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A method for estimating the nearest neighbor base‐pair content of RNAs using CD and absorption spectroscopy
Author(s) -
Johnson Kenneth H.,
Gray Donald M.
Publication year - 1991
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360310403
Subject(s) - chemistry , k nearest neighbors algorithm , base (topology) , base pair , spectral line , absorption spectroscopy , analytical chemistry (journal) , absorption (acoustics) , nucleotide , rna , crystallography , chromatography , biochemistry , dna , physics , mathematics , optics , artificial intelligence , gene , mathematical analysis , computer science , astronomy
CD and absorption spectra are sensitive to the secondary structure of RNAs. By fitting the spectra contained in our basis set to the CD and absorption spectra of an RNA of known sequence, we could determine the fractions of base pairs, the fractions of each of the nearest neighbor base pairs, and the fractions of the single‐stranded nucleotides in that RNA. The basis set included 58 CD and 58 absorption spectra. The fitting was done with a guided selection routine. The estimated error was about 0.05 for predicting the fractions of the nearest neighbor base pairs, 0.06 for predicting the fractions of A · U, G · C, and G · U base pairs, and 0.04 for predicting the fractions of the single‐stranded nucleotides.