presumably stacked monomers. In addition, comparisons of anagrams in the set (isomers having the same components in a different sequence) reveal the importance of nearest-neighbor interactions in the emissive behavior. Preliminary experiments with human tumor (HeLa) cells, observing two ODFs by laser confocal microscopy, showed that they can penetrate the outer cellular membrane, yielding cytoplasmic localization. In addition, a set of four distinctly colored ODFs was incubated with live zebrafish embryos, showing tissue penetration, apparent biostability, and no apparent toxicity. The results suggest that ODF dyes may be broadly useful as labels in biological systems, allowing the simultaneous tracking of multiple species by color, and allowing visualization in moving systems where classical fluorophores fail.
Collapse
Affiliation(s)
- Yin Nah Teo
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | | |
Collapse
|
88
|
Zhou H, Ma X, Wang J, Zhang L. Pyrene acetylide nucleotides in GNA: probing duplex formation and sensing of copper(II) ions. Org Biomol Chem 2009; 7:2297-302. [PMID: 19462038 DOI: 10.1039/b900167k] [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 synthesis and evaluation of GNA duplexes containing fluorescent pyrene and pyrene acetylide nucleotides is reported. Interestingly, only the pyrene acetylides, but not the related plain pyrene nucleotides, form strong excimers upon stacking in glycol nucleic acid (GNA) duplexes. The ability of the large pyrene acetylide nucleotide to be accommodated in GNA duplexes opposite an abasic site was investigated by molecular modeling. The interstrand pyrene acetylide excimer formation was used to monitor GNA duplex formation and was applied to the design of a copper(II)-selective "turn-on" fluorescence sensor.
Collapse
Affiliation(s)
- Hui Zhou
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, D-35032, Marburg, Germany
| | | | | | | |
Collapse
|
89
|
Varghese R, Wagenknecht HA. DNA as a supramolecular framework for the helical arrangements of chromophores: towards photoactive DNA-based nanomaterials. Chem Commun (Camb) 2009:2615-24. [PMID: 19532903 DOI: 10.1039/b821728a] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nucleic acids have been emerging as supramolecular structural scaffolds for the helical organization of chromophores in the creation of functional nanomaterials mainly because of the their unique structural features and synthetic accessibility. A large number of chromophores have been successfully incorporated into DNA or RNA as C-nucleosides, as base surrogates or as modified sugars using solid phase phosphoramidite chemistry. Moreover, multiple incorporations yield the helical organization of the chromophores inside or outside the DNA or RNA double helix depending upon the conjugation of the chromophores. Significant photophysical interactions are observed in the chromophore stacks resulting in unique optical properties that are significantly different from the monomer properties. In this feature article, multichromophore labelled nucleic acids are reviewed with special emphasis on the self-assembly induced modulation of the optical properties.
Collapse
Affiliation(s)
- Reji Varghese
- University of Regensburg, Institute for Organic Chemistry, D-93053 Regensburg, Germany
| | | |
Collapse
|
90
|
Wagenknecht HA. Helicale Anordnung von Porphyrinen entlang der DNA: auf dem Weg zu DNA-Nanoarchitekturen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900327] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
91
|
Wagenknecht HA. Helical Arrangement of Porphyrins along DNA: Towards Photoactive DNA-Based Nanoarchitectures. Angew Chem Int Ed Engl 2009; 48:2838-41. [DOI: 10.1002/anie.200900327] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
92
|
Jacobsen MF, Ferapontova EE, Gothelf KV. Synthesis and electrochemical studies of an anthraquinone-conjugated nucleoside and derived oligonucleotides. Org Biomol Chem 2009; 7:905-8. [PMID: 19225673 DOI: 10.1039/b816820b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The synthesis of a 2'-deoxyuridine nucleoside linked to an anthraquinone moiety, and its incorporation into oligonucleotides are described, including a facile oxidative demethylation with phenyliodine(iii) bis(trifluoroacetate) to reveal the anthraquinone motif. Furthermore, some useful physical and electrochemical properties of the obtained oligonucleotide are also reported, which allow its principal use in electrochemical DNA assays.
