scholarly journals Aromatic N versus aromatic F: bioisosterism discovered in RNA base pairing interactions leads to a novel class of universal base analogs

2010 ◽  
Vol 38 (9) ◽  
pp. 3133-3146 ◽  
Author(s):  
Alrun N. Koller ◽  
Jelena Božilović ◽  
Joachim W. Engels ◽  
Holger Gohlke
Keyword(s):  
Base Pairing ◽  
Pairing Interactions

scholarly journals A Deep Dive into DNA Base Pairing Interactions Under Water

2020 ◽  
Vol 124 (27) ◽  
pp. 5559-5570
Author(s):  
Rongpeng Li ◽  
Chi H. Mak
Keyword(s):  
Base Pairing ◽  
Deep Dive ◽  
Dna Base ◽  
Pairing Interactions

ChemInform Abstract: Porous Materials Based on Metal-Nucleobase Systems Sustained by Coordination Bonds and Base Pairing Interactions

ChemInform ◽  
2015 ◽  
Vol 46 (32) ◽  
pp. no-no
Author(s):  
Garikoitz Beobide ◽  
Oscar Castillo ◽  
Antonio Luque ◽  
Sonia Perez-Yanez
Keyword(s):  
Porous Materials ◽  
Base Pairing ◽  
Coordination Bonds ◽  
Pairing Interactions

scholarly journals Processing of Intron-Encoded Box C/D Small Nucleolar RNAs Lacking a 5′,3′-Terminal Stem Structure

2000 ◽  
Vol 20 (13) ◽  
pp. 4522-4531 ◽  
Author(s):  
Xavier Darzacq ◽  
Tamás Kiss
Keyword(s):  
Metabolic Stability ◽  
Small Nucleolar Rnas ◽  
Base Pairing ◽  
Flanking Sequences ◽  
Pairing Interactions ◽  
Precursor Rna ◽  
Nucleolar Rnas ◽  
Stem Structure

ABSTRACT The C and D box-containing (box C/D) small nucleolar RNAs (snoRNAs) function in the nucleolytic processing and 2′-O-methylation of precursor rRNA. In vertebrates, most box C/D snoRNAs are processed from debranched pre-mRNA introns by exonucleolytic activities. Elements directing accurate snoRNA excision are located within the snoRNA itself; they comprise the conserved C and D boxes and an adjoining 5′,3′-terminal stem. Although the terminal stem has been demonstrated to be essential for snoRNA accumulation, many snoRNAs lack a terminal helix. To identify thecis-acting elements supporting the accumulation of intron-encoded box C/D snoRNAs devoid of a terminal stem, we have investigated the in vivo processing of the human U46 snoRNA and an artificial snoRNA from the human β-globin pre-mRNA. We demonstrate that internal and/or external stem structures located within the snoRNA or in the intronic flanking sequences support the accumulation of mammalian box C/D snoRNAs lacking a canonical terminal stem. In the intronic precursor RNA, transiently formed external and/or stable internal base-pairing interactions fold the C and D boxes together and therefore facilitate the binding of snoRNP proteins. Since the external intronic stems are degraded during snoRNA processing, we propose that the C and D boxes alone can provide metabolic stability for the mature snoRNA.

scholarly journals RNA base pairing complexity in living cells visualized by correlated chemical probing

2019 ◽  
Author(s):  
Anthony M. Mustoe ◽  
Nicole Lama ◽  
Patrick S. Irving ◽  
Samuel W. Olson ◽  
Kevin M. Weeks
Keyword(s):  
Single Molecule ◽  
Rna Structure ◽  
Dimethyl Sulfate ◽  
Detection Methods ◽  
Base Pairing ◽  
Base Pairs ◽  
Chemical Probing ◽  
Pairing Interactions ◽  
In Cells

