Application of NIR Raman Spectroscopy to Probe the Flexibility of RNA Structure

Gaston, Hui Bon Hoa

doi:10.1007/978-1-0716-0278-2_12

Cited by 4 publications

(3 citation statements)

References 32 publications

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“…The previous studies focused only on the minimal self-cleaving sequence of RNA because of the technical difficulties, yet it is likely that sequences outside the catalytic core may affect the global conformational change and thus the fitness of the viroid in vivo. In this regard, Hui Bon Hoa et al [ 15 , 16 ] studied the structures of both, ASBVd(−) and ASBVd(+) strands ( Figure 1 ), by Raman spectroscopy and showed that both molecules exhibited a typical A-type RNA structure with an ordered double-helical content as expected. Nonetheless, small but specific differences between the two strands were found in the sugar puckering and base-stacking regions.…”

Section: Introductionmentioning

confidence: 77%

Kinetic Study of the Avocado Sunblotch Viroid Self-Cleavage Reaction Reveals Compensatory Effects between High-Pressure and High-Temperature: Implications for Origins of Life on Earth

Kaddour

Lucchi²,

Hervé

et al. 2021

Biology

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A high pressure apparatus allowing one to study enzyme kinetics under pressure was used to study the self-cleavage activity of the avocado sunblotch viroid. The kinetics of this reaction were determined under pressure over a range up to 300 MPa (1–3000 bar). It appears that the initial rate of this reaction decreases when pressure increases, revealing a positive ΔV≠ of activation, which correlates with the domain closure accompanying the reaction and the decrease of the surface of the viroid exposed to the solvent. Although, as expected, temperature increases the rate of the reaction whose energy of activation was determined, it appeared that it does not significantly influence the ΔV≠ of activation and that pressure does not influence the energy of activation. These results provide information about the structural aspects or this self-cleavage reaction, which is involved in the process of maturation of this viroid. The behavior of ASBVd results from the involvement of the hammerhead ribozyme present at its catalytic domain, indeed a structural motif is very widespread in the ancient and current RNA world.

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Section: Introductionmentioning

confidence: 77%

Kinetic Study of the Avocado Sunblotch Viroid Self-Cleavage Reaction Reveals Compensatory Effects between High-Pressure and High-Temperature: Implications for Origins of Life on Earth

Kaddour

Lucchi²,

Hervé

et al. 2021

Biology

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“…These data indicate the stability of a helical structure and have become the core of nucleic acid secondary structure prediction algorithms [ 127 , 128 ]. In addition to optical melting experiments, other spectroscopic techniques such as Fourier Transform Infrared (FT-IR) spectroscopy [ 129 , 130 , 131 ], Raman spectroscopy [ 132 , 133 , 134 , 135 , 136 ], circular dichroism [ 137 , 138 , 139 , 140 , 141 ], and fluorescence-based techniques (microscale thermophoresis) [ 142 , 143 , 144 , 145 , 146 , 147 , 148 ] have also been employed to study RNA structure. Similar experimental information (melting temperature, helical stability, enthalpy, entropy, and free energy changes) can be gleaned from each and translated to computational endeavors.…”

Section: Experiments That Can Help Validate MD Simulation Resultsmentioning

confidence: 99%

Challenges with Simulating Modified RNA: Insights into Role and Reciprocity of Experimental and Computational Approaches

D'Esposito

Myers

Chen

et al. 2022

Genes

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RNA is critical to a broad spectrum of biological and viral processes. This functional diversity is a result of their dynamic nature; the variety of three-dimensional structures that they can fold into; and a host of post-transcriptional chemical modifications. While there are many experimental techniques to study the structural dynamics of biomolecules, molecular dynamics simulations (MDS) play a significant role in complementing experimental data and providing mechanistic insights. The accuracy of the results obtained from MDS is determined by the underlying physical models i.e., the force-fields, that steer the simulations. Though RNA force-fields have received a lot of attention in the last decade, they still lag compared to their protein counterparts. The chemical diversity imparted by the RNA modifications adds another layer of complexity to an already challenging problem. Insight into the effect of RNA modifications upon RNA folding and dynamics is lacking due to the insufficiency or absence of relevant experimental data. This review provides an overview of the state of MDS of modified RNA, focusing on the challenges in parameterization of RNA modifications as well as insights into relevant reference experiments necessary for their calibration.

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“…Another form of spectroscopy, near-infrared (NIR) Raman spectroscopy, is also proving useful. It provides information about the energy modes of vibrating molecules subject to modulation by the polarizability of adjacent nuclei [73]. The technique has only become viable with the latest instrumentation but allows for even dilute solutions to be reliably characterized under near-native conditions, and indeed, the avocado sunblotch viroid genome has been analyzed this way [73].…”

Section: Other Techniquesmentioning

confidence: 99%

Evaluating RNA Structural Flexibility: Viruses Lead the Way

Fairman

Lever

Kenyon

2021

Viruses

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Our understanding of RNA structure has lagged behind that of proteins and most other biological polymers, largely because of its ability to adopt multiple, and often very different, functional conformations within a single molecule. Flexibility and multifunctionality appear to be its hallmarks. Conventional biochemical and biophysical techniques all have limitations in solving RNA structure and to address this in recent years we have seen the emergence of a wide diversity of techniques applied to RNA structural analysis and an accompanying appreciation of its ubiquity and versatility. Viral RNA is a particularly productive area to study in that this economy of function within a single molecule admirably suits the minimalist lifestyle of viruses. Here, we review the major techniques that are being used to elucidate RNA conformational flexibility and exemplify how the structure and function are, as in all biology, tightly linked.

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Application of NIR Raman Spectroscopy to Probe the Flexibility of RNA Structure

Cited by 4 publications

References 32 publications

Kinetic Study of the Avocado Sunblotch Viroid Self-Cleavage Reaction Reveals Compensatory Effects between High-Pressure and High-Temperature: Implications for Origins of Life on Earth

Kinetic Study of the Avocado Sunblotch Viroid Self-Cleavage Reaction Reveals Compensatory Effects between High-Pressure and High-Temperature: Implications for Origins of Life on Earth

Challenges with Simulating Modified RNA: Insights into Role and Reciprocity of Experimental and Computational Approaches

Evaluating RNA Structural Flexibility: Viruses Lead the Way

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