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15 results on '"Eimer Tuite"'

1. Role of Order in the Mechanism of Charge Transport across Single-Stranded and Double-Stranded DNA Monolayers in Tunnel Junctions

Author

Christian A. Nijhuis, Edward A. Wilkinson, Andrew R. Pike, Ayelet Vilan, Anton Tadich, Lily Bailey, Senthil Kumar Karuppannan, Ziyu Zhang, Eimer Tuite, Dongchen Qi, Nipun Kumar Gupta, James H. R. Tucker, Hybrid Materials for Opto-Electronics, and MESA+ Institute

Subjects
Base pair, UT-Hybrid-D, DNA, Single-Stranded, 02 engineering and technology, Conductivity, 010402 general chemistry, 01 natural sciences, Biochemistry, Catalysis, Article, chemistry.chemical_compound, Molecular wire, Colloid and Surface Chemistry, Monolayer, Electrical conductor, Quantum tunnelling, Electric Conductivity, Temperature, Charge (physics), General Chemistry, 021001 nanoscience & nanotechnology, 0104 chemical sciences, chemistry, Chemical physics, Nucleic Acid Conformation, 0210 nano-technology, DNA
Abstract

Deoxyribonucleic acid (DNA) has been hypothesized to act as a molecular wire due to the presence of an extended π-stack between base pairs, but the factors that are detrimental in the mechanism of charge transport (CT) across tunnel junctions with DNA are still unclear. Here we systematically investigate CT across dense DNA monolayers in large-area biomolecular tunnel junctions to determine when intrachain or interchain CT dominates and under which conditions the mechanism of CT becomes thermally activated. In our junctions, double-stranded DNA (dsDNA) is 30-fold more conductive than single-stranded DNA (ssDNA). The main reason for this large change in conductivity is that dsDNA forms ordered monolayers where intrachain tunneling dominates, resulting in high CT rates. By varying the temperature T and the length of the DNA fragments in the junctions, which determines the tunneling distance, we reveal a complex interplay between T, the length of DNA, and structural order on the mechanism of charge transport. Both the increase in the tunneling distance and the decrease in structural order result in a change in the mechanism of CT from coherent tunneling to incoherent tunneling (hopping). Our results highlight the importance of the interplay between structural order, tunneling distance, and temperature on the CT mechanism across DNA in molecular junctions.

Published
2021

2. Diastereomeric Crowding Effects in the Competitive DNA Intercalation of Ru(phenanthroline)2dipyridophenazine2+ Enantiomers

Author

Maria Abrahamsson, Anna K. F. Mårtensson, Eimer Tuite, and Per Lincoln

Subjects
010405 organic chemistry, Chemistry, Phenanthroline, Diastereomer, chemistry.chemical_element, Isothermal titration calorimetry, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, Ruthenium, Inorganic Chemistry, Crystallography, chemistry.chemical_compound, DNA Intercalation, Molecule, Titration, Physical and Theoretical Chemistry, Binding site
Abstract

The biexponential excited-state emission decay characteristic of DNA intercalated tris-bidentate dppz-based ruthenium complexes of the general form Ru(L)2dppz2+ has previously been explained by a binding model with two distinct geometry orientations of the bound ligands, with a distinct lifetime associated with each orientation. However, it has been found that upon DNA binding of Ru(phen)2dppz2+ the fractions of short and long lifetimes are strongly dependent on environmental factors such as salt concentration and, in particular, temperature. Analyzing isothermal titration calorimetry for competitive binding of Ru(phen)2dppz2+ enantiomers to poly(dAdT)2, we find that a consistent binding model must assume that the short and long lifetimes states of intercalated complexes are in equilibrium and that this equilibrium is altered when neighboring bound ligands affect each other. The degree of intercomplex binding is found to be a subtle manifestation of several attractive and repulsive factors that are highly likely to directly reflect the strong diastereomeric difference in the binding enthalpy and entropy values. In addition, as the titration progresses and the binding sites on the DNA lattice become increasingly occupied, a general resistance for the saturation of the binding sites is observed, suggesting diastereomeric crowding of the neighboring bound ligands.

Published
2019
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3. Duplex Healing of Selectively Thiolated Guanosine Mismatches through a Cd2+ Chemical Stimulus

Author

Eimer Tuite, Michael J. Hall, Colette J. Whitfield, Andrew Houlton, Andrew R. Pike, Samantha M. L. Lunn, Agnieszka K. Bronowska, and Samira Hribesh

Subjects
010405 organic chemistry, DNA damage, Organic Chemistry, Stacking, Guanosine, 010402 general chemistry, 01 natural sciences, Biochemistry, Oligomer, 0104 chemical sciences, Nucleobase, chemistry.chemical_compound, chemistry, Duplex (building), Biophysics, Molecular Medicine, Destabilisation, Molecular Biology, DNA
Abstract

The on-column selective conversion of guanosine to thioguanosine (tG) yields modified oligomers that exhibit destabilisation over the fully complementary duplex. Restoration to a stabilised duplex is induced through thio-directed Cd2+ coordination; a route for healing DNA damage. Short oligomers are G-specifically thiolated through a modified on-column protocol without the need for costly thioguanosine phosphoramidites. Addition of Cd2+ ions to a duplex containing a highly disrupted tG central mismatch sequence, 3'-A6 tG4 T6 -5', suggests a (tG)8 Cd2 central coordination regime, resulting in increased base stacking and duplex stability. Equilibrium molecular dynamic calculations support the hypothesis of metal-induced healing of the thiolated duplex. The 2 nm displacement of the central tG mismatched region is dramatically reduced after the addition of a chemical stimuli, Cd2+ ions, returning to a minimized fluctuational state comparable to the unmodified fully complementary oligomer.

Published
2018
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4. Self-Priming Enzymatic Fabrication of Multiply Modified DNA

Author

Bernard A. Connolly, Rachel C. Little, Eimer Tuite, Kasid Khan, Andrew R. Pike, Colette J. Whitfield, and Kuniharu Ijiro

Subjects
Stereochemistry, DNA polymerase, 010402 general chemistry, 01 natural sciences, Polymerase Chain Reaction, Catalysis, Nucleobase, law.invention, chemistry.chemical_compound, law, Nucleotide, DNA slippage, Polymerase, Polymerase chain reaction, chemistry.chemical_classification, biology, Base Sequence, 010405 organic chemistry, Chemistry, Nucleotides, Organic Chemistry, General Chemistry, DNA, 0104 chemical sciences, Enzyme, Duplex (building), Modified DNA, biology.protein, Nucleic Acid Conformation, Small molecule binding
Abstract

The self-priming synthesis of multiply modified DNA by the extension of repeating unit duplex “oligoseeds” provides a source of versatile DNA. Sterically-demanding nucleotides 5-Br-dUTP, 7-deaza-7-I-dATP, 6-S-dGTP, 5-I-dCTP as well as 5-(octadiynyl)-dCTP were incorporated into two extending oligoseeds; [GATC]5/[GATC]5 and [A4G]4/[CT4]4. The products contained modifications on one or both strands of DNA, demonstrating their recognition by the polymerase as both template (reading) and substrate (writing). Nucleobase modifications that lie in the major groove were reliably read and written by the polymerase during the extension reaction, even when bulky or in contiguous sequences. Repeat sequence DNA over 500 bp long, bearing four different modified units was produced by this method. The number, position and type of modification, as well as the overall length of the DNA can be controlled to yield designer DNA that offers sequence-determined sites for further chemical adaptations, targeted small molecule binding studies, or sensing and sequencing applications.

