Pairing of the nucleobase guanine studied by IR–UV double-resonance spectroscopy and ab initio calculations

Nir, Eyal; Janzen, Christoph; Imhof, Petra; Kleinermanns, Karl; Vries, Mattanjah S. de

doi:10.1039/b110360c

Cited by 94 publications

(95 citation statements)

References 26 publications

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“…Furthermore, we note that spectrum A2, with unsubstituted guanine, shows the same broadening as the other A structures. We have also studied GG base pairs with 9-methylguanine, for which we found the triply hydrogen-bonded keto-keto structure to exhibit a sharp UV spectrum (18).…”

Section: Discussionmentioning

confidence: 99%

Photochemical selectivity in guanine–cytosine base-pair structures

Abo-Riziq

Grace

Nir

et al. 2004

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

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Prebiotic chemistry presumably took place before formation of an oxygen-rich atmosphere and thus under conditions of intense short wavelength UV irradiation. Therefore, the UV photochemical stability of the molecular building blocks of life may have been an important selective factor in determining the eventual chemical makeup of critical biomolecules. To investigate the role of UV irradiation in base-pairing we have studied guanine (G) and cytosine (C) base pairs in the absence of the RNA backbone. We distinguished base-pair structures by IR-UV hole-burning spectroscopy as well as by high-level correlated ab initio calculations. The Watson-Crick structure exhibits broad UV absorption, in stark contrast to other GC structures and other base-pair structures. This broad absorption may be explained by a rapid internal conversion that makes this specific base pair arrangement uniquely photochemically stable.ab initio computation ͉ DNA base pairs ͉ IR-UV spectroscopy ͉ jet cooling ͉ photochemistry T he DNA bases involved in reproduction have short S 1 excited state lifetimes, of the order of 1 ps or less (1-7). It has been argued that this phenomenon serves to protect these bases against photochemical damage, because after excitation they do not cross to the reactive triplet state; instead, they rapidly internally convert to the electronic ground state (8). This mechanism may have been particularly significant under the conditions of the early earth, when purines and pyrimidines presumably were assembled into the first macromolecular structures, producing RNA. At that time, the earth was exposed to shorter wavelength UV radiation than it is today. For an analysis of possible prebiotic chemistry, it is necessary not only to consider the individual bases but also to study them as they interact and to do so without the RNA backbone (9). We achieve such an analysis by studying clusters of guanine (G) and cytosine (C) in the gas phase by using double resonant laser spectroscopy techniques. The experimental studies are accompanied by stateof-the-art quantum chemical and molecular dynamics calculations of the pairing of G and C. These two bases can form many different hydrogen-bonded structures, of which at least 20 are within 12 kcal͞mol of the global minimum. Thus, the familiar Watson-Crick (WC) structure may not be unique, based on energies alone. Here, we report a remarkable difference in excited state properties among the WC structure and other structures. The former exhibits broad UV absorption features; this is in contrast with the sharp UV spectra exhibited by non-WC structures. The broad absorption can be explained by recent theoretical results, predicting a pathway for rapid internal conversion (10). If the difference is solely due to lifetime broadening, these results correspond to a lifetime for the WC structures that is at least 2 orders of magnitude shorter than those of observed non-WC structures. Thus, it appears possible that the WC recognition mechanism involves a structure that was significantly more stab...

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Section: Discussionmentioning

confidence: 99%

Photochemical selectivity in guanine–cytosine base-pair structures

Abo-Riziq

Grace

Nir

et al. 2004

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

Self Cite

245

284

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“…In REMPI spectra of homo base pair combinations the predicted lowest energy structure was not observed. This absence occurred for GG dimers 107 , CC dimers 31 , and AA dimers 37 . In these homodimers the missing structure is symmetric so it is possible that an excimer state is formed with a considerable splitting causing a shift in the UV band outside of the experimental range.…”

Section: Intermolecular Effects -Clustersmentioning

confidence: 91%

UV-Excitation from an Experimental Perspective: Frequency Resolved

Vries

2014

Topics in Current Chemistry

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Electronic spectroscopy of DNA bases in the gas phase provides detailed information about the electronic excitation, which places the molecule in the Franck-Condon region in the excited state and thus prepares the starting conditions for excited state dynamics. Double resonant or hole burning spectroscopy in the gas phase can provide such information with isomer specificity, probing the starting potential energy landscape as a function of tautomeric form, isomeric structure, or hydrogen bonded or stacked cluster structure. Action spectroscopy, such REMPI, can be affected by excited state lifetimes.

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“…The spectroscopy experiments [2][3][4][5][6] of the selected base pairs provide unique evidence about their IR spectra but do not allow extracting information about their structures or stabilization energies. On the other hand, theoretical quantum chemical studies provide a full description of molecular interactions including data on geometry, stabilization energy, electric properties, IR, visible and UV spectra, selected NMR parameters, etc.…”

Section: Introductionmentioning

confidence: 99%

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

Svozil¹,

Hobza²,

Šponer³

2010

J. Phys. Chem. B

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High level ab initio methods have been used to study stacking interactions in ten unique base pair steps both in A-RNA and in B-DNA duplexes. The protocol for selection of geometries based on molecular dynamics (MD) simulations is proposed, and its suitability is demonstrated by comparison with stacking in steps at fiber diffraction geometries. It is shown that fiber diffraction geometries are not sufficiently accurate for interaction energy calculations. In addition, the protocol for selection of geometries based on MD simulations allows for the evaluation of the variability of the intrinsic stacking energies along the MD trajectories. The uncertainty in stacking energies (difference between the most and least stable geometry) due to the dynamical nature of systems can be, in some cases, as large as 3.0 kcal · mol, which is almost 50% of the actual sequence dependence of base stacking energies (the energy difference between the most and least stable sequences). Thus, assessing the relative magnitude of the gas phase stacking energy using a single geometry for each sequence is insufficient to obtain an unambiguous order of gas phase stacking energies in canonical double helices. Though the ordering of ten unique dinucleotide steps cannot be definitive, some general conclusions were drawn. The stacking energies of base pair steps in A-RNA are more evenly separated compared to B-DNA, and their ordering is less sensitive to the dynamics of the system compared to be B-DNA. The most stable step both in B-DNA and A-RNA is the CG/CG step that is well separated from the second most stable step GC/GC. Also the least stable step (the CC/GG step) is well separated from the rest of the structures. The calculations further show that B-DNA stacking is favorable only marginally (on average by 1.14 kcal · mol -1 per base pair step) over A-RNA stacking, and this difference vanishes after subtracting the stabilizing van der Waals effect of the thymine 5-methyl group that is absent in RNA. Basically, no correlation between the sequence dependence of gas phase stacking energies and the sequence dependence of ∆G°3 7 free energies used in nearest-neighbor models was found either for B-DNA or for A-RNA. This reflects the complexity of the balance of forces that are responsible for the sequence dependence of thermodynamics stability of nucleic acids, which masks the effect of the intrinsic interactions between the stacked base pairs.

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Pairing of the nucleobase guanine studied by IR–UV double-resonance spectroscopy and ab initio calculations

Cited by 94 publications

References 26 publications

Photochemical selectivity in guanine–cytosine base-pair structures

Photochemical selectivity in guanine–cytosine base-pair structures

UV-Excitation from an Experimental Perspective: Frequency Resolved

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

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