1
|
Poddar S, Levitus M. Buffer-Dependent Photophysics of 2-Aminopurine: Insights into Fluorescence Quenching and Excited-State Interactions. J Phys Chem B 2024; 128:2640-2651. [PMID: 38452253 DOI: 10.1021/acs.jpcb.3c07269] [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: 03/09/2024]
Abstract
2-Aminopurine (2AP) is the most widely used fluorescent nucleobase analogue in DNA and RNA research. Its unique photophysical properties and sensitivity to environmental changes make it a useful tool for understanding nucleic acid dynamics and DNA-protein interactions. We studied the effect of ions present in commonly used buffer solutions on the excited-state photophysical properties of 2AP. Fluorescence quenching was negligible for tris(hydroxymethyl)aminomethane (TRIS), but significant for phosphate, carbonate, 3-(N-morpholino) propanesulfonic acid (MOPS), and 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) buffers. Results indicate that the two tautomers of 2AP (7H, 9H) are quenched by phosphate ions to different extents. Quenching by the H2PO4- ion is more pronounced for the 7H tautomer, while the opposite is true for the HPO42- ion. For phosphate ions, the results of the time-resolved fluorescence study cannot be explained using a simple collisional quenching mechanism. Instead, results are consistent with transient interactions between 2AP and the phosphate ions. We postulate that excited-state interactions between the 2AP tautomers and an H-bond acceptor (phosphate and carbonate) result in significant quenching of the singlet-excited state of 2AP. Such interactions manifest in biexponential fluorescence intensity decays with pre-exponential factors that vary with quencher concentration, and downward curvatures of the Stern-Volmer plots.
Collapse
Affiliation(s)
- Souvik Poddar
- School of Molecular Sciences, Arizona State University, 551 E. University Drive, Tempe, Arizona 85287, United States
- The Biodesign Institute Center for Single Molecule Biophysics, Arizona State University, Tempe, Arizona 85287, United States
| | - Marcia Levitus
- School of Molecular Sciences, Arizona State University, 551 E. University Drive, Tempe, Arizona 85287, United States
- The Biodesign Institute Center for Single Molecule Biophysics, Arizona State University, Tempe, Arizona 85287, United States
| |
Collapse
|
2
|
Oliveira LMF, Valverde D, Costa GJ, Borin AC. The copious photochemistry of 2,6-diaminopurine: Luminescence, triplet population, and ground state recovery. Photochem Photobiol 2024; 100:323-338. [PMID: 37403286 DOI: 10.1111/php.13833] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/06/2023]
Abstract
9H- and 7H-2,6-Diaminopurine (26DAP) photoinduced events in vacuum were studied at the MS-CASPT2/cc-pVDZ level of theory. The S1 1 (ππ* La ) state is initially populated evolving barrierless towards its minimum energy structure, from where two photochemical events can take place in both tautomers. The first is the return of the electronic population to the ground state via the C6 conical intersection (CI-C6). The second involves an internal conversion to the ground through the C2 conical intersection (CI-C2). According to our geodesic interpolated paths connecting the critical structures, the second route is less favorable in both tautomers, due to the presence of high energy barriers. Our calculations suggest a competition between fluorescence and ultrafast relaxation to the electronic ground state via internal conversion process. Based on our calculated potential energy surfaces and experimental excited state lifetimes from the literature, we can infer that the 7H- must have a greater fluorescence yield than the 9H-tautomer. We also explored the triplet state population mechanisms on the 7H-26DAP to understand their long-lived components observed experimentally.
Collapse
Affiliation(s)
- Leonardo M F Oliveira
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Danillo Valverde
- Unité de Chimie Physique Théorique et Structurale, Namur Institute of Structured Matter, Université de Namur, Namur, Belgium
| | - Gustavo J Costa
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
3
|
Gate G, Williams A, Boldissar S, Šponer J, Szabla R, de Vries M. The tautomer-specific excited state dynamics of 2,6-diaminopurine using resonance-enhanced multiphoton ionization and quantum chemical calculations. Photochem Photobiol 2024; 100:404-418. [PMID: 38124372 DOI: 10.1111/php.13897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
2,6-Diaminopurine (2,6-dAP) is an alternative nucleobase that potentially played a role in prebiotic chemistry. We studied its excited state dynamics in the gas phase by REMPI, IR-UV hole burning, and ps pump-probe spectroscopy and performed quantum chemical calculations at the SCS-ADC(2) level of theory to interpret the experimental results. We found the 9H tautomer to have a small barrier to ultrafast relaxation via puckering of its 6-membered ring. The 7H tautomer has a larger barrier to reach a conical intersection and also has a sizable triplet yield. These results are discussed relative to other purines, for which 9H tautomerization appears to be more photostable than 7H and homosubstituted purines appear to be less photostable than heterosubstituted or singly substituted purines.
Collapse
Affiliation(s)
- Gregory Gate
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Ann Williams
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Samuel Boldissar
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Olomouc-Holice, Czech Republic
| | - Rafal Szabla
- Institute of Advanced Materials, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Mattanjah de Vries
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| |
Collapse
|
4
|
Widom JR, Hoeher JE. Base-Stacking Heterogeneity in RNA Resolved by Fluorescence-Detected Circular Dichroism Spectroscopy. J Phys Chem Lett 2022; 13:8010-8018. [PMID: 35984918 PMCID: PMC9442794 DOI: 10.1021/acs.jpclett.2c01778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/17/2022] [Indexed: 06/01/2023]
Abstract
RNA plays a critical role in many biological processes, and the structures it adopts are intimately linked to those functions. Among many factors that contribute to RNA folding, van der Waals interactions between adjacent nucleobases stabilize structures in which the bases are stacked on top of one another. Here, we utilize fluorescence-detected circular dichroism spectroscopy (FDCD) to investigate base-stacking heterogeneity in RNA labeled with the fluorescent adenine analogue 2-aminopurine (2-AP). Comparison of standard (transmission-detected) CD and FDCD spectra reveals that in dinucleotides, 2-AP fluorescence is emitted almost exclusively by unstacked molecules. In a trinucleotide, some fluorescence is emitted by a population of stacked and highly quenched molecules, but more than half originates from a minor ∼10% population of unstacked molecules. The combination of FDCD and standard CD measurements reveals the prevalence of stacked and unstacked conformational subpopulations as well as their relative fluorescence quantum yields.
