2,4-Diamino-6,7-dimethylpteridine as a fluorescent ligand for binding and sensing an orphan cytosine in RNA duplexes

Double-stranded DNA (dsDNA) and RNA (dsRNA) helices display an unusual structural diversity. Some structural variations are linked to sequence and may serve as signaling units for protein-binding partners. Therefore, elucidating the mechanisms and factors that modulate these variations is of fundamental importance. While the structural diversity of dsDNA has been extensively studied, similar studies have not been performed for dsRNA. Because of the increasing awareness of RNA’s diverse biological roles, such studies are timely and increasingly important. We integrate solution x-ray scattering at wide angles (WAXS) with all-atom molecular dynamics simulations to explore the conformational ensemble of duplex topologies for different sequences and salt conditions. These tightly coordinated studies identify robust correlations between features in the WAXS profiles and duplex geometry and enable atomic-level insights into the structural diversity of DNA and RNA duplexes. Notably, dsRNA displays a marked sensitivity to the valence and identity of its associated cations.

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Regulation of RNA helicase activity: principles and examples

Biological Chemistry ◽

10.1515/hsz-2020-0362 ◽

2020 ◽

Vol 0 (0) ◽

Author(s):

Pascal Donsbach ◽

Dagmar Klostermeier

Keyword(s):

Atp Hydrolysis ◽

Wide Spectrum ◽

Mrna Translation ◽

Rna Degradation ◽

Rna Helicases ◽

Interaction Partners ◽

Rna Duplexes ◽

Self Association

Abstract RNA helicases are a ubiquitous class of enzymes involved in virtually all processes of RNA metabolism, from transcription, mRNA splicing and export, mRNA translation and RNA transport to RNA degradation. Although ATP-dependent unwinding of RNA duplexes is their hallmark reaction, not all helicases catalyze unwinding in vitro, and some in vivo functions do not depend on duplex unwinding. RNA helicases are divided into different families that share a common helicase core with a set of helicase signature motives. The core provides the active site for ATP hydrolysis, a binding site for the non-sequence-specific interactions with RNA, and in many cases a basal unwinding activity. Its activity is often regulated by flanking domains, by interaction partners, or by self-association. In this review, we summarize the regulatory mechanisms that modulate the activities of the helicase core. Case studies on selected helicases with functions in translation, splicing, and RNA sensing illustrate the various modes and layers of regulation in time and space that harness the helicase core for a wide spectrum of cellular tasks.

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Comparison of Cis- and Oxaliplatin-induced Destabilization of 15-mer DNA- and RNA Duplexes by Binding to Centrally Located GG- and GNG Sequences

Zeitschrift für anorganische und allgemeine Chemie ◽

10.1002/zaac.201300060 ◽

2013 ◽

Vol 639 (8-9) ◽

pp. 1655-1660 ◽

Cited By ~ 5

Author(s):

Christopher Polonyi ◽

Ingrid Albertsson ◽

Mariana S. Damian ◽

Sofi K. C. Elmroth

Keyword(s):

Dna And Rna ◽

Rna Duplexes

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Structural insights into RNA duplexes with multiple 2′-5′-linkages

Nucleic Acids Research ◽

10.1093/nar/gkw1307 ◽

2016 ◽

pp. gkw1307 ◽

Cited By ~ 2

Author(s):

Fusheng Shen ◽

Zhipu Luo ◽

Hehua Liu ◽

Rui Wang ◽

Shenglong Zhang ◽

...

Keyword(s):

Rna Duplexes ◽

Structural Insights

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Competitive Assay for Theophylline Based on an Abasic Site-Containing DNA Duplex Aptamer and a Fluorescent Ligand

Chemistry - A European Journal ◽

10.1002/chem.201201298 ◽

2012 ◽

Vol 18 (40) ◽

pp. 12719-12724 ◽

Cited By ~ 19

Author(s):

Yusuke Sato ◽

Yushuang Zhang ◽

Seiichi Nishizawa ◽

Takehiro Seino ◽

Kodai Nakamura ◽

...

Keyword(s):

Abasic Site ◽

Dna Duplex ◽

Competitive Assay ◽

Fluorescent Ligand

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