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Xia Z, Kondhare D, Budow-Busse S, Leonard P, Seela F. 7-Deaza-2'-deoxyisoguanosine, a Noncanonical Nucleoside for Nucleic Acid Code Expansion and New DNA Constructs: Nucleobase Functionalization of Inverse Watson-Crick and Purine-Purine Base Pairs. Bioconjug Chem 2024; 35:1233-1250. [PMID: 39088564 DOI: 10.1021/acs.bioconjchem.4c00290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
Abstract
7-Deaza-2'-deoxyisoguanosine forms stable inverse Watson-Crick base pairs with 5-methyl-2'-deoxyisocytidine and purine-purine base pairs with 2'-deoxyguanosine or 5-aza-7-deaza-2'-deoxyguanosine. Both base pairs expand the genetic coding system. The manuscript reports on the functionalization of these base pairs with halogen atoms and clickable side chains introduced at 7-position of the 7-deazapurine base. Oligonucleotides containing the functionalized base pairs were prepared by solid-phase synthesis. To this end, a series of phosphoramidites were synthesized and clickable side chains with short and long linkers were incorporated in oligonucleotides. Fluorescent pyrene conjugates were obtained by postmodification. Functionalization of DNA with a single inverse Watson-Crick base pair by halogens or clickable residues has only a minor impact on duplex stability. Pyrene click adducts increase (long linker) or decrease (short linker) the double helix stability. Stable hybrid duplexes were constructed containing three consecutive purine-purine pairs of 7-functionalized 7-deaza-2'-deoxyisoguanine with guanine or 5-aza-7-deazaguanine in the center and Watson-Crick pairs at both ends. The incorporation of a hybrid base pair tract of 7-deaza-2'-deoxyisoguanosine/5-aza-7-deaza-2'-deoxyguanosine pairs stabilizes the double helix strongly. Fluorescence intensity of pyrene short linker adducts increased when the 7-deazapurine base was positioned opposite to 5-methylisocytosine (inverse base pair) compared to purine-purine base pairs with guanine or 5-aza-7-deazaguanine in opposite positions. For long liker adducts, the situation is more complex. Circular dichroism (CD) spectra of purine DNA differ to those of Watson-Crick double helices and are indicative for the new DNA constructs. The impact of 7-deaza-2'-deoxyisoguanine base pair functionalization is studied for the first time and all experimental details are reported to prepare DNA functionalized at the 7-deazaisoguanine site. The influence of single and multiple incorporations on DNA structure and stability is shown. Clickable residues introduced at the 7-position of the 7-deazaisoguanine base provide handles for Huisgen-Sharpless-Meldal click cycloadditions without harming the stability of purine-pyrimidine and purine-purine base pairs. Other chemistries might be used for bioconjugation. Our investigation paves the way for the functionalization of a new DNA related recognition system expanding the common Watson-Crick regime.
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Affiliation(s)
- Zhenqiang Xia
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Simone Budow-Busse
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
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2
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Jin Z, Zhuang B, Deng J, Yuan S, Xiong H, Zhang Y, Fan J, Li W. Temperature Dependent Hydrogen Bond Toward High Emission in an Emerging Indium-Based Perovskite. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2302354. [PMID: 37116122 DOI: 10.1002/smll.202302354] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Indexed: 06/19/2023]
Abstract
Low-dimensional organic-inorganic hybrid perovskites (OIHPs) with broadband emission attract immense scientific interest due to their potential application for the next generation of solid-state lighting. However, due to low exciton utilization, organic cations generally adjust structure rather than contribute the band edge to affect optical properties. Based on this, OIHPs are usually allowed to obtain a low photoluminescence quantum yield (PLQY). Herein, a good charge transfer carrier (p-phenylenediamine, PPDA) as organic cation is rationally employed and a novel indium-based perovskite is synthesized. By coupling with H2 O molecules, a strong interaction between organic and inorganic components is realized by hydrogen bonding, which has good transportability and greatly improves the exciton utilization. The regions of hydrogen bonding show high electron mobility, combined with the induced recombination center, improving the progress of charge relaxation. As a result, the regulation of hydrogen bond strength based on the microstructure optimization directly determines the optical emission intensity, realizing nearly 100% PLQY. Further, the polyhydrogen bond structure makes each component a stronger interaction, showing high stability in polar, organic, and acidic solvent, as well as long-term storing, which represents one of the highest overall performances for lighting in OIHPs.