Published
2018

5. Structural Heterogeneity in Polynucleotide-Facilitated Assembly of Phenothiazine Dyes

Author

Eimer Tuite and Bengt Nordén

Subjects
Circular dichroism, Intercalation (chemistry), Polynucleotides, 010402 general chemistry, Photochemistry, Linear dichroism, 01 natural sciences, Thionine, chemistry.chemical_compound, Phenothiazine, 0103 physical sciences, Materials Chemistry, Animals, Physical and Theoretical Chemistry, Fluorescent Dyes, 010304 chemical physics, Molecular Structure, Circular Dichroism, DNA, 0104 chemical sciences, Surfaces, Coatings and Films, chemistry, Polynucleotide, Cattle, Chirality (chemistry)
Abstract

The assembly of stacked dyes on DNA is of interest for electron transfer, light harvesting, sensing, and catalysis applications. A combination of UV/vis absorption, linear dichroism (LD), and circular dichroism (CD) was applied to characterize thoroughly the aggregation with DNA of the phenothiazine dyes methylene blue, azure B, and thionine. Aggregates of each dye with [poly(dG-dC)]2, [poly(dA-dT)]2, and calf thymus DNA were explored at high dye:DNA binding ratios, where excess dye groove-binds after all intercalation sites are filled. The organization of the aggregates (dimers, trimers, and multimers) with polydeoxynucleotides displays a structural diversity that depends on DNA sequence, extent of methylation of dye exocyclic amine groups, and ionic strength. The dyes typically form right-handed H-aggregates having negative LD, consistent with stepped stacking along the minor groove. However, aggregates in some dye:DNA aggregates show left-handed chirality or positive LD, indicating unusual modes of agg...

Published
2018

6. Highlights from Faraday Discussion 185: Supramolecular Photochemistry, Cambridge, 2015

Author

Fausto Puntoriero and Eimer Tuite

Subjects
Materials science, 010405 organic chemistry, Metals and Alloys, Supramolecular chemistry, Nanotechnology, Chemistry (all), Catalysis, Ceramics and Composites, Electronic Optical and Magnetic Materials, Surfaces Coatings and Films, Materials Chemistry2506 Metals and Alloys, 2506, General Chemistry, 010402 general chemistry, 01 natural sciences, Catalysis, 0104 chemical sciences, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, law.invention, Chemical engineering, law, Materials Chemistry, Ceramics and Composites, Faraday cage
Published
2016

7. Cover Feature: Duplex Healing of Selectively Thiolated Guanosine Mismatches through a Cd2+ Chemical Stimulus (ChemBioChem 11/2018)

Author

Agnieszka K. Bronowska, Andrew R. Pike, Samantha M. L. Lunn, Samira Hribesh, Michael J. Hall, Andrew Houlton, Eimer Tuite, and Colette J. Whitfield

Subjects
chemistry.chemical_compound, chemistry, Duplex (building), Organic Chemistry, Biophysics, Molecular Medicine, Guanosine, Stimulus (physiology), Molecular Biology, Biochemistry, Nucleobase
Published
2018
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8. [Ru(phen)2dppz](2+) luminescence reveals nanoscale variation of polarity in the cyclodextrin cavity

Author

Eimer Tuite, Patrick L. Higgs, and Andrew W. McKinley

Subjects
inorganic chemicals, Stereochemistry, Polarity (physics), 010402 general chemistry, Photochemistry, 01 natural sciences, Catalysis, Materials Chemistry, Organometallic Compounds, Nanotechnology, Nanoscopic scale, chemistry.chemical_classification, Cyclodextrin, 010405 organic chemistry, Ligand, Spectrum Analysis, beta-Cyclodextrins, technology, industry, and agriculture, Metals and Alloys, General Chemistry, 0104 chemical sciences, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, chemistry, Ceramics and Composites, Luminescence, Selectivity, Chirality (chemistry)
Abstract

Phosphorylation of β-cyclodextrin enhances binding with Ru(II)polypyridyl complexes, and promotes selectivity based on chirality and ligand hydrophobicity. For [Ru(phen)2dppz](2+), inclusion of dppz results in a dramatic increase in luminescence with multiple lifetimes. The sensitive response of photophysics to the environment reveals nanoscale variation of polarity.

Published
2015

9. Spatial and Mechanical Properties of Dilute DNA Monolayers on Gold Imaged by AFM

Author

Håkan Olin, Boris Polyakov, Eimer Tuite, and Donats Erts

Subjects
Materials science, Atomic force microscopy, Thin layer, Analytical chemistry, engineering.material, Mole fraction, Oligomer, Surfaces, Coatings and Films, chemistry.chemical_compound, chemistry, Coating, Chemical physics, Monolayer, Materials Chemistry, engineering, Molecule, Physical and Theoretical Chemistry, DNA
Abstract

Spatially distributed DNA oligomer arrays on Au(111) surfaces were created by one-step co-assembly of mixed monolayers of alkanethiol-conjugated DNA and mercaptohexanol (MCH). Tapping-mode AFM was used to visualize the distribution of DNA molecules on the surface and to study the mechanical properties of individual molecules. The DNA coating density increased nonlinearly with increasing mole fraction of DNA oligomer to MCH in the coating solution. For imaging in air, where surfaces are coated with a thin layer of water, the interaction between the AFM tip and the different structures on the monolayer varies between attractive and repulsive depending on the tapping amplitude, set-point ratio, and tip shape. It was found that both duplex and single-stranded DNA molecules extend approximately vertically upward from the surface.

Published
2003
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10. Picosecond Time-Resolved Resonance Raman Probing of the Light-Switch States of [Ru(Phen)2dppz]2+

Author

Anthony William Parker, Per Lincoln, Monica Coletti, Colin G. Coates, Björn Önfelt, Eimer Tuite, Bengt Norden, Pavel Matousek, Johan Olofsson, and John J. Mcgarvey

Subjects
Chemistry, Light switch, Nanosecond, Photochemistry, Linear dichroism, Surfaces, Coatings and Films, symbols.namesake, Picosecond, Excited state, Materials Chemistry, symbols, Physical and Theoretical Chemistry, Spectroscopy, Raman spectroscopy, Ground state
Abstract

Picosecond time-resolved resonance Raman (picosecond-TR3) spectroscopy has been used to conduct an extensive photophysical characterization of the "light- switch" complex [Ru(phen)(2)dppz](2+) as a function of environment, in which studies have been carried out in aqueous and nonaqueous media and in DNA. The results are considered in rotation to a previous report describing "environment-sensitive" lowest triplet MLCT states. Vibrational marker features and enhancement patterns were used to determine the rapid progression (< 20 ps) between two triplet MLCT states in aqueous environment, followed by subnanosecond, nonradiative deactivation to the ground state. In nonaqueous environment, the long-lived, emissive triplet MLCT state is spectrally identified as the short-lived first triplet MLCT state observed in water, in agreement with the earlier proposed mechanism. The present data are shown to correlate well with previous nanosecond RR findings for the complex in each environment. Interestingly, a "precursor state" has been identified upon excitation in both nonaqueous solvent and in DNA, which precedes the triplet MLCT state, and the lifetime of which appears to be environment dependent. Observation of this state is discussed in relation to other recent femtosecond spectroscopic studies on this complex.