Collapse
|
5
|
Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
Collapse
Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| |
Collapse
|
6
|
Bull GD, Thompson KC. The oxidation of guanine by photoionized 2-aminopurine. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2021. [DOI: 10.1016/j.jpap.2021.100025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
7
|
Nobis D, Fisher RS, Simmermacher M, Hopkins PA, Tor Y, Jones AC, Magennis SW. Single-Molecule Detection of a Fluorescent Nucleobase Analogue via Multiphoton Excitation. J Phys Chem Lett 2019; 10:5008-5012. [PMID: 31397575 PMCID: PMC7024020 DOI: 10.1021/acs.jpclett.9b02108] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The ability to routinely detect fluorescent nucleobase analogues at the single-molecule level would create a wealth of opportunities to study nucleic acids. We report the multiphoton-induced fluorescence and single-molecule detection of a dimethylamine-substituted extended-6-aza-uridine (DMAthaU). We show that DMAthaU can exist in a highly fluorescent form, emitting strongly in the visible region (470-560 nm). Using pulse-shaped broadband Ti:sapphire laser excitation, DMAthaU undergoes two-photon (2P) absorption at low excitation powers, switching to three-photon (3P) absorption at high incident intensity. The assignment of a 3P process is supported by cubic response calculations. Under both 2P and 3P excitation, the single-molecule brightness was over an order of magnitude higher than reported previously for any fluorescent base analogue, which facilitated the first single-molecule detection of an emissive nucleoside with multiphoton excitation.
Collapse
Affiliation(s)
- David Nobis
- WestCHEM School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K
| | - Rachel S. Fisher
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Mats Simmermacher
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Patrycja A. Hopkins
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Anita C. Jones
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
- Corresponding Authors (A.C.J.)., (S.W.M.)
| | - Steven W. Magennis
- WestCHEM School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K
- Corresponding Authors (A.C.J.)., (S.W.M.)
| |
Collapse
|
8
|
Böhnke H, Röttger K, Ingle RA, Marroux HJB, Bohnsack M, Schwalb NK, Orr-Ewing AJ, Temps F. Electronic Relaxation Dynamics of UV-Photoexcited 2-Aminopurine-Thymine Base Pairs in Watson-Crick and Hoogsteen Conformations. J Phys Chem B 2019; 123:2904-2914. [PMID: 30875228 DOI: 10.1021/acs.jpcb.9b02361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fluorescent analogue 2-aminopurine (2AP) of the canonical nucleobase adenine (6-aminopurine) base-pairs with thymine (T) without disrupting the helical structure of DNA. It therefore finds frequent use in molecular biology for probing DNA and RNA structures and conformational dynamics. However, detailed understanding of the processes responsible for fluorescence quenching remains largely elusive on a fundamental level. Although attempts have been made to ascribe decreased excited-state lifetimes to intrastrand charge-transfer and stacking interactions, possible influences from dynamic interstrand H-bonding have been widely ignored. Here, we investigate the electronic relaxation of UV-excited 2AP·T in Watson-Crick (WC) and Hoogsteen (HS) conformations. Although the WC conformation features slowed-down, monomer-like electronic relaxation in τ ∼ 1.6 ns toward ground-state recovery and triplet formation, the dynamics associated with 2AP·T in the HS motif exhibit faster deactivation in τ ∼ 70 ps. As recent research has revealed abundant transient interstrand H-bonding in the Hoogsteen motif for duplex DNA, the established model for dynamic fluorescence quenching may need to be revised in the light of our results. The underlying supramolecular photophysical mechanisms are discussed in terms of a proposed excited-state double-proton transfer as an efficient deactivation channel for recovery of the HS species in the electronic ground state.
Collapse
Affiliation(s)
- Hendrik Böhnke
- Institute of Physical Chemistry , Christian-Albrechts-University Kiel , Olshausenstr. 40 , 24098 Kiel , Germany
| | - Katharina Röttger
- Institute of Physical Chemistry , Christian-Albrechts-University Kiel , Olshausenstr. 40 , 24098 Kiel , Germany.,School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , U.K
| | - Rebecca A Ingle
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , U.K
| | - Hugo J B Marroux
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , U.K
| | - Mats Bohnsack
- Institute of Physical Chemistry , Christian-Albrechts-University Kiel , Olshausenstr. 40 , 24098 Kiel , Germany
| | - Nina K Schwalb
- Institute of Physical Chemistry , Christian-Albrechts-University Kiel , Olshausenstr. 40 , 24098 Kiel , Germany
| | - Andrew J Orr-Ewing
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , U.K
| | - Friedrich Temps
- Institute of Physical Chemistry , Christian-Albrechts-University Kiel , Olshausenstr. 40 , 24098 Kiel , Germany
| |
Collapse
|
9
|
Fisher RS, Nobis D, Füchtbauer AF, Bood M, Grøtli M, Wilhelmsson LM, Jones AC, Magennis SW. Pulse-shaped two-photon excitation of a fluorescent base analogue approaches single-molecule sensitivity. Phys Chem Chem Phys 2018; 20:28487-28498. [PMID: 30412214 DOI: 10.1039/c8cp05496g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Fluorescent nucleobase analogues (FBAs) have many desirable features in comparison to extrinsic fluorescent labels, but they are yet to find application in ultrasensitive detection. Many of the disadvantages of FBAs arise from their short excitation wavelengths (often in the ultraviolet), making two-photon excitation a potentially attractive approach. Pentacyclic adenine (pA) is a recently developed FBA that has an exceptionally high two-photon brightness. We have studied the two-photon-excited fluorescence properties of pA and how they are affected by incorporation in DNA. We find that pA is more photostable under two-photon excitation than via resonant absorption. When incorporated in an oligonucleotide, pA has a high two-photon cross section and emission quantum yield, varying with sequence context, resulting in the highest reported brightness for such a probe. The use of a two-photon microscope with ultrafast excitation and pulse shaping has allowed the detection of pA-containing oligonucleotides in solution with a limit of detection of ∼5 molecules, demonstrating that practical single-molecule detection of FBAs is now within reach.