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Affiliation(s)
- Zicong Jin
- Institute of New Energy Technology, Department of Electronic Engineering, College of Information Science and Technology, Jinan University, Guangzhou, 510632, China
- Key Laboratory of New Semiconductors and Devices of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510631, China
| | - Bihao Zhuang
- Institute of New Energy Technology, Department of Electronic Engineering, College of Information Science and Technology, Jinan University, Guangzhou, 510632, China
- Key Laboratory of New Semiconductors and Devices of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510631, China
| | - Jiahuan Deng
- Institute of New Energy Technology, Department of Electronic Engineering, College of Information Science and Technology, Jinan University, Guangzhou, 510632, China
- Key Laboratory of New Semiconductors and Devices of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510631, China
| | - Songyang Yuan
- Institute of New Energy Technology, Department of Electronic Engineering, College of Information Science and Technology, Jinan University, Guangzhou, 510632, China
- Key Laboratory of New Semiconductors and Devices of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510631, China
| | - Hui Xiong
- Institute of New Energy Technology, Department of Electronic Engineering, College of Information Science and Technology, Jinan University, Guangzhou, 510632, China
- Key Laboratory of New Semiconductors and Devices of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510631, China
| | - Yangyi Zhang
- Institute of New Energy Technology, Department of Electronic Engineering, College of Information Science and Technology, Jinan University, Guangzhou, 510632, China
- Key Laboratory of New Semiconductors and Devices of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510631, China
| | - Jiandong Fan
- Institute of New Energy Technology, Department of Electronic Engineering, College of Information Science and Technology, Jinan University, Guangzhou, 510632, China
- Key Laboratory of New Semiconductors and Devices of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510631, China
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100, China
| | - Wenzhe Li
- Institute of New Energy Technology, Department of Electronic Engineering, College of Information Science and Technology, Jinan University, Guangzhou, 510632, China
- Key Laboratory of New Semiconductors and Devices of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510631, China
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3
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Krul SE, Hoehn SJ, Feierabend KJ, Crespo-Hernández CE. Excited state dynamics of 7-deazaguanosine and guanosine 5'-monophosphate. J Chem Phys 2021; 154:075103. [PMID: 33607894 DOI: 10.1063/5.0038123] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Minor structural modifications to the DNA and RNA nucleobases have a significant effect on their excited state dynamics and electronic relaxation pathways. In this study, the excited state dynamics of 7-deazaguanosine and guanosine 5'-monophosphate are investigated in aqueous solution and in a mixture of methanol and water using femtosecond broadband transient absorption spectroscopy following excitation at 267 nm. The transient spectra are collected using photon densities that ensure no parasitic multiphoton-induced signal from solvated electrons. The data can be fit satisfactorily using a two- or three-component kinetic model. By analyzing the results from steady-state, time-resolved, computational calculations, and the methanol-water mixture, the following general relaxation mechanism is proposed for both molecules, Lb → La → 1πσ*(ICT) → S0, where the 1πσ*(ICT) stands for an intramolecular charge transfer excited singlet state with significant πσ* character. In general, longer lifetimes for internal conversion are obtained for 7-deazaguanosine compared to guanosine 5'-monophosphate. Internal conversion of the 1πσ*(ICT) state to the ground state occurs on a similar time scale of a few picoseconds in both molecules. Collectively, the results demonstrate that substitution of a single nitrogen atom for a methine (C-H) group at position seven of the guanine moiety stabilizes the 1ππ* Lb and La states and alters the topology of their potential energy surfaces in such a way that the relaxation dynamics in 7-deazaguanosine are slowed down compared to those in guanosine 5'-monophosphate but not for the internal conversion of 1πσ*(ICT) state to the ground state.
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Affiliation(s)
- Sarah E Krul
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Sean J Hoehn
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Karl J Feierabend
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
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Patel MK, Patel U, Gandhi SA, Barot V, Jayswal J. Solvent effect on neutral Co (II) complexes of paeonol derivative –qualitative and quantitative studies from energy frame work and Hirshfeld surface analysis. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.06.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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5
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Kamal A, Sharma R, She Z, Kraatz HB. Hg(ii) interactions with T-rich regions in oligonucleotides: effects of positional variations on the electrochemical properties. Analyst 2019; 143:2844-2850. [PMID: 29786706 DOI: 10.1039/c8an00232k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Hg(ii) binding to thymine-rich oligonucleotides (ODNs) is investigated electrochemically. The focus of this study is to probe the effects of position on the electrochemical response. For this purpose, three oligonucleotides were investigated in which the position of a hexa-thymine repeat is varied within a surface-supported oligonucleotide. The hexa repeats were placed in the top, middle, and bottom positions within the strand with respect to the gold surface. The effects were monitored by electrochemical impedance spectroscopy and scanning electrochemical microscopy. Using charge transfer resistance (RCT) and tip current (I) as a measure, it was possible to monitor the effects of Hg(ii) binding to the ds-oligonucleotide. The extent of film resistance reduces as the T-rich region moves from the bottom to top position within the film. The T-rich region closer to the gold surface probably builds less flexible and more rigid T-Hg(ii)-T basepairs compared to the other two positions and is expected to stay in the upright orientation on the surface. This in turn results in significant differences in the electrochemical readout, demonstrating that the position of T-rich sequences within an oligonucleotide strand matters.
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Affiliation(s)
- Ajar Kamal
- Department of Physical and Environmental Sciences, University of Toronto, Scarborough, Toronto M1C 1A4, Canada
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6
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Capobianco A, Landi A, Peluso A. Modeling DNA oxidation in water. Phys Chem Chem Phys 2018; 19:13571-13578. [PMID: 28513687 DOI: 10.1039/c7cp02029e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A novel set of hole-site energies and electronic coupling parameters to be used, in the framework of the simplest tight-binding approximation, for predicting DNA hole trapping efficiencies and rates of hole transport in oxidized DNA is proposed. The novel parameters, significantly different from those previously reported in the literature, have been inferred from reliable density functional calculations, including both the sugar-phosphate ionic backbone and the effects of the aqueous environment. It is shown that most of the experimental oxidation free energies of DNA tracts and of oligonucleotides available from photoelectron spectroscopy and voltammetric measurements are reproduced with great accuracy, without the need for introducing sequence dependent parameters.
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Affiliation(s)
- Amedeo Capobianco
- Dipartimento di Chimica e Biologia "Adolfo Zambelli", Università di Salerno, I-84084 Fisciano (SA), Italy.
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7
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Kamal A, She Z, Sharma R, Kraatz HB. A study of the interactions of Hg(II) with T-T mispair containing hairpin loops. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2017.05.058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Kamal A, She Z, Sharma R, Kraatz HB. Interactions of Hg(ii) with oligonucleotides having thymine-thymine mispairs. Optimization of an impedimetric Hg(ii) sensor. Analyst 2017; 142:1827-1834. [PMID: 28474033 DOI: 10.1039/c7an00238f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The present work describes the effect of the number of thymine-thymine mispairs in single strand DNA probes on Hg(ii) interactions and further to develop a highly sensitive DNA based impedimetric sensor for Hg(ii) detection. To achieve this goal, the influence of the number of T-T mispairs on the signal response prompted by DNA-Hg(ii) binding interactions was examined on three designed DNA probes: 5'-OH-(CH2)6-S-S-(CH2)6-AGTCCACACGTTCCTTACGC-3', 5'-OH-(CH2)6-S-S-(CH2)6-AGTCCACATTTTCCTTTTGC-3', 5'-OH-(CH2)6-S-S-(CH2)6-AGTCCATTTTTTCCTTTTTT-3' having 2T-T, 4T-T and 6T-T mispairs with identical length, respectively. This study revealed that the number of T-T mispairs plays a critical role in maximizing the signal intensity of DNA-Hg(ii) binding interactions. Based on these results, DNA comprising maximum number of T-T mispairs was further utilized for construction of the Hg(ii) sensor, which exhibited a linear correlation between the change in charge transfer resistance (ΔRCT) and the concentration of Hg(ii) over the range of 1.0 × 10-5 M to 1.0 × 10-10 M with a lower detection limit of 3.2 × 10-11 M. The selectivity was tested against 12 different metal ions including Hg(ii). The ΔRCT response from Hg(ii) is 3 times higher than the nearest competitor Pb(ii) and approximately 10 times than other ions. The potential application of such a robust and label-free DNA sensor was demonstrated by analyzing environmental samples collected from Lake Ontario.
