An RNA folding motif: GNRA tetraloop–receptor interactions

Fiore, Julie L.; Nesbitt, David J.

doi:10.1017/s0033583513000048

Cited by 76 publications

(109 citation statements)

References 133 publications

(420 reference statements)

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“…This base-phosphate hydrogen bond is of the "5/4/3BPh" type according to a recent classification ). It ensues that the 1-4 G•A trans-Sugar/Watson-Crick pair (t-SW) occurring in GNRA loops should not be considered as a U-turn determinant although it is essential for interactions with GNRA receptors (Fiore and Nesbitt 2013).…”

Section: U-turn and U Sh -Turn Signaturesmentioning

confidence: 99%

“…Although rare, these GANC loops are examples of structured tetraloops with no oxygen-π contact. For all U-turns, it is important to note that the last three nucleobases are stacked in a manner that their exposed Watson-Crick edges can establish specific tertiary contacts such as, for example, within anticodon-codon associations or with cognate receptors (Fiore and Nesbitt 2013;Tanaka et al 2013). …”

Section: U-turn and U Sh -Turn Signaturesmentioning

confidence: 99%

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Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops

D’Ascenzo¹,

Leonarski²,

Vicens³

et al. 2016

RNA

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When thinking about RNA three-dimensional structures, coming across GNRA and UNCG tetraloops is perceived as a boon since their folds have been extensively described. Nevertheless, analyzing loop conformations within RNA and RNP structures led us to uncover several instances of GNRA and UNCG loops that do not fold as expected. We noticed that when a GNRA does not assume its "natural" fold, it adopts the one we typically associate with a UNCG sequence. The same folding interconversion may occur for loops with UNCG sequences, for instance within tRNA anticodon loops. Hence, we show that some structured tetranucleotide sequences starting with G or U can adopt either of these folds. The underlying structural basis that defines these two fold types is the mutually exclusive stacking of a backbone oxygen on either the first (in GNRA) or the last nucleobase (in UNCG), generating an oxygen-π contact. We thereby propose to refrain from using sequences to distinguish between loop conformations. Instead, we suggest using descriptors such as U-turn (for "GNRA-type" folds) and a newly described Z-turn (for "UNCG-type" folds). Because tetraloops adopt for the largest part only two (inter)convertible turns, we are better able to interpret from a structural perspective loop interchangeability occurring in ribosomes and viral RNA. In this respect, we propose a general view on the inclination for a given sequence to adopt (or not) a specific fold. We also suggest how long-noncoding RNAs may adopt discrete but transient structures, which are therefore hard to predict.

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Section: U-turn and U Sh -Turn Signaturesmentioning

confidence: 99%

Section: U-turn and U Sh -Turn Signaturesmentioning

confidence: 99%

Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops

D’Ascenzo¹,

Leonarski²,

Vicens³

et al. 2016

RNA

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“…RNA architectures are formed by long-range tertiary interaction networks involving secondary structure elements such as tetraloops (1). Among those, GNRAs—N = any nucleotide, R = A or G—are more common than UNCGs (e.g.…”

Section: Introductionmentioning

confidence: 99%

“…To rationalize this discrepancy, it was proposed that tetraloop frequencies correlate better to the loop potential to establish 3D interactions than to their thermodynamic stability (1,4,5). Indeed, GNRAs were recognized to be central to the folding of large RNAs and RNPs like group I introns (6–8), group II introns (9), ribonuclease P (10–12) and ribosomes (13,14), as a result of their ability to form a characteristic U-turn (15) that allows the Watson–Crick edges of the three stacked nucleobases to interact with double helical receptors (Figure 1B).…”

Section: Introductionmentioning

confidence: 99%

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Identification of receptors for UNCG and GNRA Z-turns and their occurrence in rRNA

D’Ascenzo

Vicens

Auffinger

2018

Nucleic Acids Research

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In contrast to GNRA tetraloop receptors that are common in RNA, receptors for the more thermostable UNCG loops have remained elusive for almost three decades. An analysis of all RNA structures with resolution ≤3.0 Å from the PDB allowed us to identify three previously unnoticed receptors for UNCG and GNRA tetraloops that adopt a common UNCG fold, named ‘Z-turn’ in agreement with our previously published nomenclature. These receptors recognize the solvent accessible second Z-turn nucleotide in different but specific ways. Two receptors participating in a complex network of tertiary interactions are associated with the rRNA UUCG and GAAA Z-turns capping helices H62 and H35a in rRNA large subunits. Structural comparison of fully assembled ribosomes and comparative sequence analysis of >6500 rRNA sequences helped us recognize that these motifs are almost universally conserved in rRNA, where they may contribute to organize the large subunit around the subdomain-IV four-way junction. The third UCCG receptor was identified in a rRNA/protein construct crystallized at acidic pH. These three non-redundant Z-turn receptors are relevant for our understanding of the assembly of rRNA and other long-non-coding RNAs, as well as for the design of novel folding motifs for synthetic biology.

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RNA Structure: Tetraloops

Cheong

Kim

Cheong

2015

Encyclopedia of Life Sciences

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RNA hairpins are among the most common RNA secondary structural elements and are frequently capped by RNA tetraloops. RNA tetraloops are composed of characteristic four‐loop nucleotides that form a compact and stable structure. While they can be formed by many different nucleotide sequences, UNCG (N = A, C, G, or U), GNRA (R = A or G), and CUUG tetraloops are found most often. Tetraloops usually help initiate RNA ‐folding processes and provide sites for tertiary contacts within or between RNAs and for protein binding, thereby facilitating the assembly of ribonucleoprotein particles. Tetraloop interactions can be either sequence‐ or structure‐specific. Herein, we discuss the structures of RNA tetraloops and their interactions with other RNA structural motifs and with RNA ‐binding proteins. Key Concepts RNA hairpins play important structural and functional roles in RNA. RNA tetraloops are composed of four‐loop nucleotides that form a compact and stable structure. Tetraloops assist RNA folding and provide sites for RNA–RNA and RNA–protein interactions. Tetraloop interactions can be either sequence‐ or structure‐specific. We discuss the structures of RNA tetraloops and their interactions with other RNAs and proteins.

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An RNA folding motif: GNRA tetraloop–receptor interactions

Cited by 76 publications

References 133 publications

Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops

Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops

Identification of receptors for UNCG and GNRA Z-turns and their occurrence in rRNA

RNA Structure: Tetraloops

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