scholarly journals Analysis of Ultrafast Transient Absorption Spectroscopy Data using Integrative Data Analysis Platform: 1. Data Processing, Fitting, and Model Selection

2017 ◽  
Author(s):  
Evgenii L. Kovrigin
Keyword(s):  
Data Analysis ◽  
Transient Absorption ◽  
Model Fitting ◽  
Information Criterion ◽  
Transient Absorption Spectroscopy ◽  
Isosbestic Point ◽  
Spectroscopy Data ◽  
Integrative Data Analysis ◽  
Protein Label ◽  
Analysis Platform

ABSTRACTThis manuscript describes a workflow for analysis of transient absorption (TA) spectroscopy data using Integrative Data Analysis Platforms (IDAP) software package. Time-dependent spectral series are analyzed through evaluation of the isosbestic point and kinetics of excited state and ground-state bleach decays. Model fitting and selection based on Akaike’s Information Criterion is discussed. As a practical example, we analyze excitation decays of a common protein label, Alexa Fluor 647.

Fusion of Ultraviolet–Visible and Infrared Transient Absorption Spectroscopy Data to Model Ultrafast Photoisomerization

2017 ◽  
Vol 8 (15) ◽  
pp. 3530-3535 ◽  
Author(s):  
Bruno Debus ◽  
Maylis Orio ◽  
Julien Rehault ◽  
Gotard Burdzinski ◽  
Cyril Ruckebusch ◽  
...  
Keyword(s):  
Absorption Spectroscopy ◽  
Transient Absorption ◽  
Transient Absorption Spectroscopy ◽  
Spectroscopy Data

Thymine Dimerization Induced by Oxidative DNA Lesions and Epigenetic Intermediates via Triplet-Triplet Energy Transfer

2020 ◽  
Author(s):  
Mauricio Lineros-Rosa ◽  
Antonio Francés-Monerris ◽  
Antonio Monari ◽  
Miguel Angél Miranda ◽  
Virginie Lhiaubet-Vallet
Keyword(s):  
Energy Transfer ◽  
Excitation Energy ◽  
Transient Absorption ◽  
Theoretical Calculations ◽  
Dna Lesions ◽  
Transient Absorption Spectroscopy ◽  
Triplet Energy ◽  
Pyrimidine Dimers ◽  
Triplet Energy Transfer ◽  
Dna Nucleobases

Interaction of nucleic acids with light is a scientific question of paramount relevance not only in the understanding of life functioning and evolution, but also in the insurgence of diseases such as malignant skin cancer and in the development of biomarkers and novel light-assisted therapeutic tools. This work shows that the UVA portion of sunlight, not absorbed by canonical DNA nucleobases, can be absorbed by 5-formyluracil (ForU) and 5-formylcytosine (ForC), two ubiquitous oxidative lesions and epigenetic intermediates present in living beings in natural conditions. We measure the strong propensity of these molecules to populate triplet excited states able to transfer the excitation energy to thymine-thymine dyads, inducing the formation of the highly toxic and mutagenic cyclobutane pyrimidine dimers (CPDs). By using steady-state and transient absorption spectroscopy, NMR, HPLC, and theoretical calculations, we quantify the differences in the triplet-triplet energy transfer mediated by ForU and ForC, revealing that the former is much more efficient in delivering the excitation energy and producing the CPD photoproduct. Although significantly slower than ForU, ForC is also able to harm DNA nucleobases and therefore this process has to be taken into account as a viable photosensitization mechanism. The present findings evidence a rich photochemistry crucial to understand DNA photodamage and of potential use in the development of biomarkers and non-conventional photodynamic therapy agents.

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

2019 ◽  
Author(s):  
Matthew M. Brister ◽  
Carlos Crespo-Hernández
Keyword(s):  
Excited State ◽  
Excited States ◽  
Ground State ◽  
Transient Absorption ◽  
Electronic Energy ◽  
Transient Absorption Spectroscopy ◽  
Electronic Relaxation ◽  
Vibrationally Excited ◽  
Excited State Dynamics ◽  
Π State

<p></p><p> Damage to RNA from ultraviolet radiation induce chemical modifications to the nucleobases. Unraveling the excited states involved in these reactions is essential, but 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 longlived <sup>1</sup>n<sub>O</sub>π* state, and a receiver triplet state within 200 fs. The receiver state internally convert to the long-lived <sup>3</sup>ππ* 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.</p><p></p>

Integrative Data Analysis from a Unifying Research Synthesis Perspective

2018 ◽  
Author(s):  
Eun-Young Mun ◽  
Anne E. Ray
Keyword(s):  
Data Analysis ◽  
Large Scale ◽  
Research Synthesis ◽  
Alcohol Intervention ◽  
Data Set ◽  
Integrative Data Analysis ◽  
Level Data ◽  
Model Complex ◽  
Wide Range ◽  
Individual Participant

Integrative data analysis (IDA) is a promising new approach in psychological research and has been well received in the field of alcohol research. This chapter provides a larger unifying research synthesis framework for IDA. Major advantages of IDA of individual participant-level data include better and more flexible ways to examine subgroups, model complex relationships, deal with methodological and clinical heterogeneity, and examine infrequently occurring behaviors. However, between-study heterogeneity in measures, designs, and samples and systematic study-level missing data are significant barriers to IDA and, more broadly, to large-scale research synthesis. Based on the authors’ experience working on the Project INTEGRATE data set, which combined individual participant-level data from 24 independent college brief alcohol intervention studies, it is also recognized that IDA investigations require a wide range of expertise and considerable resources and that some minimum standards for reporting IDA studies may be needed to improve transparency and quality of evidence.

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