Electronic Transition Moments of 2-Aminopurine

Holmén, Anders; Nordén, Bengt; Albinsson, Bo

doi:10.1021/ja9635600

Cited by 132 publications

(203 citation statements)

References 54 publications

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“…Analysis of monomer calculations indicates the accuracy with which TDDFT describes spectral properties: excited-state transition energies, transition dipole directions, and oscillator strengths for 2AP, thymine, cytosine, adenine, and guanine (see figures) are in excellent agreement with experimental measurements (16)(17)(18) and with complete active subspace self-consistent field calculations (19,20). Therefore, 5Ј 2AP-N dimers of these bases were built, and TDDFT calculations done on these ''supermolecules,'' so-called because their electronic properties are neither a sum nor perturbation of monomer properties.…”

mentioning

confidence: 64%

2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking

Jean¹

2000

Proceedings of the National Academy of Sciences

133

121

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2-Aminopurine (2AP) is a fluorescent analog of guanosine and adenosine and has been used to probe nucleic acid structure and dynamics. Its spectral features in nucleic acids have been interpreted phenomenologically, in the absence of a rigorous electronic description of the context-dependence of 2AP fluorescence. Now, by using time-dependent density functional theory, we describe the excited-state properties of 2AP in a B-form dinucleotide stacked with guanosine, adenosine, cytosine, or thymine. Calculations predict that 2AP fluorescence is quenched statically when stacked with purines, because of mixing of the molecular orbitals in the ground state. In contrast, quenching is predicted to be dynamic when 2AP is stacked with pyrimidines, because of formation of a low-lying dark excited state. The different quenching mechanisms will result in different experimentally measured fluorescence lifetimes and quantum yields.T he nucleotide 2-aminopurine (2AP) has been used as a site-specific probe of nucleic acid structure and dynamics (1-11) because it base pairs with cytosine in a wobble configuration (4,5,12) or with thymine in a Watson-Crick geometry (7,11). Thermodynamic measurements of DNAs containing 2AP:C or 2AP:T show that the former pairing is more destabilizing (11,12). Incorporating 2AP into DNA quenches its fluorescence (2, 8, 11), reducing its quantum yield from that of the free nucleoside (0.65 in aqueous solution). This reduction is attributed to stacking interactions with nearest neighbor nucleobases, and, therefore, fluorescence properties of 2AP have been used to probe the equilibrium stacking properties of DNA duplexes containing these mismatched pairs (2,8,10). Although the fluorescence decay of 2AP in solution is single exponential, with a lifetime of Ϸ10 ns, in the context of a DNA molecule, four decay components, from 50 ps to 8 ns, are typically needed to describe its lifetime (2). The short decay time observed for 2AP in a duplex is attributed to the fully stacked state, whereas the longest lifetime comes from unstacked 2AP (2, 7). The distribution of stacked states can be altered by temperature, solvent, flanking bases, and bound protein, and so all of these conditions can be probed by using 2AP fluorescence. Dynamics of stacked bases adjacent to a mutagenic mismatch in DNA (such as 2AP:C and 2AP:T) may be part of the recognition mechanism by replication͞repair enzymes (3, 13), so interpretation of 2AP fluorescence data is critical for describing these environments.To understand the effect of base stacking on fluorescent properties of 2AP, we have used time-dependent density functional theory (TDDFT) (14, 15) to calculate the excited-state properties of 2AP alone and in stacked B-and A-form dinucleotides (dimers). Analysis of monomer calculations indicates the accuracy with which TDDFT describes spectral properties: excited-state transition energies, transition dipole directions, and oscillator strengths for 2AP, thymine, cytosine, adenine, and guanine (see figures) are in excellent agreement w...

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confidence: 64%

2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking

Jean¹

2000

Proceedings of the National Academy of Sciences

133

121

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“…3 Upper Right. The transients at wavelengths 430 and 440 nm show a small component (Ϸ10%) of decays with a time constant of Ϸ10 ns; the fluorescence lifetime of Ap in water is 11.8 ns (21).…”