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Affiliation(s)
- Ajar Kamal
- Department of Physical and Environmental Sciences, University of Toronto, Scarborough, Toronto M1C 1A4, Canada.
| | - Zhe She
- Department of Physical and Environmental Sciences, University of Toronto, Scarborough, Toronto M1C 1A4, Canada.
| | - Renu Sharma
- Department of Physical and Environmental Sciences, University of Toronto, Scarborough, Toronto M1C 1A4, Canada.
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences, University of Toronto, Scarborough, Toronto M1C 1A4, Canada.
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9
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Abstract
Biological electron transfer reactions between metal cofactors are critical to many essential processes within the cell. Duplex DNA is, moreover, capable of mediating the transport of charge through its π-stacked nitrogenous bases. Increasingly, [4Fe4S] clusters, generally redox-active cofactors, have been found to be associated with enzymes involved in DNA processing. DNA-binding enzymes containing [4Fe4S] clusters can thus utilize DNA charge transport (DNA CT) for redox signaling to coordinate reactions over long molecular distances. In particular, DNA CT signaling may represent the first step in the search for DNA lesions by proteins containing [4Fe4S] clusters that are involved in DNA repair. Here we describe research carried out to examine the chemical characteristics and biological consequences of DNA CT. We are finding that DNA CT among metalloproteins represents powerful chemistry for redox signaling at long range within the cell.
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Affiliation(s)
- Elizabeth O’Brien
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
| | - Rebekah M.B. Silva
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
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10
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Labib M, Sargent EH, Kelley SO. Electrochemical Methods for the Analysis of Clinically Relevant Biomolecules. Chem Rev 2016; 116:9001-90. [DOI: 10.1021/acs.chemrev.6b00220] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Mahmoud Labib
- Department
of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | | | - Shana O. Kelley
- Department
of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario M5S 3M2, Canada
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G4, Canada
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11
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Cabeza de Vaca I, Acebes S, Guallar V. Ecoupling server: A tool to compute and analyze electronic couplings. J Comput Chem 2016; 37:1740-5. [DOI: 10.1002/jcc.24392] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/28/2016] [Accepted: 03/31/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Israel Cabeza de Vaca
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Life Science Department, Electronic and Atomic Modeling Group; Nexus II, C/Jordi Girona, 29 Barcelona 08034 Spain
- Department of Chemistry; Yale University; New Haven Connecticut 06520-8107
| | - Sandra Acebes
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Life Science Department, Electronic and Atomic Modeling Group; Nexus II, C/Jordi Girona, 29 Barcelona 08034 Spain
| | - Victor Guallar
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Life Science Department, Electronic and Atomic Modeling Group; Nexus II, C/Jordi Girona, 29 Barcelona 08034 Spain
- Institució Catalana De Recerca I Estudis Avançats (ICREA); Barcelona Spain
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12
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Interactions of fluorescent dye SYBR Green I with natural and 7-deazaguanine-modified DNA studied by fluorescence and electrochemical methods. MONATSHEFTE FUR CHEMIE 2015. [DOI: 10.1007/s00706-015-1578-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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13
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Dunn MR, Larsen AC, Zahurancik WJ, Fahmi NE, Meyers M, Suo Z, Chaput JC. DNA Polymerase-Mediated Synthesis of Unbiased Threose Nucleic Acid (TNA) Polymers Requires 7-Deazaguanine To Suppress G:G Mispairing during TNA Transcription. J Am Chem Soc 2015; 137:4014-7. [DOI: 10.1021/ja511481n] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
| | | | - Walter J. Zahurancik
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | | | | | - Zucai Suo
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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14
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Ménová P, Dziuba D, Güixens-Gallardo P, Jurkiewicz P, Hof M, Hocek M. Fluorescence quenching in oligonucleotides containing 7-substituted 7-deazaguanine bases prepared by the nicking enzyme amplification reaction. Bioconjug Chem 2015; 26:361-6. [PMID: 25599383 DOI: 10.1021/acs.bioconjchem.5b00006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently, we reported the use of the Nicking Enzyme Amplification Reaction (NEAR) for the enzymatic synthesis of short oligonucleotides (ONs) containing 5-substituted pyrimidine or 7-substituted 7-deazaadenine nucleotides. Since no oligonucleotide products were visible on agarose gels stained by an intercalating dye (GelRed), we assumed that the method did not work for 7-substituted 7-deazaguanine deoxyribonucleoside triphosphates. We revisited the work and found that the NEAR method works for 7-deazaguanine nucleotides as well but that the resulting modified ONs quench the fluorescence of DNA intercalators, rendering them invisible on gel electrophoresis stained by them. Here, we report on the modified methodology for the NEAR synthesis and analysis of G-modified ONs and on quantification of the fluorescence quenching.
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Affiliation(s)
- Petra Ménová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center , Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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15
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Liu L, Hao J, Shi Y, Qiu J, Hao C. Roles of hydrogen bonds and π–π stacking in the optical detection of nitro-explosives with a luminescent metal–organic framework as the sensor. RSC Adv 2015. [DOI: 10.1039/c4ra12835d] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The nitro explosive detecting mechanism of a luminescent MOF sensor is revealed from the viewpoint of analyte–sensor interactions.
