Resonance Enhanced Multi-photon Spectroscopy of DNA

ABSTRACTResonance Enhanced Multi-photon Spectroscopy of DNAbyMarshall Robert LigareFor over 50 years DNA has been studied to better understand its connection to life and evolution. These past experiments have led to our understanding of its structure and function in the biological environment but the interaction of DNA with UV radiation at the molecular level is still not very well understood. Unique mechanisms in nucleobase chromaphores protect us from adverse chemical reactions after UV absorption. Studying these processes can help develop theories for prebiotic chemistry and the possibility of alternative forms of DNA. Using resonance enhanced multi-photon spectroscopic techniques in the gas phase allow for the structure and dynamics of individual nucleobases to be studied in detail. Experiments studying different levels of structure/complexity with relation to their biological function are presented. Resonant IR multiphoton dissociation spectroscopy in conjunction with molecular mechanics and DFT calculations are used to determine gas phase structures of anionic nucleotide clusters. A comparison of the identified structures with known biological function shows how the hydrogen bonding of the nucleotides and their clusters free of solvent create favorable structures for quick incorporation into enzymes such as DNA polymerase. Resonance enhanced multi-photon ionization (REMPI) spectroscopy techniques such as resonant two photon ionization (R2PI) and IR-UV double resonance are used to further elucidate the structure and excited state dynamics of the bare nucleobases thymine and uracil. Both exhibit long lived excited electronic states that have been implicated in DNA photolesions which can ultimately lead to melanoma and carcinoma. Our experimental data in comparison with many quantum chemical calculations suggest a new picture for the dynamics of thymine and uracil in the gas phase. A high probability of UV absorption from a vibrationally hot ground state to the excited electronic state shows that the stability of thymine and uracil comes from its intrinsic molecular properties and possibly a hydrogen bonding solvent capable of dissipating excess vibrational energy. Due to the high specificity and sensitivity of resonant two photon ionization coupled with molecular beam mass spectrometry a new analytical technique for identifying molecular markers in archaeological vessels is presented. The xanthine alkaloids theobromine, theophylline and caffeine are identified in Central American and North American pottery sherds by direct desorption/resonant laser ionization mass spectrometry

Spectroscopy of Isolated Prebiotic Nucleobases

We use multiphoton ionization and double resonance spectroscopy to study the excited state dynamics of biologically relevant molecules as well as prebiotic nucleobases, isolated in the gas phase. Molecules that are biologically relevant to life today tend to exhibit short excited state lifetimes compared to similar but non-biologically relevant analogs. The mechanism is internal conversion, which may help protect the biologically active molecules from UV damage. This process is governed by conical intersections that depend very strongly on molecular structure. Therefore we have studied purines and pyrimidines with systematic variations of structure, including substitutions, tautomeric forms, and cluster structures that represent different base pair binding motifs. These structural variations also include possible alternate base pairs that may shed light on prebiotic chemistry. With this in mind we have begun to probe the ultrafast dynamics of molecules that exhibit very short excited states and search for evidence of internal conversions

SLIM Ultrahigh Resolution Ion Mobility Spectrometry Separations of Isotopologues and Isotopomers Reveal Mobility Shifts due to Mass Distribution Changes

We report on separations of ion isotopologues and isotopomers using ultrahigh-resolution traveling wave-based Structures for Lossless Ion Manipulations with serpentine ultralong path and extended routing ion mobility spectrometry coupled to mass spectrometry (SLIM SUPER IMS-MS). Mobility separations of ions from the naturally occurring ion isotopic envelopes (e.g., [M], [M+1], [M+2], ... ions) showed the first and second isotopic peaks (i.e., [M+1] and [M+2]) for various tetraalkylammonium ions could be resolved from their respective monoisotopic ion peak ([M]) after SLIM SUPER IMS with resolving powers of ∼400–600. Similar separations were obtained for other compounds (e.g., tetrapeptide ions). Greater separation was obtained using argon versus helium drift gas, as expected from the greater reduced mass contribution to ion mobility described by the Mason–Schamp relationship. To more directly explore the role of isotopic substitutions, we studied a mixture of specific isotopically substituted (15N, 13C, and 2H) protonated arginine isotopologues. While the separations in nitrogen were primarily due to their reduced mass differences, similar to the naturally occurring isotopologues, their separations in helium, where higher resolving powers could also be achieved, revealed distinct additional relative mobility shifts. These shifts appeared correlated, after correction for the reduced mass contribution, with changes in the ion center of mass due to the different locations of heavy atom substitutions. The origin of these apparent mass distribution-induced mobility shifts was then further explored using a mixture of Iodoacetyl Tandem Mass Tag (iodoTMT) isotopomers (i.e., each having the same exact mass, but with different isotopic substitution sites). Again, the observed mobility shifts appeared correlated with changes in the ion center of mass leading to multiple monoisotopic mobilities being observed for some isotopomers (up to a ∼0.04% difference in mobility). These mobility shifts thus appear to reflect details of the ion structure, derived from the changes due to ion rotation impacting collision frequency or momentum transfer, and highlight the potential for new approaches for ion structural characterization