Published
2001
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11. Contributory presentations/posters

Author

N. Manoj, V. R. Srinivas, A. Surolia, M. Vijayan, K. Suguna, R. Ravishankar, R. Schwarzenbacher, K. Zeth, null Diederichs, G. M. Kostner, A. Gries, P. Laggner, R. Prassl, null Madhusudan, Pearl Akamine, Nguyen-huu Xuong, Susan S. Taylor, M. Bidva Sagar, K. Saikrishnan, S. Roy, K. Purnapatre, P. Handa, U. Varshney, B. K. Biswal, N. Sukumar, J. K. Mohana Rao, A. Johnson, Vasantha Pattabhi, S. Sri Krishna, Mira Sastri, H. S. Savithri, M. R. N. Murthy, Bindu Pillai, null Kannan, M. V. Hosur, Mukesh Kumar, Swati Patwardhan, K. K. Kannan, B. Padmanabhaa, S. Sasaki-Sugio, M. Nukaga, T. Matsuzaki, S. Karthikevan, S. Sharma, A. K. Sharma, M. Paramasivam, P. Kumar, J. A. Khan, S. Yadav, A. Srinivasan, T. P. Singh, S. Gourinath, Neelima Alam, A. Srintvasan, Vikas Chandra, Punit Kaur, Ch. Betzel, S. Ghosh, A. K. Bera, S. Bhattacharya, S. Chakraborty, A. K. Pal, B. P. Mukhopadhyay, I. Dey, U. Haldar, Asok Baneriee, Jozef Sevcik, Adriana Solovicova, K. Sekar, M. Sundaralingam, N. Genov, Dong-cai Liang, Tao Jiang, Ji-ping Zhang, Wen-rui Chang, Wolfgang Jahnke, Marcel Blommers, S. C. Panchal, R. V. Hosur, Bindu Pillay, Puniti Mathur, S. Srivatsun, Ratan Mani Joshi, N. R. Jaganathan, V. S. Chauhan, H. S. Atreya, S. C. Sahu, K. V. R. Chary, Girjesh Govil, Elisabeth Adjadj, Éric Quinjou, Nadia Izadi-Pruneyre, Yves Blouquit, Joël Mispelter, Bernadette Heyd, Guilhem Lerat, Philippe Milnard, Michel Desmadreil, Y. Lin, B. D. Nageswara Rao, Vidva Raghunathan, Mei H. Chau, Prashant Pesais, Sudha Srivastava, Evans Coutinho, Anil Saran, Leizl F. Sapico, Jayson Gesme, Herbert Lijima, Raymond Paxton, Thamarapu Srikrishnan, C. R. Grace, G. Nagenagowda, A. M. Lynn, Sudha M. Cowsik, Sarata C. Sahu, S. Chauhan, A. Bhattacharya, G. Govil, Anil Kumar, Maurizio Pellecchia, Erik R. P. Zuiderweg, Keiichi Kawano, Tomoyasu Aizawa, Naoki Fujitani, Yoichi Hayakawa, Atsushi Ohnishi, Tadayasu Ohkubo, Yasuhiro Kumaki, Kunio Hikichi, Katsutoshi Nitta, V. Rani Parvathy, R. M. Kini, Takumi Koshiba, Yoshihiro Kobashigawa, Min Yao, Makoto Demura, Astushi Nakagawa, Isao Tanaka, Kunihiro Kuwajima, Jens Linge, Seán O. Donoghue, Michael Nilges, G. Chakshusmathi, Girish S. Ratnaparkhi, P. K. Madhu, R. Varadarajan, C. Tetreau, M. Tourbez, D. Lavalette, M. Manno, P. L. San Biagio, V. Martorana, A. Emanuele, S. M. Vaiana, D. Bulone, M. B. Palma-Vittorelli, M. U. Palma, V. D. Trivedi, S. F. Cheng, W. J. Chien, S. H. Yang, S. Francis, D. K. Chang, Renn Batra, Michael A. Geeves, Dietmar J. Manstein, Joanna Trvlska, Pawel Grochowski, Maciej Geller, K. Ginalski, P. Grochowski, B. Lesyng, P. Lavalette, Y. Blouquit, D. Roccatano, A. Amadei, A. Di Nola, H. J. C. Berendsen, Bosco Ho, P. M. G. Curmi, H. Berry, D. Lairez, E. Pauthe, J. Pelta, V. Kothekar, Shakti Sahi, M. Srinivasan, Anil K. Singh, Kartha S. Madhusudnan, Fateh S. Nandel, Harpreet Kaur, Balwinder Singh, D. V. S. Jain, K. Anton Feenstra, Herman J. C. Berendsen, F. Tama, Y. -H. Sanejouand, N. Go, Deepak Sharma, Sunita Sharma, Santosh Pasha, Samir K. Brahmachari, R. Viiavaraghavan, Jyoti Makker, Sharmisllia Dey, S. Kumar, G. S. Lakshmikanth, G. Krishnamoorthy, V. M. Mazhul, E. M. Zaitseva, Borys Kierdaszuk, J. Widengren, B. Terry, Ü. Mets, R. Rigler, R. Swaminathan, S. Thamotharan, N. Yathindra, Y. Shibata, H. Chosrowjan, N. Mataga, I. Morisima, Tania Chakraharty, Ming Xiao, Roger Cooke, Paul Selvin, C. Branca, A. Faraone, S. Magazù, G. Maisano, P. Migliardo, V. Villari, Digambar V. Behere, M. Sharique Zahida Waheed Deva, M. Brunori, F. Cutruzzolà, Q. H. Gibson, C. Savino, C. Travaglini-Allocatelli, B. Vallone, Swati Prasad, Shyamalava Mazumdar, Samaresh Mitra, P. Soto, R. Fayad, I. E. Sukovataya, N. A. Tyulkova, Sh. V. Mamedov, B. Aktas, M. Canturk, B. Aksakal, R. Yilgin, K. I. Bogutska, N. S. Miroshnichenko, S. Chacko, M. DiSanto, J. A. Hypolite, Y-M. Zheng, A. J. Wein, M. Wojciechowski, T. Grycuk, J. Antosiewicz, Marc A. Ceruso, Alfredo Di Nola, Subhasis Bandvopadhvay, Bishnu P. Chatterjee, Devapriva Choudhury, Andrew Thompson, Vivian Stojanoff, Jerome Pinkner, Scott Hultgren, Stefan Khight, Delphine Flatters, Julia Goodfellow, Fumi Takazawatt, Minoru Kanehisa, Masaki Sasai, Hironori Nakamura, Wang Bao Han, Yuan