1
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Hernández Bustos A, Martiny E, Bom Pedersen N, Parvathaneni RP, Hansen J, Ji HP, Astakhova K. Short Tandem Repeat DNA Profiling Using Perylene-Oligonucleotide Fluorescence Assay. Anal Chem 2023; 95:7872-7879. [PMID: 37183373 DOI: 10.1021/acs.analchem.3c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We report an amplification-free genotyping method to determine the number of human short tandem repeats (STRs). DNA-based STR profiling is a robust method for genetic identification purposes such as forensics and biobanking and for identifying specific molecular subtypes of cancer. STR detection requires polymerase amplification, which introduces errors that obscure the correct genotype. We developed a new method that requires no polymerase. First, we synthesized perylene-nucleoside reagents and incorporated them into oligonucleotide probes that recognize five common human STRs. Using these probes and a bead-based hybridization approach, accurate STR detection was achieved in only 1.5 h, including DNA preparation steps, with up to a 1000-fold target DNA enrichment. This method was comparable to PCR-based assays. Using standard fluorometry, the limit of detection was 2.00 ± 0.07 pM for a given target. We used this assay to accurately identify STRs from 50 human subjects, achieving >98% consensus with sequencing data for STR genotyping.
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Affiliation(s)
- Adrián Hernández Bustos
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Region Hovedstaden 2800, Denmark
| | - Elisa Martiny
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Region Hovedstaden 2800, Denmark
| | - Nadia Bom Pedersen
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Region Hovedstaden 2800, Denmark
| | - Rohith Pavan Parvathaneni
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Region Hovedstaden 2800, Denmark
| | - Jonas Hansen
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Region Hovedstaden 2800, Denmark
- School of Medicine, Stanford University, 94305 Stanford, California, United States
| | - Hanlee P Ji
- School of Medicine, Stanford University, 94305 Stanford, California, United States
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Region Hovedstaden 2800, Denmark
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2
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Dziuba D. Environmentally sensitive fluorescent nucleoside analogues as probes for nucleic acid - protein interactions: molecular design and biosensing applications. Methods Appl Fluoresc 2022; 10. [PMID: 35738250 DOI: 10.1088/2050-6120/ac7bd8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/23/2022] [Indexed: 11/12/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are indispensable in studying the interactions of nucleic acids with nucleic acid-binding proteins. By replacing one of the poorly emissive natural nucleosides, FNAs enable real-time optical monitoring of the binding interactions in solutions, under physiologically relevant conditions, with high sensitivity. Besides that, FNAs are widely used to probe conformational dynamics of biomolecular complexes using time-resolved fluorescence methods. Because of that, FNAs are tools of high utility for fundamental biological research, with potential applications in molecular diagnostics and drug discovery. Here I review the structural and physical factors that can be used for the conversion of the molecular binding events into a detectable fluorescence output. Typical environmentally sensitive FNAs, their properties and applications, and future challenges in the field are discussed.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden, Grand Est, 67401, FRANCE
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3
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Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
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4
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Mariam J, Krishnamoorthy G, Anand R. Use of 6‐Methylisoxanthopterin, a Fluorescent Guanine Analog, to Probe Fob1‐Mediated Dynamics at the Stalling Fork Barrier DNA Sequences. Chem Asian J 2019; 14:4760-4766. [DOI: 10.1002/asia.201901061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/19/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Jessy Mariam
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 Maharashtra India
| | | | - Ruchi Anand
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 Maharashtra India
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5
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Mamedov VA, Zhukova NA, Gubaidullin AT, Syakaev VV, Kadyrova MS, Beschastnova TN, Bazanova OB, Rizvanov IDK, Latypov SK. One-Pot Synthesis of 7-(Benzimidazol-2-yl)thioxolumazine and -lumazine Derivatives via H 2SO 4-Catalyzed Rearrangement of Quinoxalinones When Exposed to 5,6-Diamino-2-mercapto- and 2,5,6-Triaminopyrimidin-4-ols. J Org Chem 2018; 83:14942-14953. [PMID: 30431276 DOI: 10.1021/acs.joc.8b02161] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A facile approach to a range of substituted 7-(benzimidazol-2-yl)thioxolumazines [7-(benzimidazol-2-yl)-2-thioxo-2,3-dihydropteridin-4(1 H)-ones] and 7-(benzimidazol-2-yl)lumazines [7-(benzimidazol-2-yl)pteridine-2,4(1 H,3 H)-diones] is described. These new biheterocyclic systems are obtained via H2SO4-catalyzed rearrangement of quinoxalin-2-ones in the presence of 5,6-diamino-2-mercapto- and 2,5,6-triaminopyrimidin-4-ols. Thus, benzimidazole and pteridine rings are constructed in one synthetic step. A plausible ANRORC ( addition of nucleophile, ring opening and ring closure)-type reaction mechanism is proposed. Applying the rearrangement to the aza-analogue of 3-benzoylquinoxalin-2(1 H)-one-i.e., 3-benzoylpyrido[2,3- b]pyrazin-2(1 H)-one-with 5,6-diamino-2-mercaptopyrimidin-4-ol makes it possible to synthesize inaccessible 7-(1 H-imidazo[4,5- b]pyridin-2-yl)-6-phenyl-2-thioxo-2,3-dihydropteridin-4(1 H)-one. 7-(Benzimidazol-2-yl)-6-(2-fluorophenyl)-2-thioxo-2,3-dihydropteridin-4(1 H)-ones undergoes intramolecular nucleophilic substitution of fluorine by a nitrogen of the benzimidazole fragment with the formation of benzo[4',5']imidazo[1',2':1,2]quinolino[4,3- g]pteridine-2,4(1 H,3 H)-diones as new heterocyclic systems.
