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Sherman EM, Esquiaqui J, Elsayed G, Ye JD. An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches. RNA (NEW YORK, N.Y.) 2012; 18:496-507. [PMID: 22279151 PMCID: PMC3285937 DOI: 10.1261/rna.031286.111] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 12/14/2011] [Indexed: 05/21/2023]
Abstract
Comprised of two aptamers connected by a short nucleotide linker, the glycine riboswitch was the first example of naturally occurring RNA elements reported to bind small organic molecules cooperatively. Earlier works have shown binding of glycine to the second aptamer allows tertiary interactions to be made between the two aptamers, which facilitates binding of a separate glycine molecule to the first aptamer, leading to glycine-binding cooperativity. Prompted by a distinctive protection pattern in the linker region of a minimal glycine riboswitch construct, we have identified a highly conserved (>90%) leader-linker duplex involving leader nucleotides upstream of the previously reported consensus glycine riboswitch sequences. In >50% of the glycine riboswitches, the leader-linker interaction forms a kink-turn motif. Characterization of three glycine ribsowitches showed that the leader-linker interaction improved the glycine-binding affinities by 4.5- to 86-fold. In-line probing and native gel assays with two aptamers in trans suggested synergistic action between glycine-binding and interaptamer interaction during global folding of the glycine riboswitch. Mutational analysis showed that there appeared to be no ligand-binding cooperativity in the glycine riboswitch when the leader-linker interaction is present, and the previously measured cooperativity is simply an artifact of a truncated construct missing the leader sequence.
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Affiliation(s)
- Eileen M. Sherman
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816, USA
| | - Jackie Esquiaqui
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816, USA
| | - Galal Elsayed
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816, USA
| | - Jing-Dong Ye
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816, USA
- Corresponding author.E-mail .
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Bindewald E, Wendeler M, Legiewicz M, Bona MK, Wang Y, Pritt MJ, Le Grice SF, Shapiro BA. Correlating SHAPE signatures with three-dimensional RNA structures. RNA (NEW YORK, N.Y.) 2011; 17:1688-96. [PMID: 21752927 PMCID: PMC3162334 DOI: 10.1261/rna.2640111] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 05/27/2011] [Indexed: 05/16/2023]
Abstract
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) is a facile technique for quantitative analysis of RNA secondary structure. In general, low SHAPE signal values indicate Watson-Crick base-pairing, and high values indicate positions that are single-stranded within the RNA structure. However, the relationship of SHAPE signals to structural properties such as non-Watson-Crick base-pairing or stacking has thus far not been thoroughly investigated. Here, we present results of SHAPE experiments performed on several RNAs with published three-dimensional structures. This strategy allows us to analyze the results in terms of correlations between chemical reactivities and structural properties of the respective nucleotide, such as different types of base-pairing, stacking, and phosphate-backbone interactions. We find that the RNA SHAPE signal is strongly correlated with cis-Watson-Crick/Watson-Crick base-pairing and is to a remarkable degree not dependent on other structural properties with the exception of stacking. We subsequently generated probabilistic models that estimate the likelihood that a residue with a given SHAPE score participates in base-pairing. We show that several models that take SHAPE scores of adjacent residues into account perform better in predicting base-pairing compared with individual SHAPE scores. This underscores the context sensitivity of SHAPE and provides a framework for an improved interpretation of the response of RNA to chemical modification.
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Affiliation(s)
- Eckart Bindewald
- Basic Science Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
| | - Michaela Wendeler
- RT Biochemistry Section, HIV Drug Resistance Program, NCI-Frederick, Frederick, Maryland 21702, USA
| | - Michal Legiewicz
- RT Biochemistry Section, HIV Drug Resistance Program, NCI-Frederick, Frederick, Maryland 21702, USA
| | - Marion K. Bona
- Basic Science Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
| | - Yi Wang
- RT Biochemistry Section, HIV Drug Resistance Program, NCI-Frederick, Frederick, Maryland 21702, USA
| | - Mark J. Pritt
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, Maryland 21702, USA
| | - Stuart F.J. Le Grice
- RT Biochemistry Section, HIV Drug Resistance Program, NCI-Frederick, Frederick, Maryland 21702, USA
| | - Bruce A. Shapiro
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, Maryland 21702, USA
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Irnov I, Winkler WC. A regulatory RNA required for antitermination of biofilm and capsular polysaccharide operons in Bacillales. Mol Microbiol 2010; 76:559-75. [DOI: 10.1111/j.1365-2958.2010.07131.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Zhou J, Soontornworajit B, Snipes MP, Wang Y. Structural prediction and binding analysis of hybridized aptamers. J Mol Recognit 2010; 24:119-26. [DOI: 10.1002/jmr.1034] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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