Zheng, Wang Zhi Xin, Pan xin Min, Vlnod Bhakuni, Sangeeta Kulkarni, Atta Ahmad, Koodathingal Prakash, Shashi Prajapati, Alexey Surin, Tomoharu Matsumoto, Li Yang, Yuki Nakagawa, Kazumoto Kimura, Yoshiyuki Amemiya, Gennady V. Semisotnov, Hiroshi Kihara, Saad Tayyab, Salman Muzammil, Yogesh Kumar, Vinod Bhakuni, Monica Sundd, Suman Kundu, M. V. Jagannadham, Medicherla V. Jagannadham, Bina Chandani, Ruby Dhar, Lalankumar Sinha, Deepti Warrier, Sonam Mehrotra, Purnima Khandelwal, Subhendu Seth, Y. U. Sasidhar, C. Ratna Prabha, Arun Gidwani, K. P. Madhusudan, Akira R. Kinjo, Ken Nishikawa, Suvobrata Chakravarty, Raghavan Varadarajan, K. Noyelle, P. Haezebrouck, M. Joniau, H. Van Dael, Sheffali Dash, Indra Brata Jha, Rajiv Bhat, Prasanna Mohanty, A. K. Bandyopadhyay, H. M. Sonawat, Ch. Mohan Rao, Siddhartha Datta, K. Rajaraman, B. Raman, T. Ramakrishna, A. Pande, J. Pande, S. Betts, N. Asherie, O. Ogun, J. King, G. Benedek, I. V. Sokolova, G. S. Kalacheva, Masashi Sonoyama, Yasunori Yokoyama, Kunihiro Taira, Shigeki Mitaku, Chicko Nakazawal, Takanori Sasakil, Yuri Mukai, Naoki Kamo, Seema Dalal, Lynne Regan, Shigeki Mituku, Mihir Roychoudhury, Devesh Kumar, Dénes Lőrinczv, Franciska Könczöl, László Farkas, Joseph Belagyi, Christoph Schick, Christy A. Thomson, Vettai S. Ananthanarayanan, E. G. Alirzayeva, S. N. Baba-Zade, M. Michael Gromiha, M. Oobatake, H. Kono, J. An, H. Uedaira, A. Sarai, Kazufumi Takano, Yuriko Yamagata, Katsuhide Yutani, Gouri S. Jas, Victor Muñoz, James Hofrichter, William A. Eaton, Jonathan Penoyar, Philip T. Lo Verde, J. Kardos, Á. Bódi, I. Venekei, P. Závodszky, L. Gráf, András Szilágyi, Péter Závodszky, R. D. Allan, J. Walshaw, D. N. Woolfson, Jun Funahashi, Savan Gupta, M. Mangoni, P. Roccatano, Gosu Ramachandraiah, Nagasuma R. Chandra, Barbara Ciani, Derek N. Woolfson, Usha B. Nair, Kanwal J. Kaur, Dinakar M. Salunke, Chittoor P. Swaminathan, Avadhesha Surolia, A. Pramanik, P. Jonasson, G. Kratz, O. T. Jansson, P. -Å. Nygren, S. Ståhl, K. Ekberg, B. -L. Johansson, S. Uhlén, M. Uhlén, H. Jörnvall, J. Wahren, Karin Welfle, Rolf Misselwitz, Wolfgang Höhne, Heinz Welfle, L. G. Mitskevich, N. V. Fedurkina, B. I. Kurganov, Gotam K. Jarori, Haripada Maity, J. Guharay, B. Sengupta, P. K. Sengupta, K. Sridevi, S. R. Kasturi, S. P. Gupta, Gunjan Agarwal, Suzanne Kwong, Robin W. Briehl, O. I. Ismailova, N, A. Tyulkova, C. Hariharan, D. Pines, E. Pines, M. Zamai, R. Cohen-Luria, A. Yayon, A. H. Parola, M. J. Padya, G. A. Spooner, D. N. Woolfeon, Panchan Bakshi, D. K. Bharadwaj, U. Sharma, N. Srivastava, R. Barthwal, N. R. Jagannathan, Keiko Matsuda, Takaaki Nishioka, Nobuhiro Go, T. Aita, S. Urata, Y. Husimi, Mainak Majumder, Nicola G. A. Abrescia, Lucy Malinina, Juan A. Subirana, Juan Aymami, Ramón Eritxa, Miquel Coll, B. J. Premraj, R. Thenmalarchelvi, P. Satheesh Kumar, N. Gautham, Lou -Sing Kan, null Ming-Hou, Shwu-Bin Lin, Tapas Sana, Kanal B. Roy, N. Bruant, D. Flatters, R. Lavery, D. Genest, Remo Rons, Heinz Sklenar, Richard Lavery, Sudip Kundu, Dhananjay Bhattacharyya, Debashree Bandyopadhyay, Ashoke Ranjan Thakur, Rabi Majumdar, F. Barceló, J. Portugal, Sunita Ramanathan, B. J. Rao, Mahua Gliosli, N. Vinay Kumar, Umesh Varshney, Shashank S. Pataskar, R. Sarojini, S. Selvasekarapandian, P. Kolandaivel, S. Sukumar, P. Kolmdaivel, Motilal Maiti, Anjana Sen, Suman Das, Elisa Del Terra, Chiara Suraci, Silvia Diviacco, Franco Quadrifoglio, Luigi Xodo, Arghya Ray, G. Karthikeyan, Kandala V. R. Chary, Basuthkar J. Rao, Anwer Mujeeb, Thomas L. James, N. Kasyanenko, E. E. F. Haya, A. Bogdanov, A. Zanina, M. R. Bugs, M. L. Cornélio, M. Ye. Tolstorukov, Nitish K. Sanval, S. N. Tiwari, Nitish K. Sanyal, Mihir Roy Choudhury, P. K. Patel, Neel S. Bhavesh, Anna Gabrielian, Stefan Wennmalm, Lars Edman, Rudolf Rigler, B. Constantinescu, L. Radu, I. Radulcscu, D. Gazdaru, Sebastian Wärmländer, Mikael Leijon, Setsuyuki Aoki, Takao Kondo, Masahiro Ishiura, V. A. Pashinskaya, M. V. Kosevich, V. S. Shelkovsky, Yu. P. Blagoy, Ji-hua Wang, R. Malathi, K. Chandrasekhar, E. R. Kandimalla, S. Agrawal, V. K. Rastogi, M. Alcolea Palafox, Chatar Singh, A. D. Beniaminov, S. A. Bondarenko, E. M. Zdobnov, E. E. Minyat, N. B. Ulyanov, V. I. Ivanov, J. S. Singh, Kailas D. Sonawane, Henri Grosjean, Ravindra Tewari, Uddhavesh B. Sonavane, Annie