The Transition from Unfolded to Folded G-Quadruplex DNA Analyzed and Interpreted by Two-Dimensional Infrared Spectroscopy

A class of DNA folds/structures known collectively as G-quadruplexes (G4) commonly forms in guanine-rich areas of genomes. G4-DNA is thought to have a functional role in the regulation of gene transcription and telomerase-mediated telomere maintenance and, therefore, is a target for drugs. The details of the molecular interactions that cause stacking of the guanine-tetrads are not well-understood, which limits a rational approach to the drugability of G4 sequences. To explore these interactions, we employed electron-vibration-vibration two-dimensional infrared (EVV 2DIR) spectroscopy to measure extended vibrational coupling spectra for a parallel-stranded G4-DNA formed by the Myc2345 nucleotide sequence. We also tracked the structural changes associated with G4-folding as a function of K+-ion concentration. To classify the structural elements that the folding process generates in terms of vibrational coupling characteristics, we used quantum-chemical calculations utilizing density functional theory to predict the coupling spectra associated with given structures, which are compared against the experimental data. Overall, 102 coupling peaks are experimentally identified and followed during the folding process. Several phenomena are noted and associated with formation of the folded form. This includes frequency shifting, changes in cross-peak intensity, and the appearance of new coupling peaks. We used these observations to propose a folding sequence for this particular type of G4 under our experimental conditions. Overall, the combination of experimental 2DIR data and DFT calculations suggests that guanine-quartets may already be present before the addition of K+-ions, but that these quartets are unstacked until K+-ions are added, at which point the full G4 structure is formed

Long-lived metal complexes open up microsecond lifetime imaging microscopy under multiphoton excitation: from FLIM to PLIM and beyond

Lifetime imaging microscopy with sub-micron resolution provides essential understanding of living systems by allowing both the visualisation of their structure, and the sensing of bio-relevant analytes in vivo using external probes. Chemistry is pivotal for the development of the next generation of bio-tools, where contrast, sensitivity, and molecular specificity facilitate observation of processes fundamental to life. A fundamental limitation at present is the nanosecond lifetime of conventional fluorescent probes which typically confines the sensitivity to sub-nanosecond changes, whilst nanosecond background autofluorescence compromises the contrast. High-resolution visualization with complete background rejection and simultaneous mapping of bio-relevant analytes including oxygen – with sensitivity orders of magnitude higher than that currently attainable – can be achieved using time-resolved emission imaging microscopy (TREM) in conjunction with probes with microsecond (or longer) lifetimes. Yet the microsecond timescale has so far been incompatible with available multiphoton excitation/detection technologies. Here we realize for the first time microsecond-imaging with multiphoton excitation whilst maintaining the essential sub-micron spatial resolution. The new method is background-free and expands available imaging and sensing timescales 1000-fold. Exploiting the first engineered water-soluble member of a family of remarkably emissive platinum-based, microsecond-lived probes amongst others, we demonstrate (i) the first instance of background-free multiphoton-excited microsecond depth imaging of live cells and histological tissues, (ii) over an order-of-magnitude variation in the probe lifetime in vivo in response to the local microenvironment. The concept of two-photon TREM can be seen as “FLIM + PLIM” as it can be used on any timescale, from ultrafast fluorescence of organic molecules to slower emission of transition metal complexes or lanthanides/actinides, and combinations thereof. It brings together transition metal complexes as versatile emissive probes with the new multiphoton-excitation/microsecond-detection approach to create a transformative framework for multiphoton imaging and sensing across biological, medicinal and material sciences

A 100 kHz time-resolved multiple-probe femtosecond to second infrared absorption spectrometer

We present a dual-amplifier laser system for time-resolved multiple-probe infrared (IR) spectroscopy based on the ytterbium potassium gadolinium tungstate (Yb:KGW) laser medium. Comparisons are made between the ytterbium-based technology and titanium sapphire laser systems for time-resolved IR spectroscopy measurements. The 100 kHz probing system provides new capability in time-resolved multiple-probe experiments, as more information is obtained from samples in a single experiment through multiple-probing. This method uses the high repetition-rate probe pulses to repeatedly measure spectra at 10 μs intervals following excitation allowing extended timescales to be measured routinely along with ultrafast data. Results are presented showing the measurement of molecular dynamics over >10 orders of magnitude in timescale, out to 20 ms, with an experimental time response o

Recombination, Solvation and Reaction of CN Radicals Following Ultraviolet Photolysis of ICN in Organic Solvents

The fates of CN radicals produced by ultraviolet (UV) photolysis of ICN in various organic solvents have been examined by transient electronic and vibrational absorption spectroscopy (TEAS and TVAS). Near-UV and visible bands in the TEAS measurement enable direct observation of the CN radicals and their complexes with the solvent molecules. Complementary TVAS measurements probe the products of CN–radical reactions. Geminate recombination to form ICN and INC is a minor pathway on the 150 fs −1300 ps time scales of our experiments in the chosen organic solvents; nonetheless, large infrared transition dipole moments permit direct observation of INC that is vibrationally excited in the CN stretching mode. The time constants for INC vibrational cooling range from 30 ps in tetrahydrofuran (THF) to 1400 ps in more weakly interacting solvents such as chloroform. The major channel for CN removal in the organic solvents is reaction with solvent molecules, as revealed by depletion of solvent absorption bands and growth of product bands in the TVA spectra. HCN is a reaction product of hydrogen atom abstraction in most of the photoexcited solutions, and forms with vibrational excitation in both the C–H and CN stretching modes. The vibrational cooling rate of the CN stretch in HCN depends on the solvent, and follows the same trend as the cooling rate of the CN stretch in INC. However, in acetonitrile solution an additional reaction pathway produces C₃H₃N₂^• radicals, which release HCN on a much longer time scale