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Affiliation(s)
- Lei Liu
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian 116024
- China
- State Key Laboratory of Molecular Reaction Dynamics
| | - Juanyuan Hao
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian 116024
- China
| | - Yantao Shi
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian 116024
- China
| | - Jieshan Qiu
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian 116024
- China
| | - Ce Hao
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian 116024
- China
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16
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Jang YJ, Kim JM, Lee HM, Jin B, Cho TS. Enhancement of DNA mediated energy transfer by Mg 2+. J IND ENG CHEM 2015. [DOI: 10.1016/j.jiec.2014.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Tumir LM, Radić Stojković M, Piantanida I. Come-back of phenanthridine and phenanthridinium derivatives in the 21st century. Beilstein J Org Chem 2014; 10:2930-54. [PMID: 25550761 PMCID: PMC4273281 DOI: 10.3762/bjoc.10.312] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 11/21/2014] [Indexed: 12/23/2022] Open
Abstract
Phenanthridine derivatives are one of the most intensively studied families of biologically active compounds with efficient DNA binding capability. Attracting attention since DNA structure discovery (1960s), they were early recognized as a symbol of DNA intercalative binding, for many decades applied as gold-standard DNA- and RNA-fluorescent markers (ethidium bromide), probes for cell viability (propidium iodide), but also “ill-famed” for various toxic (genotoxic) and mutagenic effects. After two decades of low interest, the discovery of phenanthridine alkaloids and new studies of antiparasitic/antitumor properties of phenanthridine derivatives resulted in the strong increase of the scientific interest about the turn of this century. Here are summarized phenanthridine-related advances in the 21st century (2000-present period) with emphasis on the supramolecular interactions and bioorganic chemistry, as well as novel or improved synthetic approaches.
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Affiliation(s)
- Lidija-Marija Tumir
- Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, PO Box 180, HR-10002 Zagreb, Croatia
| | - Marijana Radić Stojković
- Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, PO Box 180, HR-10002 Zagreb, Croatia
| | - Ivo Piantanida
- Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, PO Box 180, HR-10002 Zagreb, Croatia
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18
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Esfandyarpour R, Javanmard M, Koochak Z, Esfandyarpour H, Harris JS, Davis RW. Label-free electronic probing of nucleic acids and proteins at the nanoscale using the nanoneedle biosensor. BIOMICROFLUIDICS 2013; 7:44114. [PMID: 24404047 PMCID: PMC3751968 DOI: 10.1063/1.4817771] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 07/24/2013] [Indexed: 05/20/2023]
Abstract
Detection of proteins and nucleic acids is dominantly performed using optical fluorescence based techniques, which are more costly and timely than electrical detection due to the need for expensive and bulky optical equipment and the process of fluorescent tagging. In this paper, we discuss our study of the electrical properties of nucleic acids and proteins at the nanoscale using a nanoelectronic probe we have developed, which we refer to as the Nanoneedle biosensor. The nanoneedle consists of four thin film layers: a conductive layer at the bottom acting as an electrode, an oxide layer on top, and another conductive layer on top of that, with a protective oxide above. The presence of proteins and nucleic acids near the tip results in a decrease in impedance across the sensing electrodes. There are three basic mechanisms behind the electrical response of DNA and protein molecules in solution under an applied alternating electrical field. The first change stems from modulation of the relative permittivity at the interface. The second mechanism is the formation and relaxation of the induced dipole moment. The third mechanism is the tunneling of electrons through the biomolecules. The results presented in this paper can be extended to develop low cost point-of-care diagnostic assays for the clinical setting.
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Affiliation(s)
- Rahim Esfandyarpour
- Center for Integrated Systems, Department of Electrical Engineering, Stanford University, 855 California Ave., Palo Alto, California 94304, USA ; Stanford Genome Technology Center, 855 California Ave., Palo Alto, California 94304, USA
| | - Mehdi Javanmard
- Stanford Genome Technology Center, 855 California Ave., Palo Alto, California 94304, USA
| | - Zahra Koochak
- University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Hesaam Esfandyarpour
- Center for Integrated Systems, Department of Electrical Engineering, Stanford University, 855 California Ave., Palo Alto, California 94304, USA
| | - James S Harris
- Center for Integrated Systems, Department of Electrical Engineering, Stanford University, 855 California Ave., Palo Alto, California 94304, USA
| | - Ronald W Davis
- Stanford Genome Technology Center, 855 California Ave., Palo Alto, California 94304, USA
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Berlin YA, Voityuk AA, Ratner MA. DNA base pair stacks with high electric conductance: a systematic structural search. ACS NANO 2012; 6:8216-8225. [PMID: 22901272 DOI: 10.1021/nn3030139] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We report a computational search for DNA π-stack structures exhibiting high electric conductance in the hopping regime, based on the INDO/S calculations of electronic coupling and the method of data analysis called k-means clustering. Using homogeneous poly(G)-poly(C) and poly(A)-poly(T) stacks as the simplest structural models, we identify the configurations of neighboring G:C and A:T pairs that allow strong electronic coupling and, therefore, molecular electric conductance much larger than the values reported for the corresponding reference systems in the literature. A computational approach for modeling the impact of thermal fluctuations on the averaged dimer structure was also proposed and applied to the [(G:C),(G:C)] and [(A:T),(A:T)] duplexes. The results of this work may provide guidance for the construction of DNA devices and DNA-based elements of nanoscale molecular circuits. Several factors that cause changes of step parameters favorable to the formation of the predicted stack conformation with high electric conductance of DNA molecules are also discussed; favorable geometries may enhance the conductivity by factors as large as 15.
