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Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis.
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Genome evolution in yeasts
TLDR
Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.
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Single Processing Center Models for Human Dicer and Bacterial RNase III
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Geometric nomenclature and classification of RNA base pairs.
TLDR
This work proposes a classification based on the observation that the planar edge-to-edge, hydrogen-bonding interactions between RNA bases involve one of three distinct edges: the Watson-Crick edge, the Hoogsteen edge, and the Sugar edge, which facilitates the recognition of recurrent three-dimensional motifs from comparison of homologous sequences.
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The non-Watson-Crick base pairs and their associated isostericity matrices.
TLDR
This paper presents the 4 x 4 'isostericity matrices' summarizing the geometric relationships between the 16 pairwise combinations of the four standard bases, A, C, G and U, and helps identify isosteric pairs that co-vary or interchange in sequences of homologous molecules while maintaining conserved three-dimensional motifs.
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Exact method for the calculation of pseudorotation parameters P, τm and their errors. A comparison of the Altona–Sundaralingam and Cremer–Pople treatment of puckering of five-membered rings
A comparison of the two methods available for describing the puckering of five-membered rings - the Altona-Sundaralingam (A-S) [Altona & Sundaralingam (1972). J. Am. Chem. Soc. 94, 8205-8212]…
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Tools for the automatic identification and classification of RNA base pairs
Three programs have been developed to aid in the classification and visualization of RNA structure. BPViewer provides a web interface for displaying three-dimensional (3D) coordinates of individual…
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Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity
TLDR
It is demonstrated that natural HHRzs require the presence of additional nonconserved sequence elements outside of the conserved catalytic core to enable intracellular activity and may be stabilized by tertiary interactions that cleave efficiently at physiological Mg2+ concentrations and are functional in vivo.
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A new understanding of the decoding principle on the ribosome
TLDR
It is shown that the 30S subunit undergoes an identical domain closure upon binding of either cognate or near-cognate tRNA, which forms a decoding centre that constrains the mRNA in such a way that the first two nucleotides of the A codon are limited to form Watson–Crick base pairs.
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A standard reference frame for the description of nucleic acid base-pair geometry.
TLDR
A common point of reference is needed to describe the three-dimensional arrangements of bases and base-pairs in nucleic acid structures and to pinpoint unique conformational features in individual structures.
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