Direct Observation of Multiple Tautomers of Oxythiamine and their Recognition by the Thiamine Pyrophosphate Riboswitch

Structural diversification of canonical nucleic acid bases and nucleotide analogues by tautomerism has been proposed to be a powerful on/off switching mechanism allowing regulation of many biological processes mediated by RNA enzymes and aptamers. Despite the suspected biological importance of tautomerism, attempts to observe minor tautomeric forms in nucleic acid or hybrid nucleic acid-ligand complexes have met with challenges due to the lack of sensitive methods. Here, a combination of spectroscopic, biochemical, and computational tools probed tautomerism in the context of an RNA aptamer-ligand complex; studies involved a model ligand, oxythiamine pyrophosphate (OxyTPP), bound to the thiamine pyrophosphate (TPP) riboswitch (an RNA aptamer) as well as its unbound nonphosphorylated form, oxythiamine (OxyT). OxyTPP, similarly to canonical heteroaromatic nucleic acid bases, has a pyrimidine ring that forms hydrogen bonding interactions with the riboswitch. Tautomerism was established using two-dimensional infrared (2D IR) spectroscopy, variable temperature FTIR and NMR spectroscopies, binding isotope effects (BIEs), and computational methods. All three possible tautomers of OxyT, including the minor enol tautomer, were directly identified, and their distributions were quantitated. In the bound form, BIE data suggested that OxyTPP existed as a 4′-keto tautomer that was likely protonated at the N1′-position. These results also provide a mechanistic framework for understanding the activation of riboswitch in response to deamination of the active form of vitamin B1 (or TPP). The combination of methods reported here revealing the fine details of tautomerism can be applied to other systems where the importance of tautomerism is suspected.National Institutes of Health (U.S.) (Grant CA080024)National Institutes of Health (U.S.) (Grant CA26731)National Institutes of Health (U.S.) (Grant ES002109)National Institutes of Health (U.S.) (Grant ES007020)National Science Foundation (U.S.) (Grant CHE-1212557)Massachusetts Institute of Technology. Center for Environmental Health Sciences (National Institutes of Health (U.S.) Center Grant P30-ES002109)Massachusetts Institute of Technology. Laser Biomedical Research Center (National Institutes of Health (U.S.) Center Grant P41-EB015871)National Institutes of Health (U.S.) (Traineeship T32 ES007020)Massachusetts Institute of Technology (Poitras Pre-Doctoral Fellowship

Sub-20 nm Core-Shell-Shell Nanoparticles for Bright Upconversion and Enhanced Förster Resonant Energy Transfer.

Upconverting nanoparticles provide valuable benefits as optical probes for bioimaging and Förster resonant energy transfer (FRET) due to their high signal-to-noise ratio, photostability, and biocompatibility; yet, making nanoparticles small yields a significant decay in brightness due to increased surface quenching. Approaches to improve the brightness of UCNPs exist but often require increased nanoparticle size. Here we present a unique core-shell-shell nanoparticle architecture for small (sub-20 nm), bright upconversion with several key features: (1) maximal sensitizer concentration in the core for high near-infrared absorption, (2) efficient energy transfer between core and interior shell for strong emission, and (3) emitter localization near the nanoparticle surface for efficient FRET. This architecture consists of β-NaYbF4 (core) @NaY0.8-xErxGd0.2F4 (interior shell) @NaY0.8Gd0.2F4 (exterior shell), where sensitizer and emitter ions are partitioned into core and interior shell, respectively. Emitter concentration is varied (x = 1, 2, 5, 10, 20, 50, and 80%) to investigate influence on single particle brightness, upconversion quantum yield, decay lifetimes, and FRET coupling. We compare these seven samples with the field-standard core-shell architecture of β-NaY0.58Gd0.2Yb0.2Er0.02F4 (core) @NaY0.8Gd0.2F4 (shell), with sensitizer and emitter ions codoped in the core. At a single particle level, the core-shell-shell design was up to 2-fold brighter than the standard core-shell design. Further, by coupling a fluorescent dye to the surface of the two different architectures, we demonstrated up to 8-fold improved emission enhancement with the core-shell-shell compared to the core-shell design. We show how, given proper consideration for emitter concentration, we can design a unique nanoparticle architecture to yield comparable or improved brightness and FRET coupling within a small volume

Melting of a beta-Hairpin Peptide Using Isotope-Edited 2D IR Spectroscopy and Simulations

Item does not contain fulltextIsotope-edited two-dimensional infrared spectroscopy has been used to characterize the conformational heterogeneity of the beta-hairpin peptide TrpZip2 (TZ2) across its thermal unfolding transition. Four isotopologues were synthesized to probe hydrogen bonding and solvent exposure of the beta-turn (K8), the N-terminus (S1), and the midstrand region (T10 and T3T10). Isotope-shifts, 2D lineshapes, and other spectral changes to the amide I 2D IR spectra of labeled TZ2 isotopologues were observed as a function of temperature. Data were interpreted on the basis of structure-based spectroscopic modeling of conformers obtained from extensive molecular dynamics simulations. The K8 spectra reveal two unique turn geometries, the type I' beta-turn observed in the NMR structure, and a less populated disordered or bulged loop. The data indicate that structures at low temperature resemble the folded NMR structure with typical cross-strand hydrogen bonds, although with a subpopulation of misformed turns. As the temperature is raised from 25 to 85 degrees C, the fraction of population with a type I' turn increases, but the termini also fray. Hydrogen bonding contacts in the midstrand region remain at all temperatures although with increasing thermal disorder. Our data show no evidence of an extended chain or random coil state for the TZ2 peptide at any temperature. The methods demonstrated here offer an approach to characterizing conformational variation within the folded or unfolded states of proteins and peptides

