Plasticity of the RNA kink turn structural motif

Antonioli, Alexandra H.; Cochrane, Jesse C.; Lipchock, Sarah V.; Strobel, Scott A.

doi:10.1261/rna.1883810

Cited by 14 publications

(30 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The C-stems and NC-stems of these K-turns are closed by C-G and sheared tandem G-A base pairs, respectively, and are separated by three- or four-nucleotide bulges (Figure 1C). This nucleotide sequence combination enables the formation of a significant bend (~120°) in the helix axis that is stabilized by protein-RNA or RNA-RNA contacts often distal to the turn itself 23. In isolation, the K-turn sequence motif has been observed to exist as a dynamic population of conformations 33 or to preferentially adopt an extended conformation 47.…”

Section: Resultsmentioning

confidence: 99%

“…The consensus K-turn sequence motif has the intrinsic capacity to adopt the familiar K-turn fold, but this conformation appears to be stabilized by intra- or inter-molecular interactions involving the flanking RNA helices distal to the kink or interactions with proteins that bind K-turns 23. Indeed, FRET measurements have shown that the K-turn motif by itself can be dynamic and converts between linear and bent conformations and that these conformational states appear to be equally populated 33, 34.…”

Section: Discussionmentioning

confidence: 99%

“…The reverse K-turn, which has been observed infrequently, leads to a bend toward the major groove 12, 22. The direction of the bend created by the K-turn is substantially influenced by elements outside the K-turn 23.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Solution Structure of the K-Turn and Specifier Loop Domains from the Bacillus subtilis tyrS T-Box Leader RNA

Wang

Nikonowicz

2011

Journal of Molecular Biology

View full text Add to dashboard Cite

In Gram-positive bacteria, the RNA transcripts of many amino acid biosynthetic and aminoacyltRNA synthetase genes contain 5' untranslated regions, or leader RNAs, that function as riboswitches. These T bxo riboswitches bind cognate tRNA molecules and regulate gene expression by a transcription attenuation mechanism. The Specifier Loop domain of the leader RNA contains nucleotides that pair with nucleotides in the tRNA anticodon loop and is flanked on one side by a kink-turn, or GA, sequence motif. We have determined the solution NMR structure of the kink-turn (K-turn) sequence element within the context of the Specifier Loop domain. The K-turn sequence motif has several non-canonical base pairs typical of K-turn structures but adopts an extended conformation. The Specifier Loop domain contains a loop E structural motif and the single strand Specifier nucleotides stack with their Watson-Crick edges displaced toward the minor groove. Mg 2+ leads to significant bending of the helix axis at the base of the Specifier Loop domain, but does not alter the K-turn. ITC indicates that the K-turn sequence causes a small enhancement of the interaction between tRNA anticodon arm with the Specifier Loop domain. One possibility is that the K-turn structure is formed and stabilized when tRNA binds the T box riboswitch and interacts with Stem I and the antiterminator helix. This motif in turn anchors the orientation of Stem I relative to the 3' half of the leader RNA, further stabilizing the tRNA-T box complex.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Solution Structure of the K-Turn and Specifier Loop Domains from the Bacillus subtilis tyrS T-Box Leader RNA

Wang

Nikonowicz

2011

Journal of Molecular Biology

View full text Add to dashboard Cite

show abstract

“…The T(GAAA)-R(11 nt) interaction also directs the bending of a kink turn in the Azoarcus group I intron (Antonioli et al 2010). Mutations of a GAAA tetraloop implicated in a tetraloop-receptor interaction in a group II intron suggested a slight morphological loop tolerance for this interaction.…”

Section: Contribution Of Gaaa Tetraloop-11 Nt Receptor Interaction Tomentioning

confidence: 99%

An RNA folding motif: GNRA tetraloop–receptor interactions

Fiore

Nesbitt

2013

Quart. Rev. Biophys.

105

View full text Add to dashboard Cite

Nearly two decades after Westhof and Michel first proposed that RNA tetraloops may interact with distal helices, tetraloop–receptor interactions have been recognized as ubiquitous elements of RNA tertiary structure. The unique architecture of GNRA tetraloops (N=any nucleotide, R=purine) enables interaction with a variety of receptors, e.g., helical minor grooves and asymmetric internal loops. The most common example of the latter is the GAAA tetraloop–11 nt tetraloop receptor motif. Biophysical characterization of this motif provided evidence for the modularity of RNA structure, with applications spanning improved crystallization methods to RNA tectonics. In this review, we identify and compare types of GNRA tetraloop–receptor interactions. Then we explore the abundance of structural, kinetic, and thermodynamic information on the frequently occurring and most widely studied GAAA tetraloop–11 nt receptor motif. Studies of this interaction have revealed powerful paradigms for structural assembly of RNA, as well as providing new insights into the roles of cations, transition states and protein chaperones in RNA folding pathways. However, further research will clearly be necessary to characterize other tetraloop–receptor and long-range tertiary binding interactions in detail – an important milestone in the quantitative prediction of free energy landscapes for RNA folding.

show abstract

“…it has plasticity to some extent. 27,28 Recently, the applications of fluorescence resonance energy transfer (FRET) 29,30 have shed light on the conformation of K-turn RNAs. Many observations show that the unbound K-turn RNA exists in an extended conformation, and the metal ions could induce it to fold with its chaperon protein (L7Ae homolog proteins).…”

Section: Introductionmentioning

confidence: 99%