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Affiliation(s)
- Yuri A Berlin
- Department of Chemistry, Northwestern University, 1145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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20
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21
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Quantum Chemical Calculation of Donor–Acceptor Coupling for Charge Transfer in DNA. Top Curr Chem (Cham) 2012. [DOI: 10.1007/b94472] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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22
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Yamada H, Kurata M, Tanabe K, Ito T, Nishimoto SI. Synthesis and photooxidation of oligodeoxynucleotides containing 5-dimethylaminocytosine as an efficient hole-trapping site in the positive-charge transfer through DNA duplexes. Org Biomol Chem 2012; 10:2035-43. [PMID: 22273807 DOI: 10.1039/c2ob06642d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have designed and synthesized DNA duplexes containing 5-dimethylaminocytosine ((DMA)C) to investigate the effects of C(5)-substituted cytosine bases on the transfer and trapping of positive charge (holes) in DNA duplexes. Fluorescence quenching experiments revealed that a (DMA)C base is more readily one-electron oxidized into a radical cation intermediate as compared with other natural nucleobases. Upon photoirradiation of the duplexes containing (DMA)C, the photosensitizer-injected hole migrated through the DNA bases and was trapped efficiently at the (DMA)C sites, where an enhanced oxidative strand cleavage occurred by hot piperidine treatment. The (DMA)C radical cation formed by hole transfer may undergo specific hydration and subsequent addition of molecular oxygen, thereby leading to its decomposition followed by a predominant strand cleavage at the (DMA)C site. This remarkable property suggests that the modified cytosine (DMA)C can function as an efficient hole-trapping site in the positive-charge transfer in DNA duplexes.
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Affiliation(s)
- Hisatsugu Yamada
- Advanced Biomedical Engineering Research Unit, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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23
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Ingale SA, Pujari SS, Sirivolu VR, Ding P, Xiong H, Mei H, Seela F. 7-Deazapurine and 8-aza-7-deazapurine nucleoside and oligonucleotide pyrene "click" conjugates: synthesis, nucleobase controlled fluorescence quenching, and duplex stability. J Org Chem 2011; 77:188-99. [PMID: 22129276 DOI: 10.1021/jo202103q] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
7-Deazapurine and 8-aza-7-deazapurine nucleosides related to dA and dG bearing 7-octadiynyl or 7-tripropargylamine side chains as well as corresponding oligonucleotides were synthesized. "Click" conjugation with 1-azidomethyl pyrene (10) resulted in fluorescent derivatives. Octadiynyl conjugates show only monomer fluorescence, while the proximal alignment of pyrene residues in the tripropargylamine derivatives causes excimer emission. 8-Aza-7-deazapurine pyrene "click" conjugates exhibit fluorescence emission much higher than that of 7-deazapurine derivatives. They are quenched by intramolecular charge transfer between the nucleobase and the dye. Oligonucleotide single strands decorated with two "double clicked" pyrenes show weak or no excimer fluorescence. However, when duplexes carry proximal pyrenes in complementary strands, strong excimer fluorescence is observed. A single replacement of a canonical nucleoside by a pyrene conjugate stabilizes the duplex substantially, most likely by stacking interactions: 6-12 °C for duplexes with a modified "adenine" base and 2-6 °C for a modified "guanine" base. The favorable photophysical properties of 8-aza-7-deazapurine pyrene conjugates improve the utility of pyrene fluorescence reporters in oligonucleotide sensing as these nucleoside conjugates are not affected by nucleobase induced quenching.
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Affiliation(s)
- Sachin A Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstraße 11, 48149 Münster, Germany
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24
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Electron delocalization in vinyl ruthenium substituted cyclophanes: Assessment of the through-space and the through-bond pathways. J Organomet Chem 2011. [DOI: 10.1016/j.jorganchem.2011.06.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Lin Z, Li X, Kraatz HB. Impedimetric Immobilized DNA-Based Sensor for Simultaneous Detection of Pb2+, Ag+, and Hg2+. Anal Chem 2011; 83:6896-901. [DOI: 10.1021/ac2014096] [Citation(s) in RCA: 246] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Zhenzhen Lin
- Department of Chemistry, Beijing Normal University, Beijing, China, 100875
| | - Xiaohong Li
- Department of Chemistry, Beijing Normal University, Beijing, China, 100875
| | - Heinz-Bernhard Kraatz
- Department of Chemistry, University of Western Ontario,1151 Richmond Street, London, N6A 5B7, Canada
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26
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Abstract
In all organisms, oxidation threatens the integrity of the genome. DNA-mediated charge transport (CT) may play an important role in the generation and repair of this oxidative damage. In studies involving long-range CT from intercalating Ru and Rh complexes to 5'-GG-3' sites, we have examined the efficiency of CT as a function of distance, temperature, and the electronic coupling of metal oxidants bound to the base stack. Most striking is the shallow distance dependence and the sensitivity of DNA CT to how the metal complexes are stacked in the helix. Experiments with cyclopropylamine-modified bases have revealed that charge occupation occurs at all sites along the bridge. Using Ir complexes, we have seen that the process of DNA-mediated reduction is very similar to that of DNA-mediated oxidation. Studies involving metalloproteins have, furthermore, shown that their redox activity is DNA-dependent and can be DNA-mediated. Long range DNA-mediated CT can facilitate the oxidation of DNA-bound base excision repair proteins to initiate a redox-active search for DNA lesions. DNA CT can also activate the transcription factor SoxR, triggering a cellular response to oxidative stress. Indeed, these studies show that within the cell, redox-active proteins may utilize the same chemistry as that of synthetic metal complexes in vitro, and these proteins may harness DNA-mediated CT to reduce damage to the genome and regulate cellular processes.