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Affiliation(s)
- Vakhid A Mamedov
- A.E. Arbuzov Institute of Organic and Physical Chemistry, RFC Kazan Scientific Center , Russian Academy of Sciences , Arbuzov Street 8 , 420088 Kazan , Russian Federation
| | - Nataliya A Zhukova
- A.E. Arbuzov Institute of Organic and Physical Chemistry, RFC Kazan Scientific Center , Russian Academy of Sciences , Arbuzov Street 8 , 420088 Kazan , Russian Federation
| | - Aidar T Gubaidullin
- A.E. Arbuzov Institute of Organic and Physical Chemistry, RFC Kazan Scientific Center , Russian Academy of Sciences , Arbuzov Street 8 , 420088 Kazan , Russian Federation
| | - Victor V Syakaev
- A.E. Arbuzov Institute of Organic and Physical Chemistry, RFC Kazan Scientific Center , Russian Academy of Sciences , Arbuzov Street 8 , 420088 Kazan , Russian Federation
| | - Milyausha S Kadyrova
- A.E. Arbuzov Institute of Organic and Physical Chemistry, RFC Kazan Scientific Center , Russian Academy of Sciences , Arbuzov Street 8 , 420088 Kazan , Russian Federation
| | - Tat'yana N Beschastnova
- A.E. Arbuzov Institute of Organic and Physical Chemistry, RFC Kazan Scientific Center , Russian Academy of Sciences , Arbuzov Street 8 , 420088 Kazan , Russian Federation
| | - Olga B Bazanova
- A.E. Arbuzov Institute of Organic and Physical Chemistry, RFC Kazan Scientific Center , Russian Academy of Sciences , Arbuzov Street 8 , 420088 Kazan , Russian Federation
| | - Il Dar Kh Rizvanov
- A.E. Arbuzov Institute of Organic and Physical Chemistry, RFC Kazan Scientific Center , Russian Academy of Sciences , Arbuzov Street 8 , 420088 Kazan , Russian Federation
| | - Shamil K Latypov
- A.E. Arbuzov Institute of Organic and Physical Chemistry, RFC Kazan Scientific Center , Russian Academy of Sciences , Arbuzov Street 8 , 420088 Kazan , Russian Federation
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6
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Castaño C, Serrano MP, Lorente C, Borsarelli CD, Thomas AH. Quenching of the Singlet and Triplet Excited States of Pterin by Amino Acids. Photochem Photobiol 2018; 95:220-226. [DOI: 10.1111/php.13046] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/25/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Carolina Castaño
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA); Departamento de Química; Facultad de Ciencias Exactas; Universidad Nacional de La Plata; CCT La Plata-CONICET; La Plata Argentina
| | - Mariana P. Serrano
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA); Departamento de Química; Facultad de Ciencias Exactas; Universidad Nacional de La Plata; CCT La Plata-CONICET; La Plata Argentina
| | - Carolina Lorente
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA); Departamento de Química; Facultad de Ciencias Exactas; Universidad Nacional de La Plata; CCT La Plata-CONICET; La Plata Argentina
| | - Claudio D. Borsarelli
- Instituto de Bionanotecnología del NOA (INBIONATEC); CONICET; Universidad Nacional de Santiago del Estero (UNSE); Santiago del Estero Argentina
| | - Andrés H. Thomas
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA); Departamento de Química; Facultad de Ciencias Exactas; Universidad Nacional de La Plata; CCT La Plata-CONICET; La Plata Argentina
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7
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Saito Y, Hudson RH. Base-modified fluorescent purine nucleosides and nucleotides for use in oligonucleotide probes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2018. [DOI: 10.1016/j.jphotochemrev.2018.07.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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8
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Passow KT, Harki DA. 4-Cyanoindole-2'-deoxyribonucleoside (4CIN): A Universal Fluorescent Nucleoside Analogue. Org Lett 2018; 20:4310-4313. [PMID: 29989830 PMCID: PMC6168291 DOI: 10.1021/acs.orglett.8b01746] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The synthesis and characterization of a universal and fluorescent nucleoside, 4-cyanoindole-2'-deoxyribonucleoside (4CIN), and its incorporation into DNA is described. 4CIN is a highly efficient fluorophore with quantum yields >0.90 in water. When incorporated into duplex DNA, 4CIN pairs equivalently with native nucleobases and has uniquely high quantum yields ranging from 0.15 to 0.31 depending on sequence and hybridization contexts, surpassing that of 2-aminopurine, the prototypical nucleoside fluorophore. 4CIN constitutes a new isomorphic nucleoside for diverse applications.
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Affiliation(s)
- Kellan T. Passow
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Daniel A. Harki
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
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9
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Goswami S, Das MK, Sain D, Goswami B. A concise treatment of pterins: some recent synthetic and methodology aspects and their applications in molecular sensors. Pteridines 2018. [DOI: 10.1515/pteridines-2018-0002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Abstract
A concise account of pterins in chemistry and biology and their applications in molecular sensors including their optical spectroscopic properties are described. Different natural, synthetic, biological and photophysical aspects are also discussed. Synthetic access to direct functionalised pterins and a recently reported new thiophene annulation technique are described for the synthesis of Form B of molybdenum cofactor. The receptor properties of fluorescent pterin molecules including selenopyrimidines which are rarely reported for their binding of anions and neutral molecules are also of major importance in this review. For such an old and still so young, unexplored pterin system on its power to be sensitive for physical studies especially the interaction with cations, anions and neutral molecules are fascinating and research in this area is relatively new and expected to increase fast. Pterin based receptors are for the first time put into a useful review for the advantage of those who want to explore pterin and modified pterin as chromogenic and fluorogenic sensors.
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Affiliation(s)
- Shyamaprosad Goswami
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, Howrah 711103, West Bengal , India
| | - Manas Kumar Das
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, Howrah 711103, West Bengal , India
| | - Dibyendu Sain
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, Howrah 711103, West Bengal , India
| | - Bhaswati Goswami
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, Howrah 711103, West Bengal , India
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10
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Wang W, Sheng X, Zhang S, Huang F, Sun C, Liu J, Chen D. Theoretical insights into the structural and fluorescence properties of DNA containing fluorescent nucleobases. Phys Chem Chem Phys 2018; 20:16641-16649. [DOI: 10.1039/c8cp02295j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The structural and fluorescence properties of DNA containing fluorescent nucleobases are explored in detail. In particular, the effect of stacking with different neighboring bases on fluorescence properties is elucidated.
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Affiliation(s)
- Wenjuan Wang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Xiehuang Sheng
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Shaolong Zhang
- College of Physics and Electronics
- Shandong Normal University
- Jinan 250014
- P. R. China
| | - Fang Huang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Chuanzhi Sun
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Jianbiao Liu
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Dezhan Chen
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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11
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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: 228] [Impact Index Per Article: 28.5] [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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12
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A new size-expanded RNA alphabet: Computational design of benzo-homologated (xtz-) isothiazole RNA and comparisons to the x-thieno RNA. J Mol Graph Model 2017; 77:339-349. [DOI: 10.1016/j.jmgm.2017.09.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 09/11/2017] [Accepted: 09/12/2017] [Indexed: 11/17/2022]
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13
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Wranne MS, Füchtbauer AF, Dumat B, Bood M, El-Sagheer AH, Brown T, Gradén H, Grøtli M, Wilhelmsson LM. Toward Complete Sequence Flexibility of Nucleic Acid Base Analogue FRET. J Am Chem Soc 2017; 139:9271-9280. [PMID: 28613885 DOI: 10.1021/jacs.7b04517] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Förster resonance energy transfer (FRET) using fluorescent base analogues is a powerful means of obtaining high-resolution nucleic acid structure and dynamics information that favorably complements techniques such as NMR and X-ray crystallography. Here, we expand the base-base FRET repertoire with an adenine analogue FRET-pair. Phosphoramidite-protected quadracyclic 2'-deoxyadenosine analogues qAN1 (donor) and qAnitro (acceptor) were synthesized and incorporated into DNA by a generic, reliable, and high-yielding route, and both constitute excellent adenine analogues. The donor, qAN1, has quantum yields reaching 21% and 11% in single- and double-strands, respectively. To the best of our knowledge, this results in the highest average brightness of an adenine analogue inside DNA. Its potent emissive features overlap well with the absorption of qAnitro and thus enable accurate FRET-measurements over more than one turn of B-DNA. As we have shown previously for our cytosine analogue FRET-pair, FRET between qAN1 and qAnitro positioned at different base separations inside DNA results in efficiencies that are highly dependent on both distance and orientation. This facilitates significantly enhanced resolution in FRET structure determinations, demonstrated here in a study of conformational changes of DNA upon binding of the minor groove binder netropsin. Finally, we note that the donor and acceptor of our cytosine FRET-pair, tCO and tCnitro, can be conveniently combined with the acceptor and donor of our current adenine pair, respectively. Consequently, our base analogues can now measure base-base FRET between 3 of the 10 possible base combinations and, through base-complementarity, between all sequence positions in a duplex.