Collapse
Affiliation(s)
- Rachel S Fisher
- EaStCHEM School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh, EH9 3JJ, UK.
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Bull GD, Thompson KC. Proton Transfer and Tautomerism in 2-Aminopurine-Thymine and Pyrrolocytosine-Guanine Base Pairs. Biochemistry 2018; 57:4547-4561. [PMID: 30024730 DOI: 10.1021/acs.biochem.8b00521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Pyrrolocytosine (PC) and 2-aminopurine (2AP) are fluorescent nucleobase analogues of the DNA nucleobases cytosine and adenine, respectively, and form base pairs with guanine and thymine. Both fluorescent nucleobases are used extensively as probes for local structure in nucleic acids as the fluorescence properties of PC and 2AP are very sensitive to changes such as helix formation, although the reasons for this sensitivity are not clear. To address this question, ab initio calculations have been used to calculate energies, at the MP2 and CIS level, of three different tautomer pairings of PC-G, and two of 2AP-T, which can potentially be interconverted by double proton transfer between the bases. Potential energy curves linking the different tautomer pairs have been calculated. For both PC-G and 2AP-T, the most stable tautomer pair in the electronic ground state is that analogous to the natural C-G and A-T base pair. In the case of 2AP-T, an alternative, stable, tautomer base pair was located in the first electronically excited state; however, it lies higher in energy than the tautomer pair analogous to A-T, making conversion to the alternative form unlikely. In contrast, in the case of PC-G, an alternative tautomer base pair is found to be the most stable form in the first electronically excited state, and this form is accessible following initial excitation from the ground state tautomer pair, thus suggesting an alternative deactivation route via double proton transfer may be possible when PC is involved in hydrogen bonding, such as occurs in helical conformations.
Collapse
Affiliation(s)
- Graham D Bull
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck , University of London , Malet Street , Bloomsbury, London WC1E 7HX , U.K
| | - Katherine C Thompson
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck , University of London , Malet Street , Bloomsbury, London WC1E 7HX , U.K
| |
Collapse
|
11
|
Mikhaylov A, de Reguardati S, Pahapill J, Callis PR, Kohler B, Rebane A. Two-photon absorption spectra of fluorescent isomorphic DNA base analogs. BIOMEDICAL OPTICS EXPRESS 2018; 9:447-452. [PMID: 29552385 PMCID: PMC5854050 DOI: 10.1364/boe.9.000447] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/12/2017] [Accepted: 12/20/2017] [Indexed: 05/14/2023]
Abstract
Fluorescent DNA base analogs and intrinsic fluorophores are gaining importance for multiphoton microscopy and imaging, however, their quantitative nonlinear excitation properties have been poorly documented. Here we present the two-photon absorption (2PA) spectra of 2-aminopurine (2AP), 7-methyl guanosine (7MG), isoxanthopterin (IXP), 6-methyl isoxanthopterin (6MI), as well as L-tryptophan (L-trp) and 3-methylindole (3MI) in aqueous solution and some organic solvents measured in the wavelength range 550 - 810 nm using femtosecond two-photon excited fluorescence (2PEF) and nonlinear transmission (NLT) methods. The peak 2PA cross section values range from 0.1 GM (1 GM = 10-50 cm4 s photon-1) for 2AP to 2.0 GM for IXP and 7MG. Assuming typical excitation conditions for a scanning 2PEF microscope, we estimate a maximum image frame rate of ~175 frames per second (FPS).
Collapse
Affiliation(s)
| | | | - Jüri Pahapill
- National Institute of Chemical Physics and Biophysics, Tallinn 12618, Estonia
| | - Patrik R. Callis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Aleksander Rebane
- Department of Physics, Montana State University, Bozeman, MT 59717, USA
- National Institute of Chemical Physics and Biophysics, Tallinn 12618, Estonia
| |
Collapse
|
12
|
Böhnke H, Röttger K, Ingle RA, Marroux HJB, Bohnsack M, Orr-Ewing AJ, Temps F. Efficient intersystem crossing in 2-aminopurine riboside probed by femtosecond time-resolved transient vibrational absorption spectroscopy. Phys Chem Chem Phys 2018; 20:20033-20042. [DOI: 10.1039/c8cp02664e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The photophysical dynamics of 2-aminopurine, a fluorescent analogue of the canonical nucleobase adenine, has been studied by femtosecond transient vibrational absorption spectroscopy.
Collapse
Affiliation(s)
- Hendrik Böhnke
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
| | - Katharina Röttger
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
- School of Chemistry
| | | | | | - Mats Bohnsack
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
| | | | - Friedrich Temps
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
| |
Collapse
|
13
|
Smith DA, Holroyd LF, van Mourik T, Jones AC. A DFT study of 2-aminopurine-containing dinucleotides: prediction of stacked conformations with B-DNA structure. Phys Chem Chem Phys 2017; 18:14691-700. [PMID: 27186599 DOI: 10.1039/c5cp07816d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The fluorescence properties of dinucleotides incorporating 2-aminopurine (2AP) suggest that the simplest oligonucleotides adopt conformations similar to those found in duplex DNA. However, there is a lack of structural data for these systems. We report a density functional theory (DFT) study of the structures of 2AP-containing dinucleotides (deoxydinucleoside monophosphates), including full geometry optimisation of the sugar-phosphate backbone. Our DFT calculations employ the M06-2X functional for reliable treatment of dispersion interactions and include implicit aqueous solvation. Dinucleotides with 2AP in the 5'-position and each of the natural bases in the 3'-position are examined, together with the analogous 5'-adenine-containing systems. Computed structures are compared in detail with typical B-DNA base-step parameters, backbone torsional angles and sugar pucker, derived from crystallographic data. We find that 2AP-containing dinucleotides adopt structures that closely conform to B-DNA in all characteristic parameters. The structures of 2AP-containing dinucleotides closely resemble those of their adenine-containing counterparts, demonstrating the fidelity of 2AP as a mimic of the natural base. As a first step towards exploring the conformational heterogeneity of dinucleotides, we also characterise an imperfectly stacked conformation and one in which the bases are completely unstacked.