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Affiliation(s)
- Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Eric D. Olmon
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Pamela A. Sontz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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27
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Zhu X, Xu H, Gao X, Li X, Liu Q, Lin Z, Qiu B, Chen G. Design of a DNA electronic logic gate (INHIBIT gate) with an assaying application for Ag+ and cysteine. Chem Commun (Camb) 2011; 47:9080-2. [DOI: 10.1039/c1cc12734a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Pivoňková H, Horáková P, Fojtová M, Fojta M. Direct Voltammetric Analysis of DNA Modified with Enzymatically Incorporated 7-Deazapurines. Anal Chem 2010; 82:6807-13. [DOI: 10.1021/ac100757v] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hana Pivoňková
- Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic, Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ-532 10 Pardubice, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic
| | - Petra Horáková
- Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic, Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ-532 10 Pardubice, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic
| | - Miloslava Fojtová
- Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic, Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ-532 10 Pardubice, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic, Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ-532 10 Pardubice, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic
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29
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Prunkl C, Pichlmaier M, Winter R, Kharlanov V, Rettig W, Wagenknecht HA. Optical, Redox, and DNA-Binding Properties of Phenanthridinium Chromophores: Elucidating the Role of the Phenyl Substituent for Fluorescence Enhancement of Ethidium in the Presence of DNA. Chemistry 2010; 16:3392-402. [DOI: 10.1002/chem.200902823] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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30
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Affiliation(s)
- Joseph C. Genereux
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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31
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Prunkl C, Berndl S, Wanninger-Weiß C, Barbaric J, Wagenknecht HA. Photoinduced short-range electron transfer in DNA with fluorescent DNA bases: lessons from ethidium and thiazole orange as charge donors. Phys Chem Chem Phys 2010; 12:32-43. [DOI: 10.1039/b914487k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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32
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Zhu X, Chen L, Lin Z, Qiu B, Chen G. A highly sensitive and selective “signal-on” electrochemiluminescent biosensor for mercury. Chem Commun (Camb) 2010; 46:3149-51. [DOI: 10.1039/b926319e] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Wanninger-Weiss C, Valis L, Wagenknecht HA. Pyrene-modified guanosine as fluorescent probe for DNA modulated by charge transfer. Bioorg Med Chem 2008; 16:100-6. [PMID: 17509886 DOI: 10.1016/j.bmc.2007.04.064] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Accepted: 04/27/2007] [Indexed: 11/24/2022]
Abstract
8-(Pyren-1-yl)-2'-deoxyguanosine (Py-G) was incorporated synthetically as a modified DNA base and optical probe into oligonucleotides. A variety of Py-G-modified DNA duplexes have been investigated by methods of optical spectroscopy. The DNA duplex hybridization can be observed by both fluorescence and absorption spectroscopy since the Py-G group exhibits altered properties in single strands versus double strands for both spectroscopy methods. The fluorescence enhancement upon DNA hybridization can be improved significantly by the presence of 7-deazaguanin as an additional modification and charge acceptor three bases away from the Py-G modification site. Moreover, Py-G in DNA can be applied as a photoinducable donor for charge transfer processes when indol is present as an artificial DNA base and charge acceptor. Correctly base-paired duplexes can be discriminated from mismatched ones by comparison of their fluorescence quenching.
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Affiliation(s)
- Claudia Wanninger-Weiss
- University of Regensburg, Institute for Organic Chemistry, Universitätstr. 31, D-93053 Regensburg, Germany
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34
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Hasegawa JY, Nakatsuji H. Exploring Photobiology and Biospectroscopy with the Sac-Ci (Symmetry-Adapted Cluster-Configuration Interaction) Method. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/978-1-4020-8184-2_4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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35
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von Feilitzsch T, Tuma J, Neubauer H, Verdier L, Haselsberger R, Feick R, Gurzadyan G, Voityuk AA, Griesinger C, Michel-Beyerle ME. Chromophore/DNA Interactions: Femto- to Nanosecond Spectroscopy, NMR Structure, and Electron Transfer Theory. J Phys Chem B 2007; 112:973-89. [DOI: 10.1021/jp076405o] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Till von Feilitzsch
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
| | - Jennifer Tuma
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
| | - Heike Neubauer
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
| | - Laurent Verdier
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
| | - Reinhard Haselsberger
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
| | - Reiner Feick
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
| | - Gagik Gurzadyan
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
| | - Alexander A. Voityuk
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
| | - Christian Griesinger
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
| | - Maria E. Michel-Beyerle
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
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36
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Gabelica V, Rosu F, De Pauw E, Antoine R, Tabarin T, Broyer M, Dugourd P. Electron photodetachment dissociation of DNA anions with covalently or noncovalently bound chromophores. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1990-2000. [PMID: 17900923 DOI: 10.1016/j.jasms.2007.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Revised: 08/17/2007] [Accepted: 08/17/2007] [Indexed: 05/17/2023]
Abstract
Double stranded DNA multiply charged anions coupled to chromophores were subjected to UV-Vis photoactivation in a quadrupole ion trap mass spectrometer. The chromophores included noncovalently bound minor groove binders (activated in the near UV), noncovalently bound intercalators (activated with visible light), and covalently linked fluorophores and quenchers (activated at their maximum absorption wavelength). We found that the activation of only chromophores having long fluorescence lifetimes did result in efficient electron photodetachment from the DNA complexes. In the case of ethidium-dsDNA complex excited at 500 nm, photodetachment is a multiphoton process. The MS(3) fragmentation of radicals produced by photodetachment at lambda = 260 nm (DNA excitation) and by photodetachment at lambda > 300 nm (chromophore excitation) were compared. The radicals keep no memory of the way they were produced. A weakly bound noncovalent ligand (m-amsacrine) allowed probing experimentally that a fraction of the electronic internal energy was converted into vibrational internal energy. This fragmentation channel was used to demonstrate that excitation of the quencher DABSYL resulted in internal conversion, unlike the fluorophore 6-FAM. Altogether, photodetachment of the DNA complexes upon chromophore excitation can be interpreted by the following mechanism: (1) ligands with sufficiently long excited-state lifetime undergo resonant two-photon excitation to reach the level of the DNA excited states, then (2) the excited-state must be coupled to the DNA excited states for photodetachment to occur. Our experiments also pave the way towards photodissociation probes of biomolecule conformation in the gas-phase by Förster resonance energy transfer (FRET).