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Affiliation(s)
- Moa S Wranne
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology , Gothenburg S-41296, Sweden
| | - Anders Foller Füchtbauer
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology , Gothenburg S-41296, Sweden
| | - Blaise Dumat
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology , Gothenburg S-41296, Sweden
| | - Mattias Bood
- Department of Chemistry and Molecular Biology, University of Gothenburg , Gothenburg S-41296, Sweden.,Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development, AstraZeneca , Mölndal S-43183, Sweden
| | - Afaf H El-Sagheer
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford , Oxford OX1 3TA, United Kingdom.,Chemistry Branch, Faculty of Petroleum and Mining Engineering, Suez University , Suez 43721, Egypt
| | - Tom Brown
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford , Oxford OX1 3TA, United Kingdom
| | - Henrik Gradén
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development, AstraZeneca , Mölndal S-43183, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg , Gothenburg S-41296, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology , Gothenburg S-41296, Sweden
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14
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Vignoni M, Walalawela N, Bonesi SM, Greer A, Thomas AH. Lipophilic Decyl Chain–Pterin Conjugates with Sensitizer Properties. Mol Pharm 2017; 15:798-807. [DOI: 10.1021/acs.molpharmaceut.7b00136] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Mariana Vignoni
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), CCT La Plata-CONICET, Casilla de Correo 16, Sucursal 4, 1900 La Plata, Argentina
- Department of Chemistry, Brooklyn College, City University of New York, Brooklyn, New York 11210, United States
| | - Niluksha Walalawela
- Department of Chemistry, Brooklyn College, City University of New York, Brooklyn, New York 11210, United States
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Sergio M. Bonesi
- CIHIDECAR-CONICET, Departamento de Química Orgánica, FCEyN, Universidad de Buenos Aires, Pabellón 2, 3er Piso, Ciudad Universitaria, Buenos Aires, Argentina
| | - Alexander Greer
- Department of Chemistry, Brooklyn College, City University of New York, Brooklyn, New York 11210, United States
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Andrés H. Thomas
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), CCT La Plata-CONICET, Casilla de Correo 16, Sucursal 4, 1900 La Plata, Argentina
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15
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Optical absorption and emission properties of benzene-expanded Janus AT nucleobase analogues: A DFT study. Struct Chem 2016. [DOI: 10.1007/s11224-016-0743-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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16
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Tinel L, Rossignol S, Ciuraru R, Dumas S, George C. Photosensitized reactions initiated by 6-carboxypterin: singlet and triplet reactivity. Phys Chem Chem Phys 2016; 18:17105-15. [DOI: 10.1039/c6cp03119f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The photophysical and photochemical properties of 6-carboxypterin, a model compound for the pterin derivatives present at the sea surface microlayer, were studied and its singlet and triplet reactivity toward halides and selected organics demonstrated.
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Affiliation(s)
- L. Tinel
- Université Lyon 1
- CNRS
- UMR 5256
- IRCELYON
- Institut de recherches sur la catalyse et l'environnement de Lyon
| | - S. Rossignol
- Université Lyon 1
- CNRS
- UMR 5256
- IRCELYON
- Institut de recherches sur la catalyse et l'environnement de Lyon
| | - R. Ciuraru
- Université Lyon 1
- CNRS
- UMR 5256
- IRCELYON
- Institut de recherches sur la catalyse et l'environnement de Lyon
| | - S. Dumas
- Université Lyon 1
- CNRS
- UMR 5256
- IRCELYON
- Institut de recherches sur la catalyse et l'environnement de Lyon
| | - C. George
- Université Lyon 1
- CNRS
- UMR 5256
- IRCELYON
- Institut de recherches sur la catalyse et l'environnement de Lyon
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Zhang L, Zhang Z, Ren T, Tian J, Wang M. New size-expanded RNA nucleobase analogs: a detailed theoretical study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 140:407-415. [PMID: 25617981 DOI: 10.1016/j.saa.2015.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 12/20/2014] [Accepted: 01/05/2015] [Indexed: 06/04/2023]
Abstract
Fluorescent nucleobase analogs have attracted much attention in recent years due to their potential applications in nucleic acids research. In this work, four new size-expanded RNA base analogs were computationally designed and their structural, electronic, and optical properties are investigated by means of DFT calculations. The results indicate that these analogs can form stable Watson-Crick base pairs with natural counterparts and they have smaller ionization potentials and HOMO-LUMO gaps than natural ones. Particularly, the electronic absorption spectra and fluorescent emission spectra are calculated. The calculated excitation maxima are greatly red-shifted compared with their parental and natural bases, allowing them to be selectively excited. In gas phase, the fluorescence from them would be expected to occur around 526, 489, 510, and 462 nm, respectively. The influences of water solution and base pairing on the relevant absorption spectra of these base analogs are also examined.
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Affiliation(s)
- Laibin Zhang
- School of Physics and Engineering, Qufu Normal University, Qufu 273165, PR China.
| | - Zhenwei Zhang
- Linyi Academy of Technology Cooperation and Application, Linyi 276001, PR China
| | - Tingqi Ren
- School of Physics and Engineering, Qufu Normal University, Qufu 273165, PR China
| | - Jianxiang Tian
- School of Physics and Engineering, Qufu Normal University, Qufu 273165, PR China.
| | - Mei Wang
- School of Physics and Engineering, Qufu Normal University, Qufu 273165, PR China
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18
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19
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Liu H, Ge C, Yu G, Qian X. Theoretical study of the structural and optical properties of cytosine analogues. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.09.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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20
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Pauszek RF, Kodali G, Stanley RJ. Excited state electronic structures of 5,10-methenyltetrahydrofolate and 5,10-methylenetetrahydrofolate determined by Stark spectroscopy. J Phys Chem A 2014; 118:8320-8. [PMID: 24814224 DOI: 10.1021/jp501143u] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Folates are ubiquitous cofactors that participate in a wide variety of critical biological processes. 5,10-Methenyltetrahydrofolate and its photodegradation product 5,10-methylenetetrahydrofolate are both associated with the light-driven DNA repair protein DNA photolyase and its homologues (e.g., cryptochromes). The excited state electronic properties of these folate molecules have been studied here using Stark spectroscopy and complementary quantum calculations. The tetrahydrofolates have relatively large difference dipole moments (ca. 6-8 Debye) and difference polarizabilities (ca. 100 Å(3)). This extensive excited state charge redistribution appears to be due largely to the pendant p-aminobenzoic acid group, which helps shuttle charge over the entirety of the molecule. Simple calculations based on the experimental difference dipole moments suggest that tetrahydrofolates should have large two photon cross sections sufficient to enable two photon microscopy to selectively detect and follow folate-containing proteins both in vitro and in vivo.