Collapse
Affiliation(s)
- Darren A Smith
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
| | - Leo F Holroyd
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Anita C Jones
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
| |
Collapse
|
14
|
Brovarets' OO, Pérez-Sánchez H. Whether 2-aminopurine induces incorporation errors at the DNA replication? A quantum-mechanical answer on the actual biological issue. J Biomol Struct Dyn 2016; 35:3398-3411. [PMID: 27794627 DOI: 10.1080/07391102.2016.1253504] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In this paper, we consider the mutagenic properties of the 2-aminopurine (2AP), which has intrigued molecular biologists, biophysicists and physical chemists for a long time and been widely studied by both experimentalists and theorists. We have shown for the first time using QM calculations, that 2AP very effectively produces incorporation errors binding with cytosine (C) into the wobble (w) C·2AP(w) mispair, which is supported by the N4H⋯N1 and N2H⋯N3 H-bonds and is tautomerized into the Watson-Crick (WC)-like base mispair C*·2AP(WC) (asterisk denotes the mutagenic tautomer of the base), that quite easily in the process of the thermal fluctuations acquires enzymatically competent conformation. 2AP less effectively produces transversions forming the wobble mispair with A base - A·2AP(w), stabilized by the participation of the N6H⋯N1 and N2H⋯N1 H-bonds, followed by further tautomerization A·2AP(w) → A*·2AP(WC) and subsequent conformational transition A*·2AP(WC) → A*·2APsyn thus acquiring enzymatically competent structure. In this case, incorporation errors occur only in those case, when 2AP belongs to the incoming nucleotide. Thus, answering the question posed in the title of the article, we affirm for certain that 2AP induces incorporation errors at the DNA replication. Obtained results are consistent well with numerous experimental data.
Collapse
Affiliation(s)
- Ol'ha O Brovarets'
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Akademika Zabolotnoho Str., Kyiv 03680 , Ukraine.,b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , 2-h Akademika Hlushkova Ave., Kyiv 03022 , Ukraine
| | - Horacio Pérez-Sánchez
- c Computer Science Department, Bioinformatics and High Performance Computing (BIO-HPC) Research Group , Universidad Católica San Antonio de Murcia (UCAM) , Murcia 30107 , Spain
| |
Collapse
|
15
|
2-aminopurine as a fluorescent probe of DNA conformation and the DNA–enzyme interface. Q Rev Biophys 2015; 48:244-79. [DOI: 10.1017/s0033583514000158] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractNearly 50 years since its potential as a fluorescent base analogue was first recognized, 2-aminopurine (2AP) continues to be the most widely used fluorescent probe of DNA structure and the perturbation of that structure by interaction with enzymes and other molecules. In this review, we begin by considering the origin of the dramatic and intriguing difference in photophysical properties between 2AP and its structural isomer, adenine; although 2AP differs from the natural base only in the position of the exocyclic amine group, its fluorescence intensity is one thousand times greater. We then discuss the mechanism of interbase quenching of 2AP fluorescence in DNA, which is the basis of its use as a conformational probe but remains imperfectly understood. There are hundreds of examples in the literature of the use of changes in the fluorescence intensity of 2AP as the basis of assays of conformational change; however, in this review we will consider in detail only a few intensity-based studies. Our primary aim is to highlight the use of time-resolved fluorescence measurements, and the interpretation of fluorescence decay parameters, to explore the structure and dynamics of DNA. We discuss the salient features of the fluorescence decay of 2AP when incorporated in DNA and review the use of decay measurements in studying duplexes, single strands and other structures. We survey the use of 2AP as a probe of DNA-enzyme interaction and enzyme-induced distortion, focusing particularly on its use to study base flipping and the enhanced mechanistic insights that can be gained by a detailed analysis of the decay parameters, rather than merely monitoring changes in fluorescence intensity. Finally we reflect on the merits and shortcomings of 2AP and the prospects for its wider adoption as a fluorescence-decay-based probe.
Collapse
|
16
|
Trachsel MA, Lobsiger S, Schär T, Leutwyler S. Low-lying excited states and nonradiative processes of 9-methyl-2-aminopurine. J Chem Phys 2014; 140:044331. [DOI: 10.1063/1.4862913] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
|
17
|
Lobsiger S, Sinha RK, Leutwyler S. Building Up Water-Wire Clusters: Isomer-Selective Ultraviolet and Infrared Spectra of Jet-Cooled 2-Aminopurine (H2O)n, n = 2 and 3. J Phys Chem B 2013; 117:12410-21. [DOI: 10.1021/jp407127c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simon Lobsiger
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
- Department
of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904-4319, United States
| | - Rajeev K. Sinha
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
- Department
of Atomic and Molecular Physics, Manipal University, Manipal-576104, Karnataka, India
| | - Samuel Leutwyler
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
| |
Collapse
|
18
|
Rios AC, Tor Y. On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution. Isr J Chem 2013; 53:469-483. [PMID: 25284884 PMCID: PMC4181368 DOI: 10.1002/ijch.201300009] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The native bases of RNA and DNA are prominent examples of the narrow selection of organic molecules upon which life is based. How did nature "decide" upon these specific heterocycles? Evidence suggests that many types of heterocycles could have been present on the early Earth. It is therefore likely that the contemporary composition of nucleobases is a result of multiple selection pressures that operated during early chemical and biological evolution. The persistence of the fittest heterocycles in the prebiotic environment towards, for example, hydrolytic and photochemical assaults, may have given some nucleobases a selective advantage for incorporation into the first informational polymers. The prebiotic formation of polymeric nucleic acids employing the native bases remains, however, a challenging problem to reconcile. Hypotheses have proposed that the emerging RNA world may have included many types of nucleobases. This is supported by the extensive utilization of non-canonical nucleobases in extant RNA and the resemblance of many of the modified bases to heterocycles generated in simulated prebiotic chemistry experiments. Selection pressures in the RNA world could have therefore narrowed the composition of the nucleic acid bases. Two such selection pressures may have been related to genetic fidelity and duplex stability. Considering these possible selection criteria, the native bases along with other related heterocycles seem to exhibit a certain level of fitness. We end by discussing the strength of the N-glycosidic bond as a potential fitness parameter in the early DNA world, which may have played a part in the refinement of the alphabetic bases.
