Thus, reliably predicting G·U pairing would be advantageous for deciphering RNA function from new transcriptome data.
However, while Watson−Crick nucleotide pairing can be predicted reasonably accurately at the sequence level,
predictions of pairing between guanines and uracils (G·U pairs) is much more difficult. Tandem G·U pairs inside a helix
can be thermodynamically destabilizing, with the notable exception of the sequence 5′-GGUC-3′/3′-CUGG-5′.11−14 In
contrast, all consecutive terminal G·U pairs are stabilizing (Table 1), and the amount of stability depends more on
sequence and context than other consecutive terminal mismatches in RNA duplexes.15 Thus, the same idiosyncratic
physical properties and non-nearest neighbor effects of G·U pairs that facilitate molecular recognition and specificity in
biological function frustrate RNA structure prediction.
Thus, reliably predicting G·U pairing would be advantageous for deciphering RNA function from new transcriptome data.However, while Watson−Crick nucleotide pairing can be predicted reasonably accurately at the sequence level,predictions of pairing between guanines and uracils (G·U pairs) is much more difficult. Tandem G·U pairs inside a helixcan be thermodynamically destabilizing, with the notable exception of the sequence 5′-GGUC-3′/3′-CUGG-5′.11−14 Incontrast, all consecutive terminal G·U pairs are stabilizing (Table 1), and the amount of stability depends more onsequence and context than other consecutive terminal mismatches in RNA duplexes.15 Thus, the same idiosyncraticphysical properties and non-nearest neighbor effects of G·U pairs that facilitate molecular recognition and specificity inbiological function frustrate RNA structure prediction.
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