Resonance Enhanced Multi-photon Spectroscopy of DNA

ABSTRACTResonance Enhanced Multi-photon Spectroscopy of DNAbyMarshall Robert LigareFor over 50 years DNA has been studied to better understand its connection to life and evolution. These past experiments have led to our understanding of its structure and function in the biological environment but the interaction of DNA with UV radiation at the molecular level is still not very well understood. Unique mechanisms in nucleobase chromaphores protect us from adverse chemical reactions after UV absorption. Studying these processes can help develop theories for prebiotic chemistry and the possibility of alternative forms of DNA. Using resonance enhanced multi-photon spectroscopic techniques in the gas phase allow for the structure and dynamics of individual nucleobases to be studied in detail. Experiments studying different levels of structure/complexity with relation to their biological function are presented. Resonant IR multiphoton dissociation spectroscopy in conjunction with molecular mechanics and DFT calculations are used to determine gas phase structures of anionic nucleotide clusters. A comparison of the identified structures with known biological function shows how the hydrogen bonding of the nucleotides and their clusters free of solvent create favorable structures for quick incorporation into enzymes such as DNA polymerase. Resonance enhanced multi-photon ionization (REMPI) spectroscopy techniques such as resonant two photon ionization (R2PI) and IR-UV double resonance are used to further elucidate the structure and excited state dynamics of the bare nucleobases thymine and uracil. Both exhibit long lived excited electronic states that have been implicated in DNA photolesions which can ultimately lead to melanoma and carcinoma. Our experimental data in comparison with many quantum chemical calculations suggest a new picture for the dynamics of thymine and uracil in the gas phase. A high probability of UV absorption from a vibrationally hot ground state to the excited electronic state shows that the stability of thymine and uracil comes from its intrinsic molecular properties and possibly a hydrogen bonding solvent capable of dissipating excess vibrational energy. Due to the high specificity and sensitivity of resonant two photon ionization coupled with molecular beam mass spectrometry a new analytical technique for identifying molecular markers in archaeological vessels is presented. The xanthine alkaloids theobromine, theophylline and caffeine are identified in Central American and North American pottery sherds by direct desorption/resonant laser ionization mass spectrometry

Resonant Infrared Multiple Photon Dissociation Spectroscopy of Anionic Nucleotide Monophosphate Clusters

We report mid-infrared spectra and potential energy surfaces of fouranionic, 2′-deoxynucleotide-5′-monophosphates (dNMPs) and the ionic DNA pairs[dGMP-dCMP−H]1−, [dAMP-dTMP−H]1− with a total charge of the complex equal to−1. We recorded IR action spectra by resonant IR multiple-photon dissociation (IRMPD)using the FELIX free electron laser. The potential energy surface study employed an onthe-fly molecular dynamics quenching method (MD/Q), using a semiempirical AM1method, followed by an optimization of the most stable structures using density functionaltheory. By employing infrared multiple-photon dissociation (IRMPD) spectroscopy incombination with high-level computational methods, we aim at a better understanding ofthe hydrogen bonding competition between the phosphate moieties and the nucleobases.We find that, unlike in multimer double stranded DNA structures, the hydrogen bonds inthese isolated nucleotide pairs are predominantly formed between the phosphate groups.This intermolecular interaction appears to exceed the stabilization energy resulting frombase pairing and directs the overall cluster structure and alignment

Direct Analysis of Xanthine Stimulants in Archaeological Vessels by Laser Desorption Resonance Enhanced Multiphoton Ionization.

Resonance enhanced multiphoton ionization spectroscopy (REMPI) generates simultaneous vibronic spectroscopy and fragment free mass spectrometry to identify molecules within a complex matrix. We combined laser desorption with REMPI spectroscopy to study organic residues within pottery sherds from Maya vessels (600-900 CE) and Mississippian vessels (1100-1200 CE), successfully detecting three molecular markers, caffeine, theobromine, and theophylline, associated with the use of cacao. This analytical approach provides a high molecular specificity, based on both wavelength and mass identification. At the same time, the high detection limit allows for direct laser desorption from sherd scrapings, avoiding the need for extracting organic constituents from the sherd matrix

Direct Analysis of Xanthine Stimulants in Archaeological Vessels by Laser Desorption Resonance Enhanced Multiphoton Ionization

Resonance enhanced multiphoton ionization spectroscopy (REMPI) generates simultaneous vibronic spectroscopy and fragment free mass spectrometry to identify molecules within a complex matrix. We combined laser desorption with REMPI spectroscopy to study organic residues within pottery sherds from Maya vessels (600–900 CE) and Mississippian vessels (1100–1200 CE), successfully detecting three molecular markers, caffeine, theobromine, and theophylline, associated with the use of cacao. This analytical approach provides a high molecular specificity, based on both wavelength and mass identification. At the same time, the high detection limit allows for direct laser desorption from sherd scrapings, avoiding the need for extracting organic constituents from the sherd matrix

Climate change and Australian marine and freshwater environments, fishes and fisheries: synthesis and options for adaptation

Anthropogenic climate change is already apparent and will have significant, ongoing impacts on Australian fishes and their habitats. Even with immediate actions to reduce greenhouse gases, there will be sustained environmental changes. Therefore, it is necessary to consider appropriate adaptations to minimise detrimental impacts for both fishes and the human populations that utilise them. Climate change will have a range of direct effects on the physiology, fitness, and survivorship of Australia’s marine, estuarine and freshwater fishes, but also indirect effects via habitat degradation and changes to ecosystems. Effects will differ across populations, species and ecosystems, with some impacts being complex and causing unexpected outcomes. The range of adaptation options and necessary levels of intervention to maintain populations and ecosystem function will largely depend on the vulnerability of species and habitats. Climate change will also have an impact on people who depend on fishes for food or livelihoods; adapting to a new climate regime will mean trade-offs between biological assets and socioeconomic drivers. Models can be used to help predict trends and set priorities; however, they must be based on the best available science and data, and include fisheries, environmental, socioeconomic and political layers to support management actions for adaptation.John D. Koehn, Alistair J. Hobday, Morgan S. Pratchett and Bronwyn M. Gillander