Collapse
Affiliation(s)
- Andro C. Rios
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358 (USA), phone: (+1) 8585346401, fax: (+1) 858534 0202
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358 (USA), phone: (+1) 8585346401, fax: (+1) 858534 0202
| |
Collapse
|
19
|
Weinberger M, Berndt F, Mahrwald R, Ernsting NP, Wagenknecht HA. Synthesis of 4-Aminophthalimide and 2,4-Diaminopyrimidine C-Nucleosides as Isosteric Fluorescent DNA Base Substitutes. J Org Chem 2013; 78:2589-99. [DOI: 10.1021/jo302768f] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael Weinberger
- Department of Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg
6, Campus Süd, Geb. 30.42, 76131 Karlsruhe, Germany
| | - Falko Berndt
- Institute of Chemistry, Humboldt University Berlin, Brook-Taylor-Strasse 2,
12489 Berlin, Germany
| | - Rainer Mahrwald
- Institute of Chemistry, Humboldt University Berlin, Brook-Taylor-Strasse 2,
12489 Berlin, Germany
| | - Nikolaus P. Ernsting
- Institute of Chemistry, Humboldt University Berlin, Brook-Taylor-Strasse 2,
12489 Berlin, Germany
| | - Hans-Achim Wagenknecht
- Department of Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg
6, Campus Süd, Geb. 30.42, 76131 Karlsruhe, Germany
| |
Collapse
|
20
|
Richardson TT, Wu X, Keith BJ, Heslop P, Jones AC, Connolly BA. Unwinding of primer-templates by archaeal family-B DNA polymerases in response to template-strand uracil. Nucleic Acids Res 2013; 41:2466-78. [PMID: 23303790 PMCID: PMC3575838 DOI: 10.1093/nar/gks1364] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Archaeal family-B DNA polymerases bind tightly to deaminated bases and stall replication on encountering uracil in template strands, four bases ahead of the primer-template junction. Should the polymerase progress further towards the uracil, for example, to position uracil only two bases in front of the junction, 3′–5′ proof-reading exonuclease activity becomes stimulated, trimming the primer and re-setting uracil to the +4 position. Uracil sensing prevents copying of the deaminated base and permanent mutation in 50% of the progeny. This publication uses both steady-state and time-resolved 2-aminopurine fluorescence to show pronounced unwinding of primer-templates with Pyrococcus furiosus (Pfu) polymerase–DNA complexes containing uracil at +2; much less strand separation is seen with uracil at +4. DNA unwinding has long been recognized as necessary for proof-reading exonuclease activity. The roles of M247 and Y261, amino acids suggested by structural studies to play a role in primer-template unwinding, have been probed. M247 appears to be unimportant, but 2-aminopurine fluorescence measurements show that Y261 plays a role in primer-template strand separation. Y261 is also required for full exonuclease activity and contributes to the fidelity of the polymerase.
Collapse
Affiliation(s)
- Tomas T Richardson
- Institute of Cell and Molecular Biosciences (ICaMB), The University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
| | | | | | | | | | | |
Collapse
|
21
|
Reichardt C, Wen C, Vogt RA, Crespo-Hernández CE. Role of intersystem crossing in the fluorescence quenching of 2-aminopurine 2′-deoxyriboside in solution. Photochem Photobiol Sci 2013; 12:1341-50. [DOI: 10.1039/c3pp25437b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
22
|
Sinha RK, Lobsiger S, Leutwyler S. Isomer- and Species-Selective Infrared Spectroscopy of Jet-Cooled 7H- and 9H-2-Aminopurine and 2-Aminopurine·H2O Clusters. J Phys Chem A 2012; 116:1129-36. [DOI: 10.1021/jp2077177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Rajeev K. Sinha
- Department of Chemistry
and Biochemistry, University of Bern, Freiestrasse 3,
CH-3012 Bern, Switzerland
| | - Simon Lobsiger
- Department of Chemistry
and Biochemistry, University of Bern, Freiestrasse 3,
CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Department of Chemistry
and Biochemistry, University of Bern, Freiestrasse 3,
CH-3012 Bern, Switzerland
| |
Collapse
|
23
|
Lane RSK, Magennis SW. Two-photon excitation of the fluorescent nucleobase analogues 2-AP and tC. RSC Adv 2012. [DOI: 10.1039/c2ra21881j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
|
24
|
Lobsiger S, Sinha RK, Trachsel M, Leutwyler S. Low-lying excited states and nonradiative processes of the adenine analogues 7H- and 9H-2-aminopurine. J Chem Phys 2011; 134:114307. [DOI: 10.1063/1.3567090] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
25
|
Sinha RK, Lobsiger S, Trachsel M, Leutwyler S. Vibronic Spectra of Jet-Cooled 2-Aminopurine·H2O Clusters Studied by UV Resonant Two-Photon Ionization Spectroscopy and Quantum Chemical Calculations. J Phys Chem A 2011; 115:6208-17. [DOI: 10.1021/jp111469n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rajeev K. Sinha
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Simon Lobsiger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Maria Trachsel
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| |
Collapse
|
26
|
Etinski M, Marian CM. Overruling the energy gap law: fast triplet formation in 6-azauracil. Phys Chem Chem Phys 2010; 12:15665-71. [DOI: 10.1039/c0cp00106f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
27
|
Neely RK, Tamulaitis G, Chen K, Kubala M, Siksnys V, Jones AC. Time-resolved fluorescence studies of nucleotide flipping by restriction enzymes. Nucleic Acids Res 2009; 37:6859-70. [PMID: 19740769 PMCID: PMC2777440 DOI: 10.1093/nar/gkp688] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Restriction enzymes Ecl18kI, PspGI and EcoRII-C, specific for interrupted 5-bp target sequences, flip the central base pair of these sequences into their protein pockets to facilitate sequence recognition and adjust the DNA cleavage pattern. We have used time-resolved fluorescence spectroscopy of 2-aminopurine-labelled DNA in complex with each of these enzymes in solution to explore the nucleotide flipping mechanism and to obtain a detailed picture of the molecular environment of the extrahelical bases. We also report the first study of the 7-bp cutter, PfoI, whose recognition sequence (T/CCNGGA) overlaps with that of the Ecl18kI-type enzymes, and for which the crystal structure is unknown. The time-resolved fluorescence experiments reveal that PfoI also uses base flipping as part of its DNA recognition mechanism and that the extrahelical bases are captured by PfoI in binding pockets whose structures are quite different to those of the structurally characterized enzymes Ecl18kI, PspGI and EcoRII-C. The fluorescence decay parameters of all the enzyme-DNA complexes are interpreted to provide insight into the mechanisms used by these four restriction enzymes to flip and recognize bases and the relationship between nucleotide flipping and DNA cleavage.