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Affiliation(s)
- Valérie Gabelica
- Mass Spectrometry Laboratory, Université de Liège, Institut de Chimie Liège, Belgium.
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37
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Rospigliosi A, Ehlich R, Hoerber H, Middelberg A, Moggridge G. Electron transfer of plurimodified DNA SAMs. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:8264-71. [PMID: 17590024 DOI: 10.1021/la063704g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
An STM-based current-voltage (I/V) investigation of deoxyribonucleic acid (DNA) 18 base pair (bp) oligonucleotide monolayers on gold is presented. Three bases of each of the immobilized and complementary strands were modified with either iodine or phenylethylene moieties. The oligonucleotides were immobilized on template stripped gold (tsg) surfaces and characterized by atomic force microscopy (AFM) and scanning tunneling microscopy (STM). AFM imaging showed that monolayers of the expected height were formed. A comparative study of normal, halogenated, and phenyl-modified DNA was made with the STM in tunneling spectroscopy (TS) mode. I/V spectroscopic measurements in the range +/-250 mV on both single- and double-stranded (ds) DNA monolayers (modified and unmodified) showed that for negative substrate bias (U(sub)) electron transfer is more efficient through a phenyl-modified monolayer than through normal or halogenated DNA. This effect was particularly clear below a threshold bias of -100 mV. For positive U(sub), unmodified ds DNA was found to conduct slightly better than the modified strands. This is presumably caused by greater order in the unmodified versus modified DNA monolayers. Modifications on the immobilized (thiolated) strand seem to improve electron transport through the DNA monolayer more than modifications on the complementary (not surface-bound) strand.
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Affiliation(s)
- Alessandro Rospigliosi
- Department of Chemical Engineering, University of Cambridge, Pembroke Street, New Museum Site, Cambridge, United Kingdom.
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38
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Tanabe K, Yamada H, Nishimoto SI. One-electron photooxidation and site-selective strand cleavage at 5-methylcytosine in DNA by sensitization with 2-methyl-1,4-naphthoquinone-tethered oligonucleotides. J Am Chem Soc 2007; 129:8034-40. [PMID: 17547405 DOI: 10.1021/ja071369s] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photosensitized one-electron oxidation was applied to discriminate a specific base site of 5-methylcytosine (mC) generated in DNA possessing a partial sequence of naturally occurring p53 gene, using a sensitizing 2-methyl-1,4-naphthoquinone (NQ) chromophore tethered to an interior of oligodeoxynucleotide (ODN) strands. Photoirradiation and subsequent hot piperidine treatment of the duplex consisting of mC-containing DNA and NQ-tethered complementary ODN led to oxidative strand cleavage selectively at the mC site, when the NQ chromophore was arranged so as to be in close contact with the target mC. The target mC is most likely to be one-electron oxidized into the radical cation intermediate by the sensitization of NQ. The resulting mC radical cation may undergo rapid deprotonation and subsequent addition of molecular oxygen, thereby leading to its degradation followed by strand cleavage at the target mC site. In contrast to mC-containing ODN, ODN analogs with replacement of normal cytosine, thymine, adenine, or guanine at the mC site underwent less amount of such an oxidative strand cleavage at the target base site, presumably due to occurrence of charge transfer and charge recombination processes between the base radical cation and the NQ radical anion. Furthermore, well designed incorporation of the NQ chromophore into an interior of ODN could suppress a competitive strand cleavage at consecutive guanines, which occurred as a result of positive charge transfer. Thus, photosensitization by an NQ-tethered ODN led to one-electron oxidative strand cleavage exclusively at the target mC site, providing a convenient method of discriminating mC in naturally occurring DNA such as human p53 gene as a positive band on a sequencing gel.
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Affiliation(s)
- Kazuhito Tanabe
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Kyoto 615-8510, Japan.
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39
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Affiliation(s)
- Matthew Ray Holman
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
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41
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Eng MP, Albinsson B. Non-Exponential Distance Dependence of Bridge-Mediated Electronic Coupling. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200601379] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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42
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Eng MP, Albinsson B. Non-Exponential Distance Dependence of Bridge-Mediated Electronic Coupling. Angew Chem Int Ed Engl 2006; 45:5626-9. [PMID: 16871599 DOI: 10.1002/anie.200601379] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mattias P Eng
- Chalmers University of Technology, Department of Chemical and Biological Engineering, 412 96 Göteborg, Sweden
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43
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Bureekaew S, Hasegawa JY, Nakatsuji H. Electronic circular dichroism spectrum of uridine studied by the SAC–CI method. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.03.102] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Valis L, Wang Q, Raytchev M, Buchvarov I, Wagenknecht HA, Fiebig T. Base pair motions control the rates and distance dependencies of reductive and oxidative DNA charge transfer. Proc Natl Acad Sci U S A 2006; 103:10192-10195. [PMID: 16801552 PMCID: PMC1502433 DOI: 10.1073/pnas.0600957103] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In 1999, Wan et al. [Proc. Natl. Acad. Sci. USA 96, 6014-6019] published a pioneering paper that established the entanglement between DNA base pair motions and the transfer time of the charge carrier. The DNA assemblies contained an ethidium covalently bound via a flexible alkyl chain to the 5' hydroxyl group of the DNA backbone. Although covalently attached, the loose way in which the ethidium was linked to DNA allowed for large degrees of conformational freedom and thus raised some concern with respect to conformational inhomogeneity. In this letter, we report studies on a different set of ethidium DNA conjugates. In contrast to the "Caltech systems," these conjugates contain ethidium tightly incorporated (as a base pair surrogate) into the DNA base stack, opposite to an abasic site analog. Despite the tight binding, we found that charge transfer from the photoexcited ethidium base pair surrogate across two or more base pairs is several orders of magnitude slower than in case of the DNA systems bearing the tethered ethidium. To further broaden the scope of this account, we compared (oxidative) electron hole transfer and (reductive) electron transfer using the same ethidium chromophore as a charge donor in combination with two different charge acceptors. We found that both electron and hole transfer are characterized by similar rates and distance dependencies. The results demonstrate the importance of nuclear motions and conformational flexibility and underline the presence of a base gating mechanism, which appears to be generic to electronic transfer processes through pi-stacked nucleic acids.