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Affiliation(s)
- Raymond F Pauszek
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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21
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Dhuguru J, Liu W, Gonzalez WG, Babinchak WM, Miksovska J, Landgraf R, Wilson JN. Emission tuning of fluorescent kinase inhibitors: conjugation length and substituent effects. J Org Chem 2014; 79:4940-7. [PMID: 24784897 PMCID: PMC4049246 DOI: 10.1021/jo500520x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
Fluorescent N-phenyl-4-aminoquinazoline probes
targeting the ATP-binding pocket of the ERBB family of receptor tyrosine
kinases are reported. Extension of the aromatic quinazoline core with
fluorophore “arms” through substitution at the 6- position
of the quinazoline core with phenyl, styryl, and phenylbutadienyl
moieties was predicted by means of TD-DFT calculations to produce
probes with tunable photoexcitation energies and excited states possessing
charge-transfer character. Optical spectroscopy identified several
synthesized probes that are nonemissive in aqueous solutions and exhibit
emission enhancements in solvents of low polarity, suggesting good
performance as turn-on fluorophores. Ligand-induced ERBB2 phosphorylation
assays demonstrate that despite chemical modification to the quinazoline
core these probes still function as ERBB2 inhibitors in MCF7 cells.
Two probes were found to exhibit ERBB2-induced fluorescence, demonstrating
the utility of these probes as turn-on, fluoroescent kinase inhibitors.
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Affiliation(s)
- Jyothi Dhuguru
- Department of Chemistry, University of Miami , 1301 Memorial Drive, Coral Gables, Florida 33146, United States
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22
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Liu H, Song Q, Yang Y, Li Y, Wang H. Theoretical study on absorption and emission spectra of adenine analogues. J Mol Model 2014; 20:2100. [PMID: 24633764 DOI: 10.1007/s00894-014-2100-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 12/01/2013] [Indexed: 11/27/2022]
Abstract
Fluorescent nucleoside analogues have attracted much attention in studying the structure and dynamics of nucleic acids in recent years. In the present work, we use theoretical calculations to investigate the structural and optical properties of four adenine analogues (termed as A1, A2, A3, and A4), and also consider the effects of aqueous solution and base pairing. The results show that the fluorescent adenine analogues can pair with thymine to form stable H-bonded WC base pairs. The excited geometries of both adenine analogues and WC base pairs are similar to the ground geometries. The absorption and emission maxima of adenine analogues are greatly red shifted compared with nature adenine, the oscillator strengths of A1 and A2 are stronger than A3 and A4 in both absorption and emission spectra. The calculated low-energy peaks in the absorption spectra are in good agreement with the experimental data. In general, the aqueous solution and base pairing can slightly red-shift both the absorption and emission maxima, and can increase the oscillator strengths of absorption spectra, but significantly decrease the oscillator strengths of A3 in emission spectra.
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Affiliation(s)
- Hongxia Liu
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
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23
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Khalifa MEA, Amin MA, Mosselhi MAN. Site selectivity in reactions of hydrazonoyl halides with heterocycles containing amino and thione groups leading to fused heterocycles of potential antimicrobial activity. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2014. [DOI: 10.1134/s1068162014010075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Tanpure AA, Pawar MG, Srivatsan SG. Fluorescent Nucleoside Analogs: Probes for Investigating Nucleic Acid Structure and Function. Isr J Chem 2013. [DOI: 10.1002/ijch.201300010] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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25
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Kovaliov M, Segal M, Fischer B. Fluorescent p-substituted-phenyl-imidazolo-cytidine analogues. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Nucleosides 8 [18]: Ribosylation of Fused Quinazolines—Synthesis of New [1,2,4]Triazolo[5,1-b]- and [1,2,4]Triazino[3,2-b]quinazoline Nucleosides of Fluorescence Interest. J CHEM-NY 2013. [DOI: 10.1155/2013/612756] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
[1,2,4]Triazolo[5,1-b]- and [1,2,4]triazino[3,2-b] quinazolines have been ribosylated by coupling with 1-O-acetyl-2,3,5-tri-O-benzoyl-β-D-ribofuranose and by using the silylation method, followed by debenzoylation by methanolic sodium methoxide to afford the corresponding free N-nucleosides. Nucleosides obtained have been identified by their spectral analysis. From the UV-visible and fluorescence studies of some nucleosides synthesized, it is found that they have fluorescence properties.
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Moreno A, Knee J, Mukerji I. Applying 6-methylisoxanthopterin-enhanced fluorescence to examine protein-DNA interactions in the picomolar range. Biochemistry 2012; 51:6847-59. [PMID: 22849374 DOI: 10.1021/bi300466d] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Incorporation of fluorescent nucleoside analogues into duplex DNA usually leads to a reduction in quantum yield, which significantly limits their potential use and application. We have identified two pentamer DNA sequences containing 6-methylisoxanthopterin (6-MI) (ATFAA and AAFTA, where F is 6-MI) that exhibit significant enhancement of fluorescence upon formation of duplex DNA with quantum yields close to that of monomeric 6-MI. The enhanced fluorescence dramatically increases the utility and sensitivity of the probe and is used to study protein-DNA interactions of nanomolar specificity in this work. The increased sensitivity of 6-MI allows anisotropy binding measurements to be performed at DNA concentrations of 1 nM and fluorescence intensity measurements at 50 pM DNA. The ATFAA sequence was incorporated into DNA constructs to measure the binding affinity of four different protein-DNA interactions that exhibit sequence-specific and non-sequence-specific recognition. In all cases, the K(d) values obtained were consistent with previously reported values measured by other methods. Time-resolved and steady-state fluorescence measurements demonstrate that 6-MI fluorescence is very sensitive to local distortion and reports on different degrees of protein-induced perturbations with single-base resolution, where the largest changes occur at the site of protein binding.