Collapse
Affiliation(s)
- Robert K Neely
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium.
| | | | | | | | | | | |
Collapse
|
28
|
Campbell CJ, Mountford CP, Stoquert HC, Buck AH, Dickinson P, Ferapontova E, Terry JG, Beattie JS, Walton AJ, Crain J, Ghazal P, Mount AR. A DNA nanoswitch incorporating the fluorescent base analogue 2-aminopurine detects single nucleotide mismatches in unlabelled targets. Analyst 2009; 134:1873-9. [PMID: 19684913 DOI: 10.1039/b900325h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
DNA nanoswitches can be designed to detect unlabelled nucleic acid targets and have been shown to discriminate between targets which differ in the identity of only one base. This paper demonstrates that the fluorescent base analogue 2-aminopurine (AP) can be used to discriminate between nanoswitches with and without targets and to discriminate between matched and mismatched targets. In particular, we have used both steady-state and time-resolved fluorescence spectroscopy to determine differences in AP environment at the branchpoint of nanoswitches assembled using complementary targets and targets which incorporate single base mismatches.
Collapse
Affiliation(s)
- Colin J Campbell
- Division of Pathway Medicine, University of Edinburgh, Edinburgh, UK EH16 4SB.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Feng K, Engler G, Seefeld K, Kleinermanns K. Dispersed Fluorescence and Delayed Ionization of Jet-Cooled 2-Aminopurine: Relaxation to a Dark State Causes Weak Fluorescence. Chemphyschem 2009; 10:886-9. [DOI: 10.1002/cphc.200800816] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
30
|
Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids. Proc Natl Acad Sci U S A 2008; 105:11176-81. [PMID: 18676615 DOI: 10.1073/pnas.0801707105] [Citation(s) in RCA: 252] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have found that the efficiency of fluorescence resonance energy transfer between Cy3 and Cy5 terminally attached to the 5' ends of a DNA duplex is significantly affected by the relative orientation of the two fluorophores. The cyanine fluorophores are predominantly stacked on the ends of the helix in the manner of an additional base pair, and thus their relative orientation depends on the length of the helix. Observed fluorescence resonance energy transfer (FRET) efficiency depends on the length of the helix, as well as its helical periodicity. By changing the helical geometry from B form double-stranded DNA to A form hybrid RNA/DNA, a marked phase shift occurs in the modulation of FRET efficiency with helix length. Both curves are well explained by the standard geometry of B and A form helices. The observed modulation for both polymers is less than that calculated for a fully rigid attachment of the fluorophores. However, a model involving lateral mobility of the fluorophores on the ends of the helix explains the observed experimental data. This has been further modified to take account of a minor fraction of unstacked fluorophore observed by fluorescent lifetime measurements. Our data unequivocally establish that Förster transfer obeys the orientation dependence as expected for a dipole-dipole interaction.
Collapse
|
31
|
Mountford CP, Buck AH, Campbell CJ, Dickinson P, Ferapontova EE, Terry JG, Beattie JS, Walton AJ, Ghazal P, Mount AR, Crain J. Molecular Recognition with DNA Nanoswitches: Effects of Single Base Mutations on Structure. J Phys Chem B 2008; 112:2439-44. [DOI: 10.1021/jp073817o] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- C. P. Mountford
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - A. H. Buck
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - C. J. Campbell
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - P. Dickinson
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - E. E. Ferapontova
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - J. G. Terry
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - J. S. Beattie
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - A. J. Walton
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - P. Ghazal
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - A. R. Mount
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - J. Crain
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| |
Collapse
|
32
|
Neely RK, Magennis SW, Parsons S, Jones AC. Photophysics and X-ray Structure of Crystalline 2-Aminopurine. Chemphyschem 2007; 8:1095-102. [PMID: 17385756 DOI: 10.1002/cphc.200600593] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
To explore the effect of intermolecular interactions on the photophysics of 2-aminopurine (2AP) in a well-defined environment, we have investigated the fluorescence properties of single 2AP crystals, having determined their X-ray structure. In the crystal, 2AP is subject to base-stacking and hydrogen-bonding interactions similar to those found in DNA. The crystal shows dual fluorescence: pi-stacked molecules in the bulk of the lattice have redshifted excitation and emission spectra, while molecules at defect sites have spectra similar to those of 2AP in solution or in DNA. Heterogeneous intermolecular interactions in the crystal give rise to multiexponential fluorescence decay characteristics similar to those observed for 2AP-labelled DNA. The presence of about 13 % of the 7H tautomer in the crystal confirms that 9H-7H tautomerisation of 2AP occurs in the ground state. Long-wavelength excitation of a 2AP-labelled oligonucleotide duplex produced redshifted emission similar to that observed in the crystal, indicating that pi-stacking interaction of 2AP with nucleobases gives rise to a low energy excited state.