Morin, Elizabeth A. Doherty, Jennifer A. Doudna, H. Tochio, S. Sato, H. Matsuo, M. Shirakawa, Y. Kyogoku, B. Javaram, Surjit B. Dixit, Piyush Shukla, Parul Kalra, Achintya Das, Kevin McConnell, David L. Beveridge, W. H. Sawyer, R. Y. S. Chan, J. F. Eccelston, Yuling Yan, B. E. Davidson, Eimer Tuite, Bengt Norden, Peter Nielsen, Masayuki Takahashi, Anirban Ghosh, Manju Bansal, Frauke Christ, Hubert Thole, Wolfgang Wende, Alfred Pingoud, Vera Pingoud, Pratibha Mehta Luthra, Ramesh Chandra, Ranjan Sen, Rodney King, Robert Weisberg, Olaf F. A. Larsen, Jos Berends, Hans A. Heus, Cornelis W. Hilbers, Ivo H. M. van Stokkum, Bas Gobets, Rienk van Grondelle, Herbert van Amerongen, HE. Sngrvan, Yu. S. Babayan, N. V. Khudaverdian, M. Gromiha, F. Pichierri, M. Aida, P. Prabakaran, K. Sayano, Saulius Serva, Eglė Merkienė, Giedrius Vilkaitis, Elmar Weinhold, Saulius Klimašauskas, Eleonora Marsich, Antonella Bandiera, Giorgio Manzini, G. Potikyan, V. Arakelyan, Yu. Babayan, Alex Ninaber, Julia M. Goodfellow, Yoichiro Ito, Shigeru Ohta, Yuzuru Husimi, J. Usukura, H. Tagami, H. Aiba, Mougli Suarez, Elia Nunes, Deborah Keszenman, E. Carmen Candreva, Per Thyberg, Zeno Földes-Papp, Amita Joshi, Dinesh Singh, M. R. Rajeswari, null Ira, M. Pregetter, H. Amenitsch, J. Chapman, B. N. Pandev, K. P. Mishra, E. E. Pohl, J. Sun, I. I. Agapov, A. G. Tonevitsky, P. Pohl, S. M. Dennison, G. P. Gorbeako, T. S. Dynbko, N. Pappavee, A. K. Mishra, Prieto Manuel, Almeida Rodrigo, Loura Luis, L. Ya. Gendel, S. Przestalski, J. Kuczera, H. Kleszczyńska, T. Kral, E. A. Chernitsky, O. A. Senkovich, V. V. Rosin, Y. M. Allakhverdieva, G. C. Papageorgiou, R. A. Gasanov, Calin Apetrei, Tudor Savopol, Marius Balea, D. Cucu, D. Mihailescu, K. V. Ramanathan, Goran Bačić, Nicolas Sajot, Norbert Garnier, Serge Crouzy, Monique Genest, Z. S. Várkonyi, O. Zsiros, T. Farkas, Z. Combos, Sophie Cribier, I. F. Fraceto, S. Schreier, A. Spisni, F. de Paula, F. Sevšek, G. Gomišček, V. Arrigler, S. Svetina, B. Žekš, Fumimasa Nomura, Miki Nagata, Kingo Takiguchi, Hirokazu Hotani, Lata Panicker, P. S. Parvathanathan, A. Ishino, A. Saitoh, H. Hotani, K. Takiguchi, S. Afonin, A. Takahashi, Y. Nakato, T. Takizawa, Dipti Marathe, Kent Jørgensen, Satinder S. Rawat, R. Rukmini, Amitabha Chattopadhyay, M. Šentiurc, J. Štrancar, Z. Stolič, K. Filipin, S. Pečar, S. C. Biswas, Satyen Sana, Anunay Samanta, Koji Kinoshita, Masahito Yamazaki, Tetsuhiko Ohba, Tai Kiuchi, null Yoshitoshi, null Kamakura, Akira Goto, Takaaki Kumeta, Kazuo Ohki, I. P. Sugar, T. E. Thompson, K. K. Thompson, R. L. Biltonen, Y. Suezaki, H. Ichinose, M. Akivama, S. Matuoka, K. Tsuchihashi, S. Gasa, P. Mattjus, J. G. Molotkovsky, H. M. Pike, R. E. Brown, Ashish Arora, Jörg H. Kleinschmidt, Lukas K. Tamm, O. G. Luneva, K. E. Kruglyakova, V. A. Fedin, O. S. Kuptsoya, J. W. Borst, N. V. Visser, A. J. W. G. Visser, T. S. Dyubko, Toshihiko Ogihara, Kiyoshi Mishima, A. L. Shvaleva, N. Č. Radenović, P. M. Minić, M. G. Jeremić, Č. N. Radenović, T. F. Aripov, E. T. Tadjibaeva, O. N. Vagina, M. V. Zamaraeva, B. A. Salakhutdinov, A. Cole, M. Poppofl, C. Naylor, R. Titball, A. K. Basak, J. T. Eaton, C. E. Naylor, N. Justin, D. S. Moss, R. W. Titball, F. Nomura, M. Nagata, S. Ishjkawa, S. Takahashi, Kaoru Obuchi, Erich Staudegger, Manfred Kriechbaum, Robert I. Lehrer, Alan J. Waring, Karl Lohner, Susanne Gangl, Bernd Mayer, Gottfried Köhler, J. Shobini, Z. Guttenberg, B. Lortz, B. Hu, E. Sackmann, N. M. Kozlova, L. M. Lukyanenko, A. N. Antonovich, E. I. Slobozhanina, Andrey V. Krylov, Yuri N. Antonenko, Elena A. Kotova, Alexander A. Yaroslavov, Subhendu Ghosh, Amal K. Bera, Sudipto Das, Eva Urbánková, Masood Jelokhani-Niaraki, Karl Freeman, Petr Jezek, P. B. Usmanov, A. Ongarbaev, A. K. Tonkikh, Peter Pohl, Sapar M. Saparov, P. Harikumar, J. P. Reeves, S. Rao, S. K. Sikdar, A. S. Ghatpande, C. Corsso, A. C. Campos de Carvalho, W. A. Varanda, C. ElHamel, E. Dé, N. Saint, G. Molle, Anurae Varshney, M. K. Mathew, E. Loots, E. Y. Isacoff, Michiki Kasai, Naohiro Yamaguchi, Paramita Ghosh, Joseph Tigyi, Gabor Tigyi, Karoly Liliom, Ricardo Miledi, Maja R. Djurisic, Pavle R. Andjus, Indira H. Shrivastava, M. S. P. Sansom, C. Barrias, P. F. Oliveira, A. C. Mauricio, A. M. Rebelo da