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Affiliation(s)
- Andrew Moreno
- Departments of Chemistry and Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, 52 Lawn Avenue, Middletown, CT 06459, USA
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Dierckx A, Miannay FA, Ben Gaied N, Preus S, Björck M, Brown T, Wilhelmsson LM. Quadracyclic adenine: a non-perturbing fluorescent adenine analogue. Chemistry 2012; 18:5987-97. [PMID: 22437923 DOI: 10.1002/chem.201103419] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Indexed: 12/26/2022]
Abstract
Fluorescent-base analogues (FBAs) comprise a group of increasingly important molecules for the investigation of nucleic acid structure and dynamics as well as of interactions between nucleic acids and other molecules. Here, we report on the synthesis, detailed spectroscopic characterisation and base-pairing properties of a new environment-sensitive fluorescent adenine analogue, quadracyclic adenine (qA). After developing an efficient route of synthesis for the phosphoramidite of qA it was incorporated into DNA in high yield by using standard solid-phase synthesis procedures. In DNA qA serves as an adenine analogue that preserves the B-form and, in contrast to most currently available FBAs, maintains or even increases the stability of the duplex. We demonstrate that, unlike fluorescent adenine analogues, such as the most commonly used one, 2-aminopurine, and the recently developed triazole adenine, qA shows highly specific base-pairing with thymine. Moreover, qA has an absorption band outside the absorption of the natural nucleobases (>300 nm) and can thus be selectively excited. Upon excitation the qA monomer displays a fluorescence quantum yield of 6.8 % with an emission maximum at 456 nm. More importantly, upon incorporation into DNA the fluorescence of qA is significantly less quenched than most FBAs. This results in quantum yields that in some sequences reach values that are up to fourfold higher than maximum values reported for 2-aminopurine. To facilitate future utilisation of qA in biochemical and biophysical studies we investigated its fluorescence properties in greater detail and resolved its absorption band outside the DNA absorption region into distinct transition dipole moments. In conclusion, the unique combination of properties of qA make it a promising alternative to current fluorescent adenine analogues for future detailed studies of nucleic acid-containing systems.
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Affiliation(s)
- Anke Dierckx
- Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, 41296 Gothenburg, Sweden
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29
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Kodali G, Narayanan M, Stanley RJ. Excited-state electronic properties of 6-methylisoxanthopterin (6-MI): an experimental and theoretical study. J Phys Chem B 2012; 116:2981-9. [PMID: 22276652 DOI: 10.1021/jp2110083] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
6-Methylisoxanthopterin (6-MI) is a pteridine-based guanine analog that has a red-shifted absorption and high fluorescence quantum yield. Its Watson-Crick base-pairing and base stacking properties are similar to guanine. The fluorescence quantum yield of 6-MI is sensitive to its nearest neighbors and base stacking, making it a very useful real-time probe of DNA structure. The fundamental photophysics underlying this fluorescence quenching by base stacking is not well understood. We have explored the excited-state electronic structure of the 6-MI in frozen 77 K LiCl glasses using Stark spectroscopy. These measurements yielded the direction and degree of charge redistribution for the S(0)→S(1) transition as manifested in the difference dipole moment, Δμ(01), and difference static polarizability, TrΔα. TDDFT (time-dependent density functional theory) was employed to calculate the transition energy, oscillator strength, and the dipole moments of the ground and lowest optically bright excited state of 6-MI (S(0)→S(1)). The direction of Δμ(01) was assigned in the molecular frame based on the Stark data and calculations. These results suggest that the C4═O and C2-NH(2) groups are electron-deficient in the excited state, a very different outcome compared with guanine. This implies that Watson-Crick hydrogen bonding in 6-MI may be modulated by absorption of a photon so as to strengthen base pairing, if only transiently. Solvatochromism was also obtained for the absorption and emission spectra of 6-MI in various solvents and compared with the Stark spectroscopic results using both the Lippert-Mataga and Bakhshiev models.
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Affiliation(s)
- Goutham Kodali
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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30
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Datta K, Johnson NP, Villani G, Marcus AH, von Hippel PH. Characterization of the 6-methyl isoxanthopterin (6-MI) base analog dimer, a spectroscopic probe for monitoring guanine base conformations at specific sites in nucleic acids. Nucleic Acids Res 2011; 40:1191-202. [PMID: 22009678 PMCID: PMC3273825 DOI: 10.1093/nar/gkr858] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We here characterize local conformations of site-specifically placed pairs of guanine (G) residues in RNA and DNA, using 6-methyl isoxanthopterin (6-MI) as a conformational probe. 6-MI is a base analog of G and spectroscopic signals obtained from pairs of adjacent 6-MI residues reflect base–base interactions that are sensitive to the sequence context, local DNA conformation and solvent environment of the probe bases. CD signals show strong exciton coupling between stacked 6-MI bases in double-stranded (ds) DNA; this coupling is reduced in single-stranded (ss) DNA sequences. Solvent interactions reduce the fluorescence of the dimer probe more efficiently in ssDNA than dsDNA, while self-quenching between 6-MI bases is enhanced in dsDNA. 6-MI dimer probes closely resemble adjacent GG residues, in that these probes have minimal effects on the stability of dsDNA and on interactions with solvent additive betaine. They also serve as effective template bases, although further polymerase-dependent extension of DNA primers past 6-MI template bases is significantly inhibited. These probes are also used to monitor DNA ‘breathing’ at model replication forks. The 6-MI dimer probe can serve in many contexts as a useful tool to investigate GG conformations at specific sites within the nucleic acid frameworks of functioning macromolecular machines in solution.
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Affiliation(s)
- Kausiki Datta
- Department of Chemistry and Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
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31
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Serrano MP, Vignoni M, Dántola ML, Oliveros E, Lorente C, Thomas AH. Emission properties of dihydropterins in aqueous solutions. Phys Chem Chem Phys 2011; 13:7419-25. [PMID: 21409193 DOI: 10.1039/c0cp02912b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Pterins belong to a class of heterocyclic compounds present in a wide range of living systems and accumulate in the skin of patients affected by vitiligo, a depigmentation disorder. The study of the emission of 7,8-dihydropterins is difficult because these compounds are more or less unstable in the presence of O(2) and their solutions are contaminated with oxidized pterins which have much higher fluorescence quantum yields (Φ(F)). In this work, the emission properties of six compounds of the dihydropterin family (6-formyl-7,8-dihydropterin (H(2)Fop), sepiapterin (Sep), 7,8-dihydrobiopterin (H(2)Bip), 7,8-dihydroneopterin (H(2)Nep), 6-hydroxymethyl-7,8-dihydropterin (H(2)Hmp), and 6-methyl-7,8-dihydropterin (H(2)Mep)) have been studied in aqueous solution. The fluorescence characteristics (spectra, Φ(F), lifetimes (τ(F))) of the neutral form of these compounds have been investigated using the single-photon-counting technique. Φ(F) and τ(F) values obtained lie in the ranges 3-9 × 10(-3) and 0.18-0.34 ns, respectively. The results are compared to those previously reported for oxidized pterins.
