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The K-turn motif in riboswitches and other RNA species.

Lilley DM - Biochim. Biophys. Acta (2014)

Bottom Line: This generally functions to mediate tertiary interactions, and to serve as a specific protein binding site.K-turns or closely related structures are found in at least seven different riboswitch structures, where they function as key architectural elements that help generate the ligand binding pocket.This article is part of a Special Issue entitled: Riboswitches.

View Article: PubMed Central - PubMed

Affiliation: Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK. Electronic address: d.m.j.lilley@dundee.ac.uk.

No MeSH data available.


Related in: MedlinePlus

A classification of K-turn structures. K-turns can be divided into simple and complex. Examples are shown for each class. Simple K-turns are further divided into standard and non-standard, with the critical G·A pairs preserved or substituted respectively. The complex K-turns exhibit a greater departure from the standard K-turn, where the primary sequence does not map onto the 3D RNA structure. k-junctions can be considered as another branch of the complex K-turns. This scheme is taken from reference [13].
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f0015: A classification of K-turn structures. K-turns can be divided into simple and complex. Examples are shown for each class. Simple K-turns are further divided into standard and non-standard, with the critical G·A pairs preserved or substituted respectively. The complex K-turns exhibit a greater departure from the standard K-turn, where the primary sequence does not map onto the 3D RNA structure. k-junctions can be considered as another branch of the complex K-turns. This scheme is taken from reference [13].

Mentions: The K-turns can be classified into different groups based on sequence and structure (Fig. 3). The simple K-turn is a double-stranded RNA with a bulge that is followed by the A·G pairs of the NC helix. The nucleotides are named according to a universal scheme [24]. This is used throughout this review, and explained in Fig. 1. The simple K-turns may be subdivided into standard and non-standard classes. The standard simple K-turn has G·A and A·G pairs at the 1b·1n and 2b·2n positions respectively, exemplified by H. marismortui Kt-7 or the human U4 snRNA K-turn. Non-standard simple K-turns have a substitution in one of the G·A pairs. In Kt-23 of the ribosomal small subunit, the 2n position has a frequency of U > C > G > A over different species; yet where it was studied it has been found that they form normal K-turn structures despite the variation from the standard sequence [25,26].


The K-turn motif in riboswitches and other RNA species.

Lilley DM - Biochim. Biophys. Acta (2014)

A classification of K-turn structures. K-turns can be divided into simple and complex. Examples are shown for each class. Simple K-turns are further divided into standard and non-standard, with the critical G·A pairs preserved or substituted respectively. The complex K-turns exhibit a greater departure from the standard K-turn, where the primary sequence does not map onto the 3D RNA structure. k-junctions can be considered as another branch of the complex K-turns. This scheme is taken from reference [13].
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Related In: Results  -  Collection

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f0015: A classification of K-turn structures. K-turns can be divided into simple and complex. Examples are shown for each class. Simple K-turns are further divided into standard and non-standard, with the critical G·A pairs preserved or substituted respectively. The complex K-turns exhibit a greater departure from the standard K-turn, where the primary sequence does not map onto the 3D RNA structure. k-junctions can be considered as another branch of the complex K-turns. This scheme is taken from reference [13].
Mentions: The K-turns can be classified into different groups based on sequence and structure (Fig. 3). The simple K-turn is a double-stranded RNA with a bulge that is followed by the A·G pairs of the NC helix. The nucleotides are named according to a universal scheme [24]. This is used throughout this review, and explained in Fig. 1. The simple K-turns may be subdivided into standard and non-standard classes. The standard simple K-turn has G·A and A·G pairs at the 1b·1n and 2b·2n positions respectively, exemplified by H. marismortui Kt-7 or the human U4 snRNA K-turn. Non-standard simple K-turns have a substitution in one of the G·A pairs. In Kt-23 of the ribosomal small subunit, the 2n position has a frequency of U > C > G > A over different species; yet where it was studied it has been found that they form normal K-turn structures despite the variation from the standard sequence [25,26].

Bottom Line: This generally functions to mediate tertiary interactions, and to serve as a specific protein binding site.K-turns or closely related structures are found in at least seven different riboswitch structures, where they function as key architectural elements that help generate the ligand binding pocket.This article is part of a Special Issue entitled: Riboswitches.

View Article: PubMed Central - PubMed

Affiliation: Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK. Electronic address: d.m.j.lilley@dundee.ac.uk.

No MeSH data available.


Related in: MedlinePlus