ABSTRACTRNA structure and dynamics are critical to biological function. However, strategies for determining RNA structure in vivo are limited, with established chemical probing and newer duplex detection methods each having notable deficiencies. Here we convert the common reagent dimethyl sulfate (DMS) into a useful probe of all four RNA nucleotides. Building on this advance, we introduce PAIR-MaP, which uses single-molecule correlated chemical probing to directly detect base pairing interactions in cells. PAIR-MaP has superior resolution and accuracy compared to alternative experiments, can resolve alternative pairing interactions of structurally dynamic RNAs, and enables highly accurate structure modeling, including of RNAs containing multiple pseudoknots and extensively bound by proteins. Application of PAIR-MaP to human RNase MRP and two bacterial mRNA 5'-UTRs reveals new functionally important and complex structures undetectable by conventional analyses. PAIR-MaP is a powerful, experimentally concise, and broadly applicable strategy for directly visualizing RNA base pairs and dynamics in cells.

scholarly journals RNA base-pairing complexity in living cells visualized by correlated chemical probing

2019 ◽  
Vol 116 (49) ◽  
pp. 24574-24582 ◽  
Author(s):  
Anthony M. Mustoe ◽  
Nicole N. Lama ◽  
Patrick S. Irving ◽  
Samuel W. Olson ◽  
Kevin M. Weeks
Keyword(s):  
Single Molecule ◽  
Rna Structure ◽  
Messenger Rna ◽  
Dimethyl Sulfate ◽  
Detection Methods ◽  
Base Pairing ◽  
Chemical Probing ◽  
Pairing Interactions ◽  
In Cells

RNA structure and dynamics are critical to biological function. However, strategies for determining RNA structure in vivo are limited, with established chemical probing and newer duplex detection methods each having deficiencies. Here we convert the common reagent dimethyl sulfate into a useful probe of all 4 RNA nucleotides. Building on this advance, we introduce PAIR-MaP, which uses single-molecule correlated chemical probing to directly detect base-pairing interactions in cells. PAIR-MaP has superior resolution compared to alternative experiments, can resolve multiple sets of pairing interactions for structurally dynamic RNAs, and enables highly accurate structure modeling, including of RNAs containing multiple pseudoknots and extensively bound by proteins. Application of PAIR-MaP to human RNase MRP and 2 bacterial messenger RNA 5′ untranslated regions reveals functionally important and complex structures undetected by prior analyses. PAIR-MaP is a powerful, experimentally concise, and broadly applicable strategy for directly visualizing RNA base pairs and dynamics in cells.

Theoretical analysis of noncanonical base pairing interactions in RNA molecules

2007 ◽  
Vol 32 (S1) ◽  
pp. 809-825 ◽  
Author(s):  
Dhananjay Bhattacharyya ◽  
Siv Chand Koripella ◽  
Abhijit Mitra ◽  
Vijay Babu Rajendran ◽  
Bhabdyuti Sinha
Keyword(s):  
Theoretical Analysis ◽  
Base Pairing ◽  
Rna Molecules ◽  
Pairing Interactions

scholarly journals The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements

2021 ◽  
Author(s):  
Katharina F Hohmann ◽  
Anja Blümler ◽  
Alexander Heckel ◽  
Boris Fürtig
Keyword(s):  
Molecular Mechanism ◽  
Fold Increase ◽  
Regulatory Elements ◽  
Regulatory State ◽  
Base Pairing ◽  
Rna Chaperone ◽  
Gene Regulatory Elements ◽  
Pairing Interactions ◽  
Rna Chaperones ◽  
Refolding Kinetics

Abstract In bacteria RNA gene regulatory elements refold dependent on environmental clues between two or more long-lived conformational states each associated with a distinct regulatory state. The refolding kinetics are strongly temperature-dependent and especially at lower temperatures they reach timescales that are biologically not accessible. To overcome this problem, RNA chaperones have evolved. However, the precise molecular mechanism of how these proteins accelerate RNA refolding reactions remains enigmatic. Here we show how the RNA chaperone StpA of Escherichia coli leads to an acceleration of a bistable RNA’s refolding kinetics through the selective destabilization of key base pairing interactions. We find in laser assisted real-time NMR experiments on photocaged bistable RNAs that the RNA chaperone leads to a two-fold increase in refolding rates at low temperatures due to reduced stability of ground state conformations. Further, we can show that upon interaction with StpA, base pairing interactions in the bistable RNA are modulated to favor refolding through the dominant pseudoknotted transition pathway. Our results shed light on the molecular mechanism of the interaction between RNA chaperones and bistable RNAs and are the first step into a functional classification of chaperones dependent on their biophysical mode of operation.

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