Costa, I. A. Lopes, S. V. Fedorovich, V. S. Chubanov, M. V. Sholukh, S. V. Konev, N. Fedirko, V. Manko, M. Klevets, N. Shvinka, B. S. Prabhananda, Mamata H. Kombrabail, S. Aravamudhan, Berenice Venegas-Cotero, Ivan Ortega Blake, Zhi-hong Zhang, Xiao-jian Hu, Han-qing Zhou, Wei-ying Cheng, Hang-fang Feng, L. O. Dubitsky, L. S. Vovkanvch, I. A. Zalyvsky, E. Savio-Galimberti, P. Bonazzola, J. E. Ponce-Homos, Mario Parisi, Claudia Capurro, Roxana Toriano, Laxma G. Ready, Larry R. Jones, David D. Thomas, B. A. Tashmukhamedov, B. T. Sagdullaev, D. Heitzmann, R. Warth, M. Bleich, R. Greger, K. T. G. Ferreira, H. G. Ferreira, Orna Zagoory, Essa Alfahel, Abraham H. Parola, Zvi Priel, H. Hama-Inaba, R. Wang, K. Choi, T. Nakajima, K. Haginoya, M. Mori, H. Ohyama, O. Yukawa, I. Hayata, Nanda B. Joshi, Sridhar K. Kannurpatti, Preeti G. Joshi, Mau Sinha, Xun Shen, Tianhui Hu, Ling Bei, Menno L. W. Knetsch, Nicole Schäfers, John Sandblom, Juris Galvanovskis, Roxana Pologea-Moraru, Eugenia Kovacs, Alexandra Dinu, S. H. Sanghvi, V. Jazbinšek, G. Thiel, W. Müller, G. Wübeller, Z. Tronteli, Leš Fajmut, Marko Marhl, Milan Brumen, I. D. Volotovski, S. G. Sokolovski, M. R. Knight, Alexei N. Vasil’ev, Alexander V. Chalyi, P. Sharma, P. J. Steinbach, M. Sharma, N. D. Amin, J. Barchir, R. W. Albers, H. C. Pant, M. Balasubramanyam, M. Condrescu, J. P. Gardner, Shamci Monajembashi, Gotz Pilarczyk, K. O. Greulich, F. M. El-Refaei, M. M. Talaat, A. I. El-Awadi, F. M. Ali, Ivan Tahradník, Jana Pavelková, Alexandra Zahradniková, Boris S. Zhorov, Vettai S. Ananthanaravanan, M. Ch. Michailov, E. Neu, W. Seidenbusch, E. Gornik, D. Martin, U. Welscher, D. G. Weiss, B. R. Pattnaik, A. Jellali, V. Forster, D. Hicks, J. Sahel, H. Dreyfus, S. Picaud, Hong-Wei Wang, Sen-fang Sui, Pradeep K. Luther, John Barry, Ed Morris, John Squire, C. Sivakama Sundari, D. Balasubramanian, K. Veluraia, T. Hema Thanka Christlet, M. Xavier Suresh, V. Laretta-Garde, Dubravka Krilov, Nataša Stojanović, Janko N. Herak, Ravi Jasuja, Maria Ivanova, Rossen Mirchev, Frank A. Ferrone, David Stopar, Ruud B. Spruijt, Cor J. A. M. Wolfs, Marcus A. Hemminga, G. Arcovito, M. De Spirito, Rajendra K. Agrawal, Amy B. Heagle, Pawel Penczek, Robert Grassucci, Joachim Frank, Manjuli R. Sharma, Loice H. Jeyakumar, Sidney Fleischer, Terence Wagenknecht, Carlo Knupp, Peter M. G. Munro, Eric Ezra, John M. Squire, Koji Ichihara, Hidefumi Kitazawa, Yusuke Iguchi, Tomohiko J. Itoh, Greta Pifat, Marina Kveder, Slavko Pečar, Milan Schara, Deepak Nair, Kavita Singh, Kanury V. S. Rao, Kanwaljeet Kaur, Deepti Jain, B. Sundaravadivel, Manisha Goel, D. M. Salunke, E. I. Kovalenko, G. N. Semenkova, S. N. Cherenkevich, T. Lakshmanan, D. Sriram, S. Srinivasan, D. Loganathan, T. S. Ramalingam, J. A. Lebrón, P. J. Bjorkman, A. K. Singh, T. N. Gayatri, Ernesto R. Caffarena, J. Raul Grigera, Paulo M. Bisch, V. Kiessling, P. Fromherz, K. N. Rao, S. M. Gaikwad, M. I. Khan, C. G. Suresh, P. Kaliannan, M. Elanthiraiyan, K. Chadha, J. Payne, J. L. Ambrus, M. P. N. Nair, Madhavan P. N. Nair, S. Mahajan, K. C. Chadha, R. Hewitt, S. A. Schwartz, J. Bourguignon, M. Faure, C. Cohen-Addad, M. Neuburger, R. Ober, L. Sieker, D. Macherel, R. Douce, D. S. Gurumurthy, S. Velmurugan, Z. Lobo, Ratna S. Phadke, Prashant Desai, I. M. Guseinova, S. Yu. Suleimanov, I. S. Zulfugarov, S. N. Novruzova, J. A. Aliev, M. A. Ismayilov, T. V. Savchenko, D. R. Alieva, Petr Ilík, Roman Kouřil, Hana Bartošková, Jan Nauš, Jvoti U. Gaikwad, Sarah Thomas, P. B. Vidyasagar, G. Garab, I. Simidjiev, S. Rajagopal, Zs. Várkonyi, S. Stoylova, Z. Cseh, E. Papp, L. Mustárdy, A. Holzenburg, R. Bruder, U. K. Genick, T. T. Woo, D. P. Millar, K. Gerwert, E. D. Getzoff, Tamás Jávorfí, Győző Garab, K. Razi Naqvi, Md. Kalimullah, Jyoti Gaikwad, Manoj Semwal, Roman Kouril, Petr Ilik, Man Naus, István Pomozi, Gábor Horváth, Rüdiger Wehner, Gary D. Bernard, Ana Damjanović, Thorsten Ritz, Klaus Schulten, Wang Jushuo, Shan Jixiu, Gong Yandao, Kuang Tingyun, Zhao Nanming, Arvi Freiberg, Kõu Timpmann, Rein Ruus, Neal W. Woodbury, E. V. Nemtseva, N. S. Kudryasheva, A. G. Sizykh, V. N. Shikhov, T. V. Nesterenko, A. A. Tikhomirov, Giorgio Forti, Giovanni Finazzi, Alberto Furia, Romina Paola Barbagallo, S. Iskenderova, R. Agalarov, R. Gasanov, Miyashita Osamu, G. O. Nobuhiro, R. K. Soni, M. Ramrakhiani, Hiromasa Yagi, Kacko Tozawa, Nobuaki Sekino, Tomoyuki