Section: Resultsmentioning

confidence: 98%

Site- and sequence-selective ultrafast hydration of DNA

Pal

Zhao

Xia

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

107

137

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Water molecules in the DNA grooves are critical for maintaining structural integrity, conformational changes, and molecular recognition. Here we report studies of site-and sequence-specific hydration dynamics, using 2-aminopurine (Ap) as the intrinsic fluorescence probe and with femtosecond resolution. The dodecamer d[CGCA(Ap)ATTTGCG]2 was investigated, and we also examined the effect of a specific minor groove-binding drug, pentamidine, on hydration dynamics. Two time scales were observed: Ϸ1 ps (bulklike) and 10 -12 ps (weakly bound type), consistent with layer hydration observed in proteins and DNA. However, for denatured DNA, the cosolvent condition of 40% formamide hydration is very different: it becomes that of bulk (in the presence of formamide). Well known electron transfer between Ap and nearby bases in stacked assemblies becomes inefficient in the single-stranded state. The rigidity of Ap in the single strands is significantly higher than that in bulk water and that attached to deoxyribose, suggesting a unique role for the dynamics of the phosphate-sugarbase in helix formation. The disparity in minor and major groove hydration is evident because of the site selection of Ap and in the time scale observed here (in the presence and absence of the drug), which is different by a factor of 2 from that observed in the minor groove-drug recognition.T he influence of hydration on the conformation and interactions of DNA has been the subject of many investigations using x-ray crystallography, NMR, molecular dynamics, and thermodynamic techniques (for recent reviews see refs. 1-4). The important role of water in the three-dimensional structures adopted by DNA is summarized in one of these reviews (1). At the interface between DNA and proteins (5, 6), water molecules in the first hydration shell of DNA ''mark'' the positions where protein residues hydrogen-bond to DNA. Even for specificity of cleavage in DNA, water activity affects site-specific recognition of DNA by EcoRI (6) as it does in protein function (7).In the minor groove of a B-form DNA duplex, hydration and its role in drug binding are striking. In a recent publication (8) from this laboratory, we described how the drug (Hoechst 33258) bound in the minor groove of DNA can be used to probe the dynamics of the water layer. For a DNA dodecamer duplex d(CGCAAATTTGCG) 2 , two well separated hydration times were found: 1.4 and 19 ps, compared with 0.2 and 1.2 ps for the same drug in bulk water. For comparison, we also studied genomic calf thymus DNA for which the hydration exhibits time scales similar to those of the dodecamer DNA.In this study, we use a DNA base analog, 2-aminopurine (Ap), in the same dodecamer B-DNA duplex d(CGCAApATTTGCG) 2 as an intrinsic fluorescence probe. Ap has been shown by NMR spectroscopy and thermodynamic measurements to form a stable base pair with thymine in a DNA oligomer, stabilized by two hydrogen bonds in a Watson-Crick geometry (9, 10) (see Fig. 1). Thus it is reasonable to consider that the modification by Ap does not alte...

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“…The ground and lowest electronic excited states have a π-π* character [20]. In aqueous solutions the quantum efficiency is about 0.7 [3], maxima of absorption and emission are about 305 nm and 370 nm respectively [4,21] and the fluorescence intensity decays are mono-exponential with the fluorescence lifetime of about 12 ns [8,22].…”

Section: Introductionmentioning

confidence: 99%

Fluorescence intensity decays of 2-aminopurine solutions: Lifetime distribution approach

Bharill

Sarkar

Ballin

et al. 2008

Analytical Biochemistry

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The fluorescent adenine analogue 2-aminopurine (2AP) has been used extensively to monitor conformational changes and macromolecular binding events involving nucleic acids because its fluorescence properties are highly sensitive to changes in chemical environment. Furthermore, site-specific incorporation of 2AP permits local DNA and RNA conformational events to be discriminated from the global structural changes monitored by UV/Vis spectroscopy and circular dichroism. However, while the steady-state fluorescence properties of 2AP have been well defined in diverse settings, interpretation of 2AP fluorescence lifetime parameters has been hampered by the heterogeneous nature of multi-exponential 2AP intensity decays observed across populations of microenvironments. To resolve this problem, we have tested the utility of multi-exponential versus continuous Lorentzian lifetime distribution models to describe fluorescence intensity decays from 2AP in diverse chemical backgrounds and within the context of RNA. Heterogeneity was introduced into 2AP intensity decays by mixing solvents of differing polarities, or by adding quenchers under high viscosity to evaluate the transient effect. Heterogeneity of 2AP fluorescence within the context of a synthetic RNA hairpin was introduced by structural remodeling using a magnesium salt. In each case, except folded RNA which required a bimodal distribution, 2AP lifetime properties were well described by single Lorentzian distribution functions, abrogating the need to introduce additional discrete lifetime subpopulations. Rather, heterogeneity in fluorescence decay processes was accommodated by the breadth of each distribution. This approach also permitted solvent relaxation effects on 2AP emission to be assessed by comparing lifetime distributions at multiple wavelengths. Together, these studies provide a new perspective for the interpretation of 2AP fluorescence lifetime properties, which will further the utility of this Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. HHS Public Access Author Manuscript Author ManuscriptAuthor ManuscriptAuthor Manuscript fluorophore in analyses of the complex and heterogeneous structural microenvironments associated with nucleic acids.

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Electronic Transition Moments of 2-Aminopurine

Cited by 132 publications

References 54 publications

2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking

2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking

Site- and sequence-selective ultrafast hydration of DNA

Fluorescence intensity decays of 2-aminopurine solutions: Lifetime distribution approach

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