The kinetic landscape of an RNA-binding protein in cells

Gene expression in higher eukaryotic cells orchestrates interactions between thousands of RNA-binding proteins (RBPs) and tens of thousands of RNAs¹. The kinetics by which RBPs bind to and dissociate from their RNA sites are critical for the coordination of cellular RNA-protein interactions². However, these kinetic parameters have not been experimentally measured in cells. Here we show that time-resolved RNA-protein cross-linking with a pulsed femtosecond ultraviolet laser, followed by immunoprecipitation and high-throughput sequencing, allows the determination of binding and dissociation kinetics of the RBP DAZL for thousands of individual RNA-binding sites in cells. This kinetic cross-linking and immunoprecipitation (KIN-CLIP) approach reveals that DAZL resides at individual binding sites for time periods of only seconds or shorter, whereas the binding sites remain DAZL-free for markedly longer. The data also indicate that DAZL binds to many RNAs in clusters of multiple proximal sites. The effect of DAZL on mRNA levels and ribosome association correlates with the cumulative probability of DAZL binding in these clusters. Integrating kinetic data with mRNA features quantitatively connects DAZL-RNA binding to DAZL function. Our results show how kinetic parameters for RNA-protein interactions can be measured in cells, and how these data link RBP-RNA binding to the cellular function of RBPs.

On the Origin of the Photostability of DNA and RNA Monomers: Excited State Relaxation Mechanism of the Pyrimidine Chromophore

Today's genetic composition is the result of continual refinement processes on primordial heterocycles present in prebiotic Earth and at least partially regulated by ultraviolet radiation. Femtosecond transient absorption spectroscopy and state-of-the-art ab initio calculations are combined to unravel the electronic relaxation mechanism of pyrimidine, the common chromophore of the nucleobases. The excitation of pyrimidine at 268 nm populates the S₁(nπ*) state directly. A fraction of the population intersystem crosses to the triplet manifold within 7.8 ps, partially decaying within 1.5 ns, while another fraction recovers the ground state in >3 ns. The pyrimidine chromophore is not responsible for the photostability of the nucleobases. Instead, C2 and C4 amino and/or carbonyl functionalization is essential for shaping the topography of pyrimidine's potential energy surfaces and results in accessible conical intersections between the initially populated electronic excited state and the ground state.

Time-resolved ultrafast transient polarization spectroscopy to investigate nonlinear processes and dynamics in electronically excited molecules on the femtosecond time scale

We report a novel experimental technique to investigate ultrafast dynamics in photoexcited molecules by probing the 3rd-order nonlinear optical susceptibility. A non-collinear 3-pulse scheme is developed to probe the ultrafast dynamics of excited electronic states using the optical Kerr effect. Optical homodyne and optical heterodyne detections are demonstrated to measure the 3rd-order nonlinear optical response for the S₁ excited state of liquid nitrobenzene, which is populated by 2-photon absorption of a 780 nm 40 fs excitation pulse.

Excited-State Dynamics in the RNA Nucleotide Uridine 5'-Monophosphate Investigated Using Femtosecond Broadband Transient Absorption Spectroscopy

Damage to RNA from ultraviolet radiation induces chemical modifications to the nucleobases. Unraveling the excited states involved in these reactions is essential; however, investigations aimed at understanding the electronic-energy relaxation pathways of the RNA nucleotide uridine 5'-monophosphate (UMP) have not received enough attention. In this Letter, the excited-state dynamics of UMP is investigated in aqueous solution. Excitation at 267 nm results in a trifurcation event that leads to the simultaneous population of the vibrationally excited ground state, a long-lived ¹nπ* state, and a receiver triplet state within 200 fs. The receiver state internally converts to the long-lived ³ππ* state in an ultrafast time scale. The results elucidate the electronic relaxation pathways and clarify earlier transient absorption experiments performed for uracil derivatives in solution. This mechanistic information is important because long-lived nπ* and ππ* excited states of both singlet and triplet multiplicities are thought to lead to the formation of harmful photoproducts.

Photochemical Relaxation Pathways in Dinitropyrene Isomer Pollutants

Dinitropyrenes are polycyclic aromatic pollutants prevalent in the environment. While their transformations by sunlight in the environment have been documented, the effect that the nitro-group substitution pattern has on the relaxation pathways has not been extensively studied. In this contribution, the steady-state and femtosecond-to-microsecond excited-state dynamics of 1,3-dinitropyrene and 1,8-dinitropyrene isomers are investigated upon visible light excitation at 425 nm and compared with those recently reported for the 1,6-dinitropyrene isomer. The experimental results are complemented with ground- and excited-state density functional calculations. It is shown that excitation at 425 nm results in the ultrafast branching of the excited-state population in the S₁ state to populate the triplet state in ca. 90% yield and to form a nitropyrenoxy radical in less than 10% yield. In addition, the position of the NO₂ group does not affect significantly the excited-state relaxation mechanism, while it does influence the absorption and fluorescence spectra, the fluorescence, triplet, singlet oxygen, and photodegradation yields, as well as the relative yield of radical formation. Radical formation is implicated in the photodegradation of these pollutants, while in the presence of hydrogen donors, direct reactions from the triplet state are also observed.

The Photochemical Branching Ratio in 1,6-Dinitropyrene Depends on the Excitation Energy

Nitropolycyclic aromatic hydrocarbons constitute one of the most disconcerting classes of pollutants. Photochemical degradation is thought to be a primary mode of their natural removal from the environment, but the microscopic mechanism leading to product formation as a function of excitation wavelength is poorly understood. In this Letter, it is revealed that excitation of 1,6-dinitropyrene with 425, 415, or 340 nm radiation leads to an increasing amount of radical production through photodissociation at the expense of triplet-state population-the two primary reaction pathways in this class of pollutants. Radical formation requires overcoming an energy barrier in the excited singlet manifold. This activation energy explains the large fraction of the initial singlet-state population that intersystem crosses to a doorway triplet state, instead of leading overwhelmingly to photodissociation. The unforeseen excitation wavelength dependence of this branching process is expected to regulate the photochemistry of 1,6-dinitropyrene and possibly of other nitroaromatic pollutants in the environment.

Correction: Photochemical etiology of promising ancestors of the RNA nucleobases

Correction for 'Photochemical etiology of promising ancestors of the RNA nucleobases' by M. M. Brister et al., Phys. Chem. Chem. Phys., 2016, DOI: .

Direct Observation of Triplet-State Population Dynamics in the RNA Uracil Derivative 1-Cyclohexyluracil

Investigation of the excited-state dynamics in nucleic acid monomers is an area of active research due to the crucial role these early events play in DNA and RNA photodamage. The dynamics and rate at which the triplet state is populated are key mechanistic pathways yet to be fully elucidated. Direct spectroscopic evidence is presented in this contribution for intersystem crossing dynamics in a uracil derivative, 1-cyclohexyluracil. It is shown that intersystem crossing to the triplet manifold occurs in one picosecond or less in acetonitrile solution-at least an order of magnitude faster than previously estimated experimentally. Broadband transient absorption measurements also reveal the primary electronic relaxation pathways of the uracil chromophore, including the absorption spectra of the (1)ππ*, (1)nπ*, and (3)ππ* states and the rates of vibrational cooling in the ground and (3)ππ* states. The experimental results are supported by density functional calculations.