Iwabuchi, Masasuke Yoshida, Hideo Akutsu, A. V. Avetisyan, A. D. Kaulen, V. P. Skulachev, B. A. Feniouk, Cécile Breyton, Werner Kühlbrandt, Maria Assarsson, Astrid Gräslund, G. Horváth, B. Libisch, Z. Gombos, N. V. Budagovskaya, N. Kudryasheva, Erisa Harada, Yuki Fukuoka, Tomoaki Ohmura, Arima Fukunishi, Gota Kawai, Kimitsuna Watanabe, Jure Derganc, Bojan Božič, Saša Svetina, Boštjan Žekš, J. F. Y. Hoh, Z. B. Li, G. H. Rossmanith, E. L. de Beer, B. W. Treijtel, P. L. T. M. Frederix, T. Blangè, S. Hénon, F. Galtet, V. Laurent, E. Planus, D. Isabey, L. S. Rath, P. K. Dash, M. K. Raval, C. Ramakrishnan, R. Balaram, Milan Randic, Subhash C. Basak, Marjan Vracko, Ashesh Nandy, Dragan Amic, Drago Beslo, Sonja Nikolic, Nenad Trinajstic, J. Walahaw, Marc F. J. Lensink, Boojala V. B. Reddy, Ilya N. Shindylov, Philip E. Bourne, M. C. Donnamaria, J. de Xammar Oro, J. R. Grigera, Monica Neagu, Adrian Neagu, Matej Praprotnik, Dušanka Janežič, Pekka Mark, Lennart Nilsson, L. La Fata, Laurent E. Dardenne, Araken S. Werneck, Marçal de O. Neto, N. Kannan, S. Vishveshwara, K. Veluraja, Gregory D. Grunwald, Alexandra T. Balaban, Kanika Basak, Brian D. Gute, Denise Mills, David Opitz, Krishnan Balasubramanian, G. I. Mihalas, Diana Lungeanu, G. Macovievici, Raluca Gruia, C. Cortez-Maghelly, B. Dalcin, E. P. Passos, S. Blesic, M. Ljubisavljevic, S. Milosevic, D. J. Stratimirovic, Nandita Bachhawat, Shekhar C. Mande, A. Nandy, Ayumu Saito, Koichi Nishigaki, Mohammed Naimuddin, Takatsugu Hirokawa, Mitsuo Ono, Hirotomo Takaesu, M. I. El Gohary, Abdalla S. Ahmed, A. M. Eissa, Hiroshi Nakashima, G. P. S. Raghava, N. Kurgalvuk, O. Goryn, Bernard S. Gerstman, E. V. Gritsenko, N. N. Remmel, O. M. Maznyak, V. A. Kratasyuk, E. N. Esimbekova, D. Tchitchkan, S. Koulchitsky, A. Tikhonov, A. German, Y. Pesotskaya, S. Pashkevich, S. Pletnev, V. Kulchitsky, Umamaheswar Duvvuri, Sridhar Charagundla, Rahim Rizi, John S. Leigh, Ravinder Reddy, Mahesh Kumar, O. Coshic, P. K. Julka, O. K. Rath, NR. Jagannathan, Karina Roxana Iliescu, Maria Sajin, Nicolcta Moisoi, Ileana Petcu, A. I. Kuzmenko, R. P. Morozova, I. A. Nikolenko, G. V. Donchenko, M. K. Rahman, M. M. Ahmed, Takehiro Watanabe, Y. Rubin, H. Gilboa, R. Sharony, R. Ammar, G. Uretzky, M. Khubchandani, H. N. Mallick, V. Mohan Kumar, Arijitt Borthakur, Erik M. Shapiro, M. Gulnaz Begum, Mahaveer N. Degaonkar, S. Govindasamy, Ivan Dimitrov, T. A. Kumosani, W. Bild, I. Stefanescu, G. Titescu, R. Iliescu, C. Lupusoru, V. Nastasa, I. Haulica, Gopal Khetawat, N. Faraday, M. Nealen, S. Noga, P. F. Bray, T. V. Ananieva, E. A. Lycholat, MV. Kosevich, S. G. Stepanyan, S. V. Antonyuk, R. Khachatryan, H. Arakelian, A. Kumar, S. Ayrapetyan, V. Mkheyan, S. Agadjanyan, A. Khachatryan, S. S. Rajan, V. Kabaleeswaran, Geetha Gopalakrishnan, T. R. Govindachari, Meera Ramrakhiani, Phillip Lowe, Andrew Badley, David C. Cullen, H. Hermel, W. Schmahl, H. Möhwald, Nirmalya Majumdar, Joydip Das, András Dér, Loránd Kelemen, László Oroszi, András Hámori, Jeremy J. Ramsden, Pál Ormos, D. Savitri, Chanchal K. Mitra, Toshio Yanagida, Seiji Esaki, Yuji Kimura, Tomoyuki Nishida, Yosiyuki Sowa, M. Radu, V. K. Koltover, Ya. I. Estrin, L. A. Kasumova, V. P. Bubnov, E. E. Laukhina, Rajiv Dotta, M. Degaonkar, P. Raghunathan, Rama Jayasundar, Pavel Novák, Milan Marko, Ivan Zahradník, Hiroaki Hirata, Hidetake Miyata, J. Balaji, P. Sengupta, S. Maiti, M. Gonsalves, A. L. Barker, J. V. Macpherson, D. O’Hare, C. P. Winlove, P. R. Unwin, R. Phillip, S. Banerjee, G. Ravindra Kumar, K. Nagayaka, R. Danev, S. Sugitani, K. Murata, Michael Gősch, H. Blom, P. Thyberg, Z. Földes-Papp, G. Björk, J. Holm, T. Heino, Masashi Yokochi, Fuyuhiko Inagaki, Masami Kusunoki, E. K. Matthews, J. Pines, Yu. P. Chukova, Vitaly K. Koltover, Geetanjali Bansal, Uma Singh, M. P. Bansal, Kotoko Nakata, Tastuya Nakano, Tsuguchika Kaminuma, B. P. S. Kang, U. Singh, Bonn Kirn, Neja Potocnik, Vito Stare, Latal Shukla, V. Natarajan, T. P. A. Devasagayam, M. D. Sastry, P. C. Kesavan, R. Sayfutdinov, V. V. Adamovich, D. Yu. Rogozin, A. G. Degermendzhy, C. L. Khetrapal, G. A. Nagana Gowda, Kedar Nath Ghimire, Ishida Masaru, H. Fujita, S. Ishiwata, Y. Kishimoto, S. Kawahara, M. Suzuki, H. Mori, M. Mishina, Y. Kirino, H. Ohshima, A. S. Dukhin, V. N. Shilov, P. J. Goetz, and R. K. Mishra