Collapse
Affiliation(s)
- Robert K Neely
- School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
| | | | | | | |
Collapse
|
33
|
Lenz T, Bonnist EYM, Pljevaljcić G, Neely RK, Dryden DTF, Scheidig AJ, Jones AC, Weinhold E. 2-Aminopurine Flipped into the Active Site of the Adenine-Specific DNA Methyltransferase M.TaqI: Crystal Structures and Time-Resolved Fluorescence. J Am Chem Soc 2007; 129:6240-8. [PMID: 17455934 DOI: 10.1021/ja069366n] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the crystal structure of the DNA adenine-N6 methyltransferase, M.TaqI, complexed with DNA, showing the fluorescent adenine analog, 2-aminopurine, flipped out of the DNA helix and occupying virtually the same position in the active site as the natural target adenine. Time-resolved fluorescence spectroscopy of the crystalline complex faithfully reports this state: base flipping is accompanied by the loss of the very short ( approximately 50 ps) lifetime component associated with fully base-stacked 2-aminopurine in DNA, and 2-aminopurine is subject to considerable quenching by pi-stacking interactions with Tyr108 in the catalytic motif IV (NPPY). This proves 2-aminopurine to be an excellent probe for studying base flipping by M.TaqI and suggests similar quenching in the active sites of DNA and RNA adenine-N6 as well as DNA cytosine-N4 methyltransferases sharing the conserved motif IV. In solution, the same distinctive fluorescence response confirms complete destacking from DNA and is also observed when the proposed key residue for base flipping by M.TaqI, the target base partner thymine, is substituted by an abasic site analog. The corresponding cocrystal structure shows 2-aminopurine in the active site of M.TaqI, demonstrating that the partner thymine is not essential for base flipping. However, in this structure, a shift of the 3' neighbor of the target base into the vacancy left after base flipping is observed, apparently replicating a stabilizing role of the missing partner thymine. Time-resolved fluorescence and acrylamide quenching measurements of M.TaqI complexes in solution provide evidence for an alternative binding site for the extra-helical target base within M.TaqI and suggest that the partner thymine assists in delivering the target base into the active site.
Collapse
Affiliation(s)
- Thomas Lenz
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Abstract
The excited state dynamics of protonated adenine in the gas phase were investigated by femtosecond pump-probe transient mass spectroscopy. Adenine was protonated in an electrospray ionization source and transferred to a Paul trap. Two femtosecond laser pulses at 266 nm and 800 nm excited the lowest electronic pipi* state and probed the excited-state dynamics by monitoring ion fragment formation. The measured excited state decay is monoexponential with a lifetime shorter than 161 fs. This agrees with a theoretical prediction of very fast internal conversion via a conical intersection with the ground state.
Collapse
Affiliation(s)
- Dirk Nolting
- Max Born Institute, Max-Born-Strasse 2a, 12489 Berlin, Germany.
| | | | | | | |
Collapse
|
35
|
Kuimova MK, Gill PMW, Lin CY, Matousek P, Towrie M, Sun XZ, George MW, Parker AW. Picosecond time-resolved infrared study of 2-aminopurine ionisation in solution. Photochem Photobiol Sci 2007; 6:949-55. [PMID: 17721593 DOI: 10.1039/b705801b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two photon ionisation of 2-aminopurine (2AP) has been monitored following 267 nm irradiation in neutral and acidic aqueous solutions using picosecond time-resolved infrared spectroscopy (ps-TRIR). The transient infrared spectra obtained in neutral and acidic conditions show significant differences that are consistent with the formation of different species, namely the 2AP radical cation, 2AP+*, in acidic conditions and the uncharged radical, 2AP*(-H+), in neutral conditions. The ps-TRIR data indicate that deprotonation of 2AP+* in neutral solution takes place within <2 ps following photoionisation. DFT calculations (EDF1/6-31+G*) were used to support the assignment of the intermediates observed in these spectroscopic experiments.
Collapse
Affiliation(s)
- Marina K Kuimova
- School of Chemistry, University of Nottingham, University Park, Nottingham, UK.
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Hardman SJO, Thompson KC. Influence of base stacking and hydrogen bonding on the fluorescence of 2-aminopurine and pyrrolocytosine in nucleic acids. Biochemistry 2006; 45:9145-55. [PMID: 16866360 DOI: 10.1021/bi060479t] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescent nucleobase analogues are used extensively to probe the structure and dynamics of nucleic acids. The fluorescence of the adenine analogue 2-aminopurine and the cytosine analogue pyrrolocytosine is significantly quenched when the bases are located in regions of double-stranded nucleic acids. To allow more detailed structural information to be obtained from fluorescence studies using these bases, we have studied the excited-state properties of the bases at the CIS and TDB3LYP level in hydrogen-bonded and base-stacked complexes. The results reveal that the first excited state (the fluorescent state) of a hydrogen-bonded complex containing 2-aminopurine and thymine is just the first excited state of 2-aminopurine alone. However, the same cannot be said for structures in which 2-aminopurine is base stacked with other nucleobases. Stacking causes the molecular orbitals involved in the fluorescence transition to spread over more than one base. The predicted rate for the fluorescence transition is reduced, thus reducing the fluorescence quantum yield. The decrease in radiative rate varies with the stacking arrangement (e.g., A- or B-form DNA) and with the identity of the nucleobase with which 2-aminopurine is stacked. Stacking 2-aminopurine between two guanine moieties is shown to significantly decrease the energy gap between the first and second excited states. We do not find reliable evidence for a low-energy charge-transfer state in any of the systems that were studied. In the case of pyrrolocytosine, base stacking was found to reduce the oscillator strength for the fluorescence transition, but very little spreading of molecular orbitals across more than one base was observed.
