Sequence-dependent conformational preferences of disordered single-stranded RNA.

IF 7.9 2区 综合性期刊 Q1 CHEMISTRY, MULTIDISCIPLINARY
Cell Reports Physical Science Pub Date : 2024-11-20 Epub Date: 2024-10-29 DOI:10.1016/j.xcrp.2024.102264
Tong Wang, Weiwei He, Suzette A Pabit, Lois Pollack, Serdal Kirmizialtin
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引用次数: 0

Abstract

Disordered single-stranded RNA (ssRNA) molecules, like their well-folded counterparts, have crucial functions that depend on their structures. However, since native ssRNAs constitute a highly heterogeneous conformer population, their structural characterization poses challenges. One important question regards the role of sequence in influencing ssRNA structure. Here, we adopt an integrated approach that combines solution-based measurements, including small-angle X-ray scattering (SAXS) and Förster resonance energy transfer (FRET), with experimentally guided all-atom molecular dynamics (MD) simulations, to construct structural ensembles of a 30-nucleotide RNA homopolymer (rU30) and a 30-nucleotide RNA heteropolymer with an A-/C-rich sequence. We compare the size, shape, and flexibility of the two different ssRNAs. While the average properties align with polymer-physics descriptions of flexible polymers, we discern distinct, sequence-dependent conformations at the molecular level that demand a more detailed representation than provided by polymer models. These findings emphasize the role of sequence in shaping the overall properties of ssRNA.

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来源期刊
Cell Reports Physical Science
Cell Reports Physical Science Energy-Energy (all)
CiteScore
11.40
自引率
2.20%
发文量
388
审稿时长
62 days
期刊介绍: Cell Reports Physical Science, a premium open-access journal from Cell Press, features high-quality, cutting-edge research spanning the physical sciences. It serves as an open forum fostering collaboration among physical scientists while championing open science principles. Published works must signify significant advancements in fundamental insight or technological applications within fields such as chemistry, physics, materials science, energy science, engineering, and related interdisciplinary studies. In addition to longer articles, the journal considers impactful short-form reports and short reviews covering recent literature in emerging fields. Continually adapting to the evolving open science landscape, the journal reviews its policies to align with community consensus and best practices.
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