Methanol-to-olefins studied by UV Raman spectroscopy as compared to visible wavelength: capitalization on resonance enhancement

Resonance Raman spectroscopy can provide insights into complex reaction mechanisms by selectively enhancing the signals of specific molecular species. In this work, we demonstrate that, by changing the excitation wavelength, Raman bands of different intermediates in the methanol-to-hydrocarbons reactions can be identified. We show in particular how UV excitation enhances signals from short-chain olefins and cyclopentadienyl cations during the induction period, while visible excitation better detects later-stage aromatics. However, visible excitation is prone to fluorescence that can obscure Raman signals, and hence, we show how fast fluorescence rejection techniques like Kerr gating are necessary for extracting useful information from visible excitation measurements

Kerr gated Raman spectroscopy of LiPF6 salt and LiPF6-based organic carbonate electrolyte for Li-ion batteries

Fluorescent species are formed during cycling of lithium ion batteries as a result of electrolyte decomposition due to the instability of the non-aqueous electrolytes and side reactions that occur at the electrode surface. The increase in the background fluorescence due to the presence of these components makes it harder to analyse data due to the spectroscopic overlap of Raman scattering and fluorescence. Herein, Kerr gated Raman spectroscopy was shown to be an effective technique for the isolation of the scattering effect from the fluorescence enabling the collection of the Raman spectra of LiPF6 salt and LiPF6-based organic carbonate electrolyte, without the interference of the fluorescence component. Kerr gated Raman was able to identify POF3 on the LiPF6 particle surface, after the addition of trace water

Reversal of a single base pair step controls guanine photo-oxidation by an intercalating Ru(II) dipyridophenazine complex

Small changes in DNA sequence can often have major biological effects. Here the rates and yields of guanine photo-oxidation by Λ [Ru(TAP)2(dppz)]2+ have been compared in 5′-{CCGGATCCGG}2 and 5′-{CCGGTACCGG}2 using ps/ns transient visible and time-resolved IR (TRIR) spectroscopy. The inefficiency of electron transfer in the TA sequence is consistent with the 5′-TA-3′ vs. 5′-AT-3′ binding preference predicted by X-ray crystallography. The TRIR spectra also reveal the differences in binding sites in the two oligonucleotides

Contrasting ring-opening propensities in UV-excited α-pyrone and coumarin

Ring-opening quantum yields following UV-photoexcitation of coumarin and α-pyrone are influenced by the dynamics through, rather than just the geometries of, conical intersections.</p

Understanding the factors controlling the photo-oxidation of natural DNA by enantiomerically pure intercalating ruthenium polypyridyl complexes through TA/TRIR studies with polydeoxynucleotides and mixed sequence oligodeoxynucleotides

Ruthenium polypyridyl complexes which can sensitise the photo-oxidation of nucleic acids and other biological molecules show potential for photo-therapeutic applications. In this article a combination of transient visible absorption (TrA) and time-resolved infra-red (TRIR) spectroscopy are used to compare the photo-oxidation of guanine by the enantiomers of [Ru(TAP)2(dppz)]2+ in both polymeric {poly(dG-dC), poly(dA-dT) and natural DNA} and small mixed-sequence duplex-forming oligodeoxynucleotides. The products of electron transfer are readily monitored by the appearance of a characteristic TRIR band centred at ca. 1700 cm?1 for the guanine radical cation and a band centered at ca. 515 nm in the TrA for the reduced ruthenium complex. It is found that efficient electron transfer requires that the complex be intercalated at a G-C base-pair containing site. Significantly, changes in the nucleobase vibrations of the TRIR spectra induced by the bound excited state before electron transfer takes place are used to identify preferred intercalation sites in mixed-sequence oligodeoxynucleotides and natural DNA. Interestingly, with natural DNA, while it is found that quenching is inefficient in the picosecond range, a slower electron transfer process occurs, which is not found with the mixed-sequence duplex-forming oligodeoxynucleotides studied

Photochemical mechanism of an atypical algal phytochrome

International audiencePhytochromes are bilin-containing photoreceptors that are typically sensitive to the red/far-red region of the visible spectrum. Recently, phytochromes from certain eukaryotic algae have become attractive targets for optogenetic applications because of their unique ability to respond to multiple wavelengths of light. Herein, a combination of time-resolved spectroscopy and structural approaches across picosecond to second timescales have been used to map photochemical mechanisms and structural changes in this atypical group of phytochromes. The photochemistry of an orange/far-red light-sensitive algal phytochrome from Dolihomastix tenuilepis has been investigated by using a combination of visible, IR and X-ray scattering probes. The entire photocycle, correlated with accompanying structural changes in the cofactor/protein, are reported. This study identifies a complex photocycle for this atypical phytochrome. It also highlights a need to combine outcomes from a range of biophysical approaches to unravel complex photochemical and macromolecular processes in multi-domain photoreceptor proteins that are the basis of biological light-mediated signalling