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Affiliation(s)
- Mariana P Serrano
- INIFTA, Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CCT La Plata-CONICET., C.C. 16, Suc. 4, (1900) La Plata, Argentina
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Dierckx A, Dinér P, El-Sagheer AH, Kumar JD, Brown T, Grøtli M, Wilhelmsson LM. Characterization of photophysical and base-mimicking properties of a novel fluorescent adenine analogue in DNA. Nucleic Acids Res 2011; 39:4513-24. [PMID: 21278417 PMCID: PMC3105426 DOI: 10.1093/nar/gkr010] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
To increase the diversity of fluorescent base analogues with improved properties, we here present the straightforward click-chemistry-based synthesis of a novel fluorescent adenine-analogue triazole adenine (AT) and its photophysical characterization inside DNA. AT shows promising properties compared to the widely used adenine analogue 2-aminopurine. Quantum yields reach >20% and >5% in single- and double-stranded DNA, respectively, and show dependence on neighbouring bases. Moreover, AT shows only a minor destabilization of DNA duplexes, comparable to 2-aminopurine, and circular dichroism investigations suggest that AT only causes minimal structural perturbations to normal B-DNA. Furthermore, we find that AT shows favourable base-pairing properties with thymine and more surprisingly also with normal adenine. In conclusion, AT shows strong potential as a new fluorescent adenine analogue for monitoring changes within its microenvironment in DNA.
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Affiliation(s)
- Anke Dierckx
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, University of Gothenburg, S-41296 Gothenburg, Sweden
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Schlitt KM, Millen AL, Wetmore SD, Manderville RA. An indole-linked C8-deoxyguanosine nucleoside acts as a fluorescent reporter of Watson-Crick versus Hoogsteen base pairing. Org Biomol Chem 2011; 9:1565-71. [PMID: 21240404 DOI: 10.1039/c0ob00883d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pyrrole- and indole-linked C(8)-deoxyguanosine nucleosides act as fluorescent reporters of H-bonding specificity. Their fluorescence is quenched upon Watson-Crick H-bonding to dC, while Hoogsteen H-bonding to G enhances emission intensity. The indole-linked probe is ∼ 10-fold brighter and shows promise as a fluorescent reporter of Hoogsteen base pairing.
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Affiliation(s)
- Katherine M Schlitt
- Department of Chemistry, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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Kritsky MS, Telegina TA, Vechtomova YL, Kolesnikov MP, Lyudnikova TA, Golub OA. Excited flavin and pterin coenzyme molecules in evolution. BIOCHEMISTRY (MOSCOW) 2010; 75:1200-16. [DOI: 10.1134/s0006297910100020] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Petroselli G, Dántola ML, Cabrerizo FM, Lorente C, Braun AM, Oliveros E, Thomas AH. Quenching of the fluorescence of aromatic pterins by deoxynucleotides. J Phys Chem A 2010; 113:1794-9. [PMID: 19199487 DOI: 10.1021/jp8101496] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Steady-state and time-resolved studies of the fluorescence of four aromatic unconjugated pterins (pterin (Ptr), 6-(hydroxymethyl)pterin (Hmp), 6-methylpterin (Mep), and 6,7-dimethylpterin (Dmp)) in aqueous solutions in the presence of different nucleotides (2'-deoxyguanosine 5'-monophosphate (dGMP), 2'-deoxyadenosine 5'-monophosphate (dAMP), and 2'-deoxycytosine 5'-monophosphate (dCMP)) have been performed using the single-photon counting technique. The singlet excited states of acid forms of pterins are deactivated by purine nucleotides (dGMP and dAMP) via a combination of dynamic and static processes. The efficiency of the dynamic quenching is high, independently of the nature of the purine base of the nucleotide and of the chemical structure of the substituents linked to the pterin moiety. Analysis of the static quenching indicates that ground-state association between pterins and purine nucleotides takes place, but the formation of the corresponding complexes is significant only at relatively high reactant concentrations. The quenching of the fluorescence of acid forms of pterin derivatives by dCMP, a pyrimidine nucleotide, is slightly less efficient than the quenching by purine nucleotides and is purely dynamic. In alkaline media, the fluorescence quenching is much less efficient than in acidic media, the deactivation by purine nucleotides being purely dynamic, whereas quenching by dCMP is negligible. Possible mechanisms for the quenching of fluorescence of pterin derivatives by the different nucleotides are discussed.
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Affiliation(s)
- Gabriela Petroselli
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas, Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CCT La Plata-CONICET, Boulevard 113 y 64, 1900 La Plata, Argentina
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36
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Zheng JY, Feng XM, Zhang SF, Zhao YF. Design and synthesis of novel fluorescently labelled nucleosides. J Labelled Comp Radiopharm 2010. [DOI: 10.1002/jlcr.1813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Narayanan M, Kodali G, Singh V, Xing Y, Hawkins ME, Stanley RJ. Differential fluorescence quenching of fluorescent nucleic acid base analogues by native nucleic acid monophosphates. J Phys Chem B 2010; 114:5953-63. [PMID: 20387838 DOI: 10.1021/jp1011507] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescent nucleic acid base analogues (FBAs) are used widely as probes of DNA and RNA structure and dynamics. Of increasing utility are the pteridone adenosine analogues (6MAP, DMAP) and pteridine guanosine analogues (3MI, 6MI). These FBAs (collectively referred to as PTERs) are useful, in part, because their fluorescence quantum yields, Phi(f), are modulated by base stacking with native bases (NBs), making them sensitive reporters of DNA structure. The quenching mechanism has been hypothesized to be photoinduced electron transfer following selective excitation of the FBA, but hard evidence for this has been lacking. The degree of quenching shows some dependence on the neighboring bases, but there has been no real determination as to whether FBA*:NB complexes satisfy the basic thermodynamic requirement for spontaneous PET: a negative free energy for the electron transfer reaction. Indeed, quenching may result from entirely different mechanisms. To address these questions, Stern-Volmer (S-V) experiments were performed using the native-base monophosphate nucleotides (NMPs) GMP, AMP, CMP, and dTMP in aqueous solutions as quenchers to obtain quenching rate constants, k(q). Cyclic voltammetry (CV) and optical absorption and emission data of the PTERS were obtained in aprotic organic solvents. These data were used to obtain excited-state redox potentials from which electron transfer free energies were derived using the Rehm-Weller equation. The reorganization energies for PET were obtained using the Scandola-Balzani equation, taking into account the free energy contribution due to water. 6MAP*, DMAP*, and 3MI* gave negative free energies between -0.1 and -0.2 eV and reorganization energies of about 0.13 eV. They all displayed ET activation energies below the accessible thermal energy (0.038 eV = 3/2k(B)T, where k(B) is Boltzmann's constant) for all NMPs with the exception of CMP, whose activation barrier was only about 35% higher (approximately 0.05 eV). Thus, we conclude that these PTERs act as electron acceptors and promote NMP oxidation. However, 6MI* had positive ET free energies for all NMPs with the exception of GMP (and then only for nucleobase oxidation). The magnitudes of these free energies (> or = 0.45 eV for AMP, CMP, and dTMP) suggest that 6MI* may not quenched by PET.