Subjects
0303 health sciences, biology, General Medicine, 010402 general chemistry, 01 natural sciences, Horseradish peroxidase, General Biochemistry, Genetics and Molecular Biology, 0104 chemical sciences, 03 medical and health sciences, Biochemistry, Manganese porphyrin, biology.protein, Enzyme reconstitution, General Agricultural and Biological Sciences, 030304 developmental biology
Published
1999
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12. Difference between active and inactive nucleotide cofactors in the effect on the DNA binding and the helical structure of RecA filament dissociation of RecA--DNA complex by inactive nucleotides

Author

Hye-Kyung Kim, Bengt Nordén, Tassadite Selmane, Masayuki Takahashi, Kell Mortensen, Eimer Tuite, and Christine Ellouze

Subjects
chemistry.chemical_classification, Circular dichroism, GTP', Oligonucleotide, Nucleotides, Circular Dichroism, Guanosine, DNA, biochemical phenomena, metabolism, and nutrition, Biochemistry, Protein filament, DNA-Binding Proteins, chemistry.chemical_compound, Rec A Recombinases, chemistry, Biophysics, bacteria, Nucleic Acid Conformation, Nucleotide, Homologous recombination, Protein Binding
Abstract

The RecA protein requires ATP or dATP for its coprotease and strand exchange activities. Other natural nucleotides, such as ADP, CTP, GTP, UTP and TTP, have little or no activation effect on RecA for these activities. We have investigated the activation mechanism, and the selectivity for ATP, by studying the effect of various nucleotides on the DNA binding and the helical structure of the RecA filament. The interaction with DNA was investigated via fluorescence measurements with a fluorescent DNA analog and fluorescein-labeled oligonucleotides, assisted by linear dichroism. Filament structure was investigated via small-angle neutron scattering. There is no simple correlation between filament elongation, DNA binding affinity of RecA, and DNA structure in the RecA complex. There may be multiple conformations of RecA, Both coprotease and strand exchange activities require formation of a rigid and well organized complex. The triphosphate nucleotides which do not activate RecA, destabilize the RecA-DNA complex, indicating that the chemical nature of the nucleotide nucleobase is very important for the stability of RecA-DNA complex. Higher stability of the RecA-DNA complex in the presence of adenosine 5'-O-3-thiotriphosphate or guanosine 5'-O-3-thiotriphosphate than ATP or GTP indicates that contact between the protein and the chemical group at the gamma position of the nucleotide also affects the stability of the RecA-DNA complex. This contact appears also important for the rigid organization of DNA because ADP strongly decreases the rigidity of the complex.

Published
1999

13. Effects of minor and major groove-binding drugs and intercalators on the DNA association of minor groove-binding proteins RecA and deoxyribonuclease I detected by flow linear dichroism

Author

Masayuki Takahashi, Eimer Tuite, Per Hagmar, Ulrica Sehlstedt, and Bengt Nordén

Subjects
Circular dichroism, Indoles, Ultraviolet Rays, Plasma protein binding, Ligands, Biochemistry, DNA-binding protein, chemistry.chemical_compound, Methyl Green, Ethidium, Deoxyribonuclease I, Chemistry, Circular Dichroism, Spectrum Analysis, DNA, Ligand (biochemistry), Intercalating Agents, DNA binding site, DNA-Binding Proteins, Crystallography, Rec A Recombinases, Biophysics, Nucleic Acid Conformation, Ethidium bromide, Protein Binding
Abstract

Linear and circular dichroic spectroscopies have been employed to investigate the effects of small DNA ligands on the interactions of two proteins which bind to the minor groove of DNA, viz. RecA protein from Escherichia coli and deoxyribonuclease I (bovine pancreas). Ligands representing three specific non-covalent binding modes were investigated: 4',6-diamidino-2-phenylindole and distamycin A (minor groove binders), methyl green (major groove binder), and methylene blue, ethidium bromide and ethidium dimer (intercalators). Linear dichroism was demonstrated to be an excellent detector, in real time, of DNA double-strand cleavage by deoxyribonuclease I. Ligands bound in all three modes interfered with the deoxyribonuclease I digestion of dsDNA, although the level of interference varied in a manner which could be related to the ligand binding site, the ligand charge appearing to be less important. In particular, the retardation of deoxyribonuclease I cleavage by the major groove binder methyl green demonstrates that accessibility to the minor groove can be affected by occupancy of the opposite groove. Binding of all three types of ligand also had marked effects on the interaction of RecA with dsDNA in the presence of non-hydrolyzable cofactor adenosine 5'-O-3-thiotriphosphate, decreasing the association rate to varying extents but with the strongest effects from ligands having some minor groove occupancy. Finally, each ligand was displaced from its DNA binding site upon completion of RecA association, again demonstrating that modification of either groove can affect the properties and behaviour of the other. The conclusions are discussed against the background of previous work on the use of small DNA ligands to probe DNA-protein interactions.

Published
1997

14. Synthesis and binding of proflavine diazides as functional intercalators for directed assembly on DNA

Author

Alexandra O. Haigh, Joseph H. Hedley, Andrew R. Pike, Eimer Tuite, and Shahrbanou MoradpourHafshejani

Subjects
Conductive polymer, chemistry.chemical_compound, Aqueous solution, chemistry, Stereochemistry, General Chemical Engineering, Intercalation (chemistry), Amine gas treating, Protonation, General Chemistry, Azide, Proflavine, DNA
Abstract

Proflavine diazide (PD) with amido-azide substituents on the amine groups and its N-methylated analogue (MePD) bind strongly to DNA by nearest-neighbour intercalation with little sequence selectivity, presenting reactive azide groups in the major groove. PD is neutral in aqueous solution but experiences binding-coupled protonation on interaction with DNA with an apparent pKa shift of 2.5 units. MePD can be click modified in situ on DNA with alkyne-functionalised thienyl-pyrrole as a precursor for conducting polymer synthesis, and remains intercalated after reaction with the substituents aligned in the groove.

Published
2013
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15. Influence of polystyrenesulfonate on electron transfer quenching of ruthenium trisbipyridine luminescence by viologens: non-covalent assembly and covalent tethering of the ruthenium complex

Author

Patricia M. Ennis, David B. Rose, John M. Kelly, and Eimer Tuite

Subjects
Luminescence, Aqueous solution, Quenching (fluorescence), Molecular Structure, Chemistry, General Physics and Astronomy, chemistry.chemical_element, Viologen, DNA, Molecular Dynamics Simulation, Chromophore, Photochemistry, Viologens, Ruthenium, Electron Transport, Electron transfer, Covalent bond, Organometallic Compounds, medicine, Polystyrenes, Physical and Theoretical Chemistry, Small molecule binding, medicine.drug
Abstract

A new copolymer (RuB-PSS) of ruthenium(II)bis-(2,2'-bipyridine)(4-vinyl 2,2'-bipyridine) and styrene sulfonate was prepared which tethers the ruthenium chromophore directly to the polymer backbone. The photophysical properties of the copolymer, and its luminescence quenching by viologens, were compared with those of ruthenium(II)tris-bipyridine, [Ru(bpy)(3)](2+), bound non-covalently to polystyrenesulfonate (PSS) via hydrophobic and electrostatic interactions. Enhancement of ruthenium polypyridyl complex luminescence in both systems is due to decreased rates of non-radiative decay when removed from bulk water as well as reduced oxygen quenching. Molecular dynamics simulations show an open PSS chain conformation with induction of local curvature around the ruthenium centres. Hence, the complexes remain exposed to water, albeit less so than in bulk solution, as evidenced by low enhancement of bound [Ru(phen)(2)dppz](2+) emission. Quenching by O(2) is hindered for both systems due to combined polarity, ionic strength, and viscosimetric effects that influence local concentrations and diffusion of reactants. Electron transfer quenching of the Ru centre by zwitterionic propyl viologen sulfonate (PVS(0)) and cationic methyl viologen (MV(2+)) is enhanced for [Ru(bpy)(3)](2+)/PSS, but retarded for RuB-PSS, despite the attraction of the quenchers for PSS. PSS binding hinders separation of the electron transfer products relative to aqueous solution, excepting an increase for RuB-PSS/PVS(0). We conclude that anionic hydrophobic polymers such as PSS can differentially influence forward- and reverse- electron transfer reactions depending on the charge and hydrophobicity of the reactants. In the context of small molecule binding, we find that PSS provides a tenable model for DNA.

Published
2012
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