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Affiliation(s)
- Linda Valis
- Institute for Organic Chemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Qiang Wang
- Eugene F. Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467; and
| | - Milen Raytchev
- Eugene F. Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467; and
| | - Ivan Buchvarov
- Eugene F. Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467; and
| | | | - Torsten Fiebig
- Eugene F. Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467; and
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Wagenknecht HA. Electron transfer processes in DNA: mechanisms, biological relevance and applications in DNA analytics. Nat Prod Rep 2006; 23:973-1006. [PMID: 17119642 DOI: 10.1039/b504754b] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In principle, DNA-mediated charge transfer processes can be categorized as oxidative hole transfer and reductive electron transfer. With respect to the routes of DNA damage most of the past research has been focused on the investigation of oxidative hole transfer or transport. On the other hand, the transport or transfer of excess electrons has a large potential for biomedical applications, mainly for DNA chip technology.
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Affiliation(s)
- Hans-Achim Wagenknecht
- University of Regensburg, Institute for Organic Chemistry, D-93040, Regensburg, Germany.
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Li H, Seela F. Parallel and antiparallel DNA: fluorescence quenching of ethidium bromide by 7-deazapurines. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:865-8. [PMID: 16248051 DOI: 10.1081/ncn-200059214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The fluorescence quenching of ethidium bromide caused by 7-deaza-2'-deoxyguanosine or 7-deaza2'-deoxyisoguanosine is observed in DNA with parallel or anti-parallel chain orientation.
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Affiliation(s)
- Hong Li
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Germany
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Dohno C, Saito I. Discrimination of single-nucleotide alterations by G-specific fluorescence quenching. Chembiochem 2005; 6:1075-81. [PMID: 15852333 DOI: 10.1002/cbic.200400325] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A new strategy for the detection of single-base alterations through fluorescence quenching by guanine (G) is described. We have devised a novel base-discriminating fluorescent (BDF) nucleoside, 4'PyT, that contains a pyrenecarboxamide fluorophore at the thymidine sugar's C4'-position. 4'PyT-containing oligodeoxynucleotides only exhibited enhanced fluorescence in response to the presence of a complementary adenine base. In contrast, the fluorescence of mismatched duplexes containing 4'PyT/N base pairs (N = C, G, or T) was considerably weaker. This highly A-selective fluorescence was a product of guanine-specific quenching efficiency; when the complementary base to 4'PyT was a mismatch, the pyrenecarboxamide fluorophore was able to interact intimately with neighboring G bases (the most likely interaction in the case of intercalation), so effective quenching by the G bases occurred in the mismatched duplexes. In contrast, duplexes containing 4'PyT/A base pairs exhibited strong emission, since in this case the fluorophores were positioned in the minor groove and able to escape fluorescence quenching by the G bases.
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Affiliation(s)
- Chikara Dohno
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, 615-8510 Kyoto, Japan
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Sandin P, Wilhelmsson LM, Lincoln P, Powers VEC, Brown T, Albinsson B. Fluorescent properties of DNA base analogue tC upon incorporation into DNA--negligible influence of neighbouring bases on fluorescence quantum yield. Nucleic Acids Res 2005; 33:5019-25. [PMID: 16147985 PMCID: PMC1201328 DOI: 10.1093/nar/gki790] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The quantum yield of the fluorescent tricyclic cytosine analogue, 1,3-diaza-2-oxophenothiazine, tC, is high and virtually unaffected by incorporation into both single- and double-stranded DNA irrespective of neighbouring bases (0.17-0.24 and 0.16-0.21, respectively) and the corresponding fluorescence decay curves are all mono-exponential, properties that are unmatched by any base analogue so far. The fluorescence lifetimes increase when going from tC free in solution (3.2 ns) to single- and double-stranded DNA (on average 5.7 and 6.3 ns, respectively). The mono-exponential decays further support previous NMR results where it was found that tC has a well-defined position and geometry within the DNA helix. Furthermore, we find that the oxidation potential of tC is 0.4 V lower than for deoxyguanosine, the natural base with the lowest oxidation potential. This suggests that tC may be of interest in charge transfer studies in DNA as an electron hole acceptor. We also present a novel synthetic route to the phosphoramidite form of tC. The results presented here together with previous work show that tC is a very good C-analogue that induces minimal perturbation to the native structure of DNA. This makes tC unique as a fluorescent base analogue and is thus highly interesting in a range of applications for studying e.g. structure, dynamics and kinetics in nucleic acid systems.
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Affiliation(s)
| | - L. Marcus Wilhelmsson
- To whom the correspondence should be addressed. Tel: +46 31 7723051; Fax: +46 31 7723858;
| | | | - Vicki E. C. Powers
- School of Chemistry, University of SouthamptonHighfield, Southampton SO17 1BJ, UK
| | - Tom Brown
- School of Chemistry, University of SouthamptonHighfield, Southampton SO17 1BJ, UK
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Wan C, Xia T, Becker HC, Zewail AH. Ultrafast unequilibrated charge transfer: A new channel in the quenching of fluorescent biological probes. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2005.06.101] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Seela F, Peng X. Synthesis and Properties of 7‐Substituted 7‐Deazapurine (Pyrrolo[2,3‐d]pyrimidine) 2′‐Deoxyribonucleosides. ACTA ACUST UNITED AC 2005; Chapter 1:Unit 1.10. [DOI: 10.1002/0471142700.nc0110s21] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Frank Seela
- Universität Osnabrück Osnabrück Germany
- Center for Nanotechnology (CeNTech) Münster Germany
| | - Xiaohua Peng
- Universität Osnabrück Osnabrück Germany
- Center for Nanotechnology (CeNTech) Münster Germany
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