Collapse
Affiliation(s)
- Samantha J O Hardman
- School of Biological and Chemical Sciences, Birkbeck University of London, Malet Street, London WC1E 7HX, UK
| | | |
Collapse
|
37
|
Serrano-Andrés L, Merchán M, Borin AC. Adenine and 2-aminopurine: paradigms of modern theoretical photochemistry. Proc Natl Acad Sci U S A 2006; 103:8691-6. [PMID: 16731617 PMCID: PMC1482641 DOI: 10.1073/pnas.0602991103] [Citation(s) in RCA: 241] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Indexed: 11/18/2022] Open
Abstract
Distinct photophysical behavior of nucleobase adenine and its constitutional isomer, 2-aminopurine, has been studied by using quantum chemical methods, in particular an accurate ab initio multiconfigurational second-order perturbation theory. After light irradiation, the efficient, ultrafast energy dissipation observed for nonfluorescent 9H-adenine is explained here by the nonradiative internal conversion process taking place along a barrierless reaction path from the initially populated 1(pipi* La) excited state toward a low-lying conical intersection (CI) connected with the ground state. In contrast, the strong fluorescence recorded for 2-aminopurine at 4.0 eV with large decay lifetime is interpreted by the presence of a minimum in the 1(pipi* La) hypersurface lying below the lowest CI and the subsequent potential energy barrier required to reach the funnel to the ground state. Secondary deactivation channels were found in the two systems related to additional CIs involving the 1(pipi* Lb) and 1(npi*) states. Although in 9H-adenine a population switch between both states is proposed, in 7H-adenine this may be perturbed by a relatively larger barrier to access the 1(npi*) state, and, therefore, the 1(pipi* Lb) state becomes responsible for the weak fluorescence measured in aqueous adenine at approximately 4.5 eV. In contrast to previous models that explained fluorescence quenching in adenine, unlike in 2-aminopurine, on the basis of the vibronic coupling of the nearby 1(pipi*) and 1(npi*) states, the present results indicate that the 1(npi*) state does not contribute to the leading photophysical event and establish the prevalence of a model based on the CI concept in modern photochemistry.
Collapse
Affiliation(s)
- Luis Serrano-Andrés
- Instituto de Ciencia Molecular, Universitat de València, Dr. Moliner 50, Burjassot, ES-46100 Valencia, Spain.
| | | | | |
Collapse
|
38
|
He RX, Duan XH, Li XY. Theoretical investigation of spectral properties and tautomerization mechanism of 2-aminopurine. Phys Chem Chem Phys 2006; 8:587-91. [PMID: 16482300 DOI: 10.1039/b512242b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In this work the spectral properties and tautomerization mechanism of 2-aminopurine are investigated using quantum chemical calculations. TD-DFT results lead to a conclusion that two tautomers of 2-aminopurine discussed in this work are fluorescent and present the pi-->pi* transition feature of vertical excitation and emission. It is predicted that the tautomerization of 2-aminopurine hardly occurs in a direct isomerization mechanism because of the high barrier. However, the explicit involvement of water molecules into the system reduces the barrier height considerably and hence makes the ground state reaction feasible. An explanation for the almost equal populations of the two tautomers in polar solvent is given through reaction mechanism analysis.
Collapse
Affiliation(s)
- Rong-Xing He
- College of Chemical Engineering, Sichuan University, Chengdu, PR China
| | | | | |
Collapse
|
39
|
Seefeld KA, Plützer C, Löwenich D, Häber T, Linder R, Kleinermanns K, Tatchen J, Marian CM. Tautomers and electronic states of jet-cooled 2-aminopurine investigated by double resonance spectroscopy and theory. Phys Chem Chem Phys 2005; 7:3021-6. [PMID: 16186905 DOI: 10.1039/b505954b] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present resonant two-photon ionization (R2PI), IR-UV, and UV-UV double resonance spectra of jet-cooled 2-aminopurine (2AP) as well as Fourier transform infrared (FTIR) gas phase spectra. 2AP is a fluorescing isomer of the nucleobase adenine. The results show that there is only one tautomer of 2AP which absorbs in the wavelength range 32,300-34,500 cm(-1). The comparison with the calculated IR spectra of 9H- and 7H-2AP points to 9H-2AP as the dominating tautomer in the gas phase but the spectra are too similar to allow an unambiguous assignment to the respective tautomer. Hence, we determined vertical and adiabatic excitation energies of both tautomers employing combined density functional theory and multi-reference configuration interaction techniques. For the 0-0 band of the first 1pipi* transition of 9H-2AP we obtain a theoretical value of 32,328 cm(-1), in excellent agreement with the band origin of our R2PI spectrum at 32,371 cm(-1). The first singlet pipi* transition of the less stable 7H-2AP tautomer is predicted to be red-shifted by about 1700 cm(-1) with respect to the corresponding transition in 9H-2AP. From the absence of experimental bands in the energy region between 30,300 and 32,350 cm(-1) we conclude that 7H-2AP is not present to an appreciable extent in the molecular beam. Our calculations yield nearly equal energies for the 1npi* and 1pipi* minima of isolated 2AP, similar to the situation in adenine. The hitherto existing argument that the energetic order of states is responsible for the different spectroscopic properties of these isomers therefore does not hold. Rather, vibronic levels close to the origin of the 1pipi* transition cannot access the conical intersection between the 1pipi* and S(0) states along a puckering coordinate of the six-membered ring, in contrast to the situation in electronically excited 9H-adenine. As a consequence, a rich vibrational structure can be observed in the R2PI spectrum of 2AP whereas the spectrum of 9H-adenine breaks off at low energies.
Collapse
Affiliation(s)
- Kai A Seefeld
- Institute of Physical Chemistry, Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | | | | | | | | | | | | | | |
Collapse
|