Two-dimensional infrared spectroscopy of nucleic acids : application to tautomerism and DNA aptamer unfolding dynamics

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2014.Cataloged from PDF version of thesis. Vita.Includes bibliographical references.The structural dynamics of nucleic acids are intimately related to their biological functions; however, our ability to study these molecular dynamics has been largely impeded by the lack of techniques that possess both high time resolution and structural sensitivity. The motivation for the work in this thesis was to develop and apply two-dimensional infrared spectroscopy (2D IR) as a new experimental tool to investigate nucleic acid dynamics. Infrared spectroscopy is sensitive to structural changes of nucleic acids and 2D IR offers sub-picosecond time resolution. 2D IR spectroscopy is advantageous over the linear infrared absorption spectroscopy because the vibrational spectrum is spread onto two frequency axes, giving rise to the structurally sensitive cross-peaks. These cross-peaks allow the determination of vibrational couplings, which encode chemical bond connectivity, distance and orientation. However, 2D IR spectroscopy of nucleic acids is underdeveloped due to the difficulties in modeling highly delocalized and coupled vibrations of nucleobases. This thesis initiated the efforts to develop 2D IR spectroscopy of nucleic acids by first characterizing the 2D IR spectra and vibrational eigenstates of nucleobases, using a model of multiple anharmonically coupled oscillators. With pronounced cross-peaks existing between all the vibrations for a give nucleobase, 2D IR spectroscopy was shown to be capable of distinguishing between different tautomers, using pyridone as a model system. Coupled with a laser-induced temperature-jump (T-jump), 2D IR was used to monitor rapidly exchanging tautomers in real time under physiological conditions on the nanosecond timescale. Systematically characterizing the tautomer exchange rates as a function of various experimental variables lead to a two-state concerted mechanism involving bridging water wires for the lactam-lactim tautomerization of 6-chloro-2-pyridone. This method was then applied to study the tautomerism of a deoxycytidine analog, KP1212, which is an anti-HIV drug. Multiple tautomers, including the normally rare enol tautomers, were found under physiological conditions. This observation supports the rare tautomer hypothesis, which states that each tautomer displays a distinct base-pairing preference, eventually leading to mutations and population collapse of the HIV viruses. Beyond studies on the single nucleotide level, 2D IR was used to characterize the structural dynamics of thrombin-binding aptamer (TBA), which is a 15mer DNA folded into a guanine-quadruplex (G-quadruplex). The 2D IR spectral signatures of G-quadruplex were established, and T-jump transient 2D IR was employed to investigate the unfolding dynamics of TBA. A mechanism of the early unfolding of TBA was proposed: A ~100 nanosecond response was attributed to the local deformation of the G-quadruplex, and a few-microsecond response was ascribed to be the fraying of the 3'-tail of TBA. This observation was consistent with a mechanism suggested by molecular dynamics simulations. Finally, the dissociation of double-stranded DNA formed by TBA and its complementary strand was found to be on the timescale of tens to hundreds of microseconds. The experiments in this thesis demonstrate the capability of 2D IR to investigate nucleic acid dynamics spanning a wide range of timescales.by Chunte Sam Peng.Ph. D

Identification of Lactam–Lactim Tautomers of Aromatic Heterocycles in Aqueous Solution Using 2D IR Spectroscopy

The tautomerism of aromatic heterocycles is of great interest because it directly affects their chemical properties and biological function. The tautomerism of 2-pyridone, 6-chloro-2-pyridone, and 4-pyrimidinone has been examined in D₂O using FTIR, two-dimensional IR (2D IR) spectroscopy, and density functional theory (DFT) calculations. Using the 2D IR cross-peak patterns, the lactim tautomer of 6-chloro-2-pyridone was separated from the lactam tautomer, and its population was observed to increase with temperature. The equilibrium constant of [lactam]/[lactim] was determined to be 2.1 at room temperature for 6-chloro-2-pyridone. Similarly, the N1H and N3H lactam tautomers of 4-pyrimidinone were identified with 2D IR. To assign the vibrational modes of different tautomers, DFT calculations of these chemical species were performed with explicit water molecules, and the hydration effects on the vibrational frequencies and intensities were established

Direct observation of ground-state lactam-lactim tautomerization using temperature-jump transient 2D IR spectroscopy

We provide a systematic characterization of the nanosecond ground-state lactam-lactim tautomerization of pyridine derivatives in aqueous solution under ambient conditions using temperature-jump transient 2D IR spectroscopy. Although electronic excited-state tautomerization has been widely studied, experimental work on the ground electronic state, most relevant to chemistry and biology, is lacking. Using 2D IR spectroscopy, lactam and lactim tautomers of 6- chloro-2-pyridoneand2-chloro-4-pyridone are unambiguously identified by their unique cross-peak patterns. Monitoring the correlated exponential relaxation of these signals in response to a laser temperature jump provides a direct measurement of the nanosecond tautomerization kinetics. By studying the temperature, concentration, solvent, and pH dependence, we extract a thermodynamic and kinetic characterization and conclude that the tautomerization proceeds through a two-state concerted mechanism. We find that the intramolecular proton transfer is mediated by bridging water molecules and there action barrier is dictated by the release of a proton from pyridone, as would be expected for an efficient Grothuss-type proton transfer mechanism.National Science Foundation (U.S.) (Grant CHE-1212557)Massachusetts Institute of Technology. Center for Environmental Health Sciences (NIH) Center Grant P30-ES002109))Massachusetts Institute of Technology. Laser Biomedical Research Center (NIH Center Grant P41-EB015871)Agilent TechnologiesNational Institutes of Health (U.S.) (Ruth L. Kirschstein National Research Service Award