Effects of flanking G . C base pairs on internal Watson-Crick, G . U, and nonbonded base pairs within a short ribonucleic acid duplex

A series of pentaribonucleotides, ApGpXpGpU (where X identical to A, G, C, or U), was synthesized to investigate the effects of flanking G . C pairs on internal Watson-Crick