Collapse
Affiliation(s)
- Mikkel F Jacobsen
- Danish National Research Foundation: Centre for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the Department of Chemistry, University of Aarhus, Langelandsgade 140, 8000 Aarhus C, Denmark
| | | | | |
Collapse
|
93
|
Filichev V, Astakhova I, Malakhov A, Korshun V, Pedersen E. 1-, 2-, and 4-Ethynylpyrenes in the Structure of Twisted Intercalating Nucleic Acids: Structure, Thermal Stability, and Fluorescence Relationship. Chemistry 2008; 14:9968-80. [DOI: 10.1002/chem.200800380] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
94
|
Han KH, Lee E, Kim JS, Cho BK. An Extraordinary Cylinder-to-Cylinder Transition in the Aqueous Assemblies of Fluorescently Labeled Rod−Coil Amphiphiles. J Am Chem Soc 2008; 130:13858-9. [DOI: 10.1021/ja806128e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kyung-Hee Han
- Department of Chemistry, Dankook University, Gyeonggi-Do, 448-701, Korea, Department of Chemistry, Yonsei University, Seoul, 120-749, Korea, and Department of Chemistry, Korea University, Seoul,136-704, Korea
| | - Eunji Lee
- Department of Chemistry, Dankook University, Gyeonggi-Do, 448-701, Korea, Department of Chemistry, Yonsei University, Seoul, 120-749, Korea, and Department of Chemistry, Korea University, Seoul,136-704, Korea
| | - Jong Seung Kim
- Department of Chemistry, Dankook University, Gyeonggi-Do, 448-701, Korea, Department of Chemistry, Yonsei University, Seoul, 120-749, Korea, and Department of Chemistry, Korea University, Seoul,136-704, Korea
| | - Byoung-Ki Cho
- Department of Chemistry, Dankook University, Gyeonggi-Do, 448-701, Korea, Department of Chemistry, Yonsei University, Seoul, 120-749, Korea, and Department of Chemistry, Korea University, Seoul,136-704, Korea
| |
Collapse
|
95
|
Baumstark D, Wagenknecht HA. Fluorescent Hydrophobic Zippers inside Duplex DNA: Interstrand Stacking of Perylene-3,4:9,10-tetracarboxylic Acid Bisimides as Artificial DNA Base Dyes. Chemistry 2008; 14:6640-5. [DOI: 10.1002/chem.200800514] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
96
|
Seo YJ, Lee IJ, Kim BH. Detection of structure-switching in G-quadruplexes using end-stacking ability. Bioorg Med Chem Lett 2008; 18:3910-3. [PMID: 18585032 DOI: 10.1016/j.bmcl.2008.06.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 06/04/2008] [Accepted: 06/11/2008] [Indexed: 10/21/2022]
Abstract
G-quadruplex-forming ODNs containing nonpolar aromatic fluorophore moiety, A(PY) at the dangling ends undergo pi-stacking on surface of G-quadruplex, and the fluorescence change can be used to distinguish the structure-switching between the mixed parallel/antiparallel structure and antiparallel structure.
Collapse
Affiliation(s)
- Young Jun Seo
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | | | | |
Collapse
|
97
|
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.
Collapse
Affiliation(s)
- Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furocho, Chikusa, Nagoya, 464-8603, Japan
| | | | | |
Collapse
|
98
|
Nakamura M, Murakami Y, Sasa K, Hayashi H, Yamana K. Pyrene-zipper array assembled via RNA duplex formation. J Am Chem Soc 2008; 130:6904-5. [PMID: 18473465 DOI: 10.1021/ja801054t] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a new strategy for multipyrene modification of RNA sequences to form unique structures of pyrene aromatic arrays, the "pyrene-zipper array", on duplex RNA that exhibits remarkably strong excimer fluorescence.
Collapse
Affiliation(s)
- Mitsunobu Nakamura
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
| | | | | | | | | |
Collapse
|
99
|
Srivatsan SG, Weizman H, Tor Y. A highly fluorescent nucleoside analog based on thieno[3,4-d]pyrimidine senses mismatched pairing. Org Biomol Chem 2008; 6:1334-8. [PMID: 18385838 PMCID: PMC5263222 DOI: 10.1039/b801054d] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A highly emissive nucleobase analog, based on a thieno[3,4-d]pyrimidine core, is enzymatically incorporated into RNA oilgonucleotides that function as base discriminating fluorescent probes.
Collapse
Affiliation(s)
- Seergazhi G Srivatsan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, USA
| | | | | |
Collapse
|
100
|
Hocek M, Fojta M. Cross-coupling reactions of nucleoside triphosphates followed by polymerase incorporation. Construction and applications of base-functionalized nucleic acids. Org Biomol Chem 2008; 6:2233-41. [PMID: 18563253 DOI: 10.1039/b803664k] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Construction of functionalized nucleic acids (DNA or RNA) via polymerase incorporation of modified nucleoside triphosphates is reviewed and selected applications of the modified nucleic acids are highlighted. The classical multistep approach for the synthesis of modified NTPs by triphosphorylation of modified nucleosides is compared to the novel approach consisting of direct aqueous cross-coupling reactions of unprotected halogenated nucleoside triphosphates. The combination of cross-coupling of NTPs with polymerase incorporation gives an efficient and straightforward two-step synthesis of modified nucleic acids. Primer extension using biotinylated templates followed by separation using streptavidine-coated magnetic beads and DNA duplex denaturation is used for preparation of modified single stranded oligonucleotides. Examples of using this approach for electrochemical DNA labelling and bioanalytical applications are given.
Collapse
Affiliation(s)
- Michal Hocek
- 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
|