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Affiliation(s)
- Madhavan Narayanan
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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Abstract
The use of fluorescent nucleic acid base analogues is becoming increasingly important in the fields of biology, biochemistry and biophysical chemistry as well as in the field of DNA nanotechnology. The advantage of being able to incorporate a fluorescent probe molecule close to the site of examination in the nucleic acid-containing system of interest with merely a minimal perturbation to the natural structure makes fluorescent base analogues highly attractive. In recent years, there has been a growing interest in developing novel candidates in this group of fluorophores for utilization in various investigations. This review describes the different classes of fluorophores that can be used for studying nucleic acid-containing systems, with an emphasis on choosing the right kind of probe for the system under investigation. It describes the characteristics of the large group of base analogues that has an emission that is sensitive to the surrounding microenvironment and gives examples of investigations in which this group of molecules has been used so far. Furthermore, the characterization and use of fluorescent base analogues that are virtually insensitive to changes in their microenvironment are described in detail. This group of base analogues can be used in several fluorescence investigations of nucleic acids, especially in fluorescence anisotropy and fluorescence resonance energy transfer (FRET) measurements. Finally, the development and characterization of the first nucleic base analogue FRET pair, tC(O)-tC(nitro), and its possible future uses are discussed.
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Jungmann O, Pfleiderer W. Nucleosides part LXVI I: synthesis of 4-amino-7(8H)pteridinone-N8-nucleosides-structural analogs of adenosine. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2010; 28:550-85. [PMID: 20183602 DOI: 10.1080/15257770903054241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Various 4-amino-7(8H)pteridones (6, 12, 14, 15, 20, 22) have been glycosylated with 1-chloro-2'-deoxy-D-ribofuranose derivatives (25, 26) applying the new DBU-salt method to form the N(8)-2'-deoxy-D-ribofuranosides (27-36) which can be regarded as 2'-deoxyadenosine analogs. Analogously reacted the 2-N,N-dimethyl-amino-methyleneimino-7(8H)pteridones (43-48) to give preferentially the corresponding N(8)-beta-D-anomers (49-55). Ribosylation with 1-bromo-2,3,5-tri-O-benzoyl-a-D-ribofuranose (56) proceeded as well with 6, 12, 15, 45, and 46 to yield to N(8)-beta-D-ribofuranosides 57-61. Sugar deprotection led to the free N(8)-2'-deoxy-beta-D-ribofuranosides 37-42 and N(8)-beta-D-ribofurano-sides 62-65, respectively. Glycosylations via the silyl-method under Vorbruggen conditions led with 6, 12 and 15 to the same results, however, 4-amino-6-phenyl-7(8H)pteridone (14) reacted differently forming the N(1)-beta-D-ribofuranosides (71, 79) and the N(1)-2'-deoxy-alpha-and ss-D-ribofuranosides 73, 74, 77, 78. The assignments of the structures have been achieved by (1)H-NMR- and UV-spectra. C,H,N-elemental analyses account for the composition.
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Affiliation(s)
- Oliver Jungmann
- Fachbereich Chemie, Universitat Konstanz, Postfach, Konstanz, Germany
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40
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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: 681] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [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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41
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Goswami S, Hazra A, Jana S, Fun HK. Recognition study of substituted benzoic acids by 7-substituted pterin receptors in solution and solid phases. CrystEngComm 2010. [DOI: 10.1039/b917092h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Kodali G, Kistler KA, Narayanan M, Matsika S, Stanley RJ. Change in Electronic Structure upon Optical Excitation of 8-Vinyladenosine: An Experimental and Theoretical Study. J Phys Chem A 2009; 114:256-67. [DOI: 10.1021/jp908055h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Goutham Kodali
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Kurt A. Kistler
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Madhavan Narayanan
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Robert J. Stanley
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
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43
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Steinlin T, Vasella A. Acylation of a 6-(Methylamino)-5-nitrosopyrimidine and 1,3-Dipolar Cycloaddition of an 8-MethylisoxanthopterinN(5)-Oxide. Synthesis ofC(6),N(8)-Disubstituted Isoxanthopterins. Helv Chim Acta 2009. [DOI: 10.1002/hlca.200900009] [Citation(s) in RCA: 7] [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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44
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Zhang L, Bu Y. Photophysical Characters of Rationally Designed Hetero-Ring-Expanded Guanine Analogues and Effect of Cytosine Pairing. J Phys Chem B 2008; 112:10723-31. [DOI: 10.1021/jp802556a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laibin Zhang
- The Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P. R. China
| | - Yuxiang Bu
- The Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P. R. China
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45
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Abstract
This chapter is focused on the fluorescent pteridine guanine analogs, 3MI and 6MI and on the pteridine adenine analog, 6MAP. A brief overview of commonly used methods to fluorescently label oligonucleotides reveals the role the pteridines play in the extensive variety of available probes. We describe the fluorescence characteristics of the pteridine probes as monomers and incorporated into DNA and review a variety of applications including changes in fluorescence intensity, anisotropies, time resolved studies, two photon excitation and single molecule detection.
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46
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Yang K, Stanley RJ. The extent of DNA deformation in DNA photolyase-substrate complexes: a solution state fluorescence study. Photochem Photobiol 2007; 84:741-9. [PMID: 18086248 DOI: 10.1111/j.1751-1097.2007.00251.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Cyclobutylpyrimidine dimers (CPDs) are the major UV photoproduct formed in DNA containing adjacent pyrimidines. These lesions can be repaired by DNA photolyase, a flavoprotein that utilizes blue light in a direct reversal of the cyclobutane ring. Previous studies have shown that the CPD is base flipped into the protein, with concomitant disruption of the substrate around the CPD. In this study, we use a fluorescent cytidine analog, pyrrolo-dC (PC), to probe how far base flipping propagates along the duplex. From these measurements, the degree of base destacking in the two bases flanking the adenines opposing the CPD appears to be minimal, which was consistent with the protein:substrate crystal structure. Fluorescence-detected melting temperatures for duplexes with and without a CPD were obtained, suggesting that a 5'-pyrimidine-PC-purine-3' motif is more stable than the 5'-purine-PC-pyrimidine-3' motif. This stability trend was reflected in the fluorescence intensities of ss-PC oligos but not for duplexes. The melting point depression due to the PC probe was found to be comparable to other popular fluorescent base analogs.
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Affiliation(s)
- Kongsheng Yang
- Department of Chemistry, Temple University, Philadelphia, PA, USA
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47
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Sandin P, Börjesson K, Li H, Mårtensson J, Brown T, Wilhelmsson LM, Albinsson B. Characterization and use of an unprecedentedly bright and structurally non-perturbing fluorescent DNA base analogue. Nucleic Acids Res 2007; 36:157-67. [PMID: 18003656 PMCID: PMC2248743 DOI: 10.1093/nar/gkm1006] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
This article presents the first evidence that the DNA base analogue 1,3-diaza-2-oxophenoxazine, tC(O), is highly fluorescent, both as free nucleoside and incorporated in an arbitrary DNA structure. tC(O) is thoroughly characterized with respect to its photophysical properties and structural performance in single- and double-stranded oligonucleotides. The lowest energy absorption band at 360 nm (epsilon = 9000 M(-1) cm(-1)) is dominated by a single in-plane polarized electronic transition and the fluorescence, centred at 465 nm, has a quantum yield of 0.3. When incorporated into double-stranded DNA, tC(O) shows only minor variations in fluorescence intensity and lifetime with neighbouring bases, and the average quantum yield is 0.22. These features make tC(O), on average, the brightest DNA-incorporated base analogue so far reported. Furthermore, it base pairs exclusively with guanine and causes minimal perturbations to the native structure of DNA. These properties make tC(O) a promising base analogue that is perfectly suited for e.g. photophysical studies of DNA interacting with macromolecules (proteins) or for determining size and shape of DNA tertiary structures using techniques such as fluorescence anisotropy and fluorescence resonance energy transfer (FRET).
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Affiliation(s)
- Peter Sandin
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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48
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Nonogawa M, Pack SP, Arai T, Endo N, Sommani P, Kodaki T, Kotake Y, Makino K. Synthesis of 6-formylpterin nucleoside analogs and their ROS generation activities in the presence of NADH in the dark. Org Biomol Chem 2007; 5:3314-9. [PMID: 17912384 DOI: 10.1039/b710466a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We demonstrated previously that 3-position-modified 6-formylpterin (6FP) derivatives produce reactive oxygen species (ROS) such as hydrogen peroxide (H(2)O(2)) from oxygen in the presence of NADH in the dark. It has been shown that 6FP derivatives markedly generate ROS, which gives rise to their particular physiological activities, such as induction of apoptosis in cellular and living systems, suggesting that such compounds provide a hint for the design of a ROS controlling agent in vivo. However, it is not well understood why such unique activities appear on chemical modification. In the present study, in order to see the effect on ROS generation activity in the dark by the modification of the 1-position in 6FP, we have developed a new synthetic procedure for nucleoside analogs of 6FP and prepared 1-(beta-d-ribofuranosyl)-2-(N,N-diethylaminomethyleneamino)-6-formylpteridin-4-one (RDEF) and 1-(beta-d-ribofuranosyl)-2-(piperidine-1-ylmethyleneamino)-6-formylpteridin-4-one (RPIF) in which the 1-position of 6FP is glycosylated. At pH 7.4, NADH was spontaneously oxidized to NAD(+) in the presence of RDEF in the dark. Using electron paramagnetic resonance analysis coupled with the spin trapping technique, we show that O(2) was converted to H(2)O(2)via superoxide anion radical ( O(2)(-)) during this reaction. The modification of the 1-position of 6FP did not cancel ROS generation activities, which were demonstrated in 3-position-modified 6FPs. Since the 6FP derivatives developed in the present study have a ribose moiety, these compounds can be subjected to further derivatization, such as incorporation into oligonucleotides, oligosaccharides, proteins, or any other compounds that recognize and interact with specific biomolecules, and therefore would be useful in pharmaceutical investigations that need generation of appropriate and controllable amounts of ROS in vivo.
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Affiliation(s)
- Mitsuru Nonogawa
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji 611-0011, Japan
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49
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Shi ZD, Wu H, Ruddy B, Griffiths GL. Imaging Probe Development Center: a National Institutes of Health core synthesis resource for imaging probes. JOURNAL OF BIOMEDICAL OPTICS 2007; 12:051502. [PMID: 17994866 DOI: 10.1117/1.2778702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The Imaging Probe Development Center (IPDC) has been set up under the auspices of the National Institutes of Health (NIH) Roadmap as part of the molecular libraries and imaging initiatives. It comprises a core synthesis facility dedicated to the preparation of imaging probes, initially for intramural NIH scientists, and later, for the extramural scientific community. The facility opened fully in late 2006, in refurbished laboratories in Rockville, Maryland, and a staff of around a dozen was recruited into place by early 2007; the director was hired in late 2005. The IPDC provides a mechanism for the production of sensitive probes for use by imaging scientists who cannot obtain such probes commercially. The probes to be made will encompass all major imaging modalities including radionuclide, magnetic resonance, and optical. The operation of the IPDC is outlined, together with the results of interim achievements while the IPDC maintained a small temporary laboratory in Bethesda. As of December 2006, a total of eleven probe compositions had been made, and several of these are described with particular mention of those probes intended for use in optical applications.
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Affiliation(s)
- Zhen-Dan Shi
- National Institutes of Health, Imaging Probe Development Center, National Heart, Lung, and Blood Institute, 9800 Medical Center Drive, Building 2B, Suite 3042, Bethesda, Maryland 20892, USA
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50
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Yang K, Matsika S, Stanley RJ. 6MAP, a fluorescent adenine analogue, is a probe of base flipping by DNA photolyase. J Phys Chem B 2007; 111:10615-25. [PMID: 17696385 DOI: 10.1021/jp071035p] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cyclobutylpyrimidine dimers (CPDs) are formed between adjacent pyrimidines in DNA when it absorbs ultraviolet light. CPDs can be directly repaired by DNA photolyase (PL) in the presence of visible light. How PL recognizes and binds its substrate is still not well understood. Fluorescent nucleic acid base analogues are powerful probes of DNA structure. We have used the fluorescent adenine analogue 6MAP, a pteridone, to probe the local double helical structure of the CPD substrate when bound by photolyase. Duplex melting temperatures were obtained by both UV-vis absorption and fluorescence spectroscopies to ascertain the effect of the probe and the CPD on DNA stability. Steady-state fluorescence measurements of 6MAP-containing single-stranded and doubled-stranded oligos with and without protein show that the local region around the CPD is significantly disrupted. 6MAP shows a different quenching pattern compared to 2-aminopurine, another important adenine analogue, although both probes show that the structure of the complementary strand opposing the 5'-side of the CPD lesion is more destacked than that opposing the 3'-side in substrate/protein complexes. We also show that 6MAP/CPD duplexes are substrates for PL. Vertical excitation energies and transition dipole moment directions for 6MAP were calculated using time-dependent density functional theory. Using these results, the Förster resonance energy transfer efficiency between the individual adenine analogues and the oxidized flavin cofactor was calculated to account for the observed intensity pattern. These calculations suggest that energy transfer is highly efficient for the 6MAP probe and less so for the 2Ap probe. However, no experimental evidence for this process was observed in the steady-state emission spectra.
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Affiliation(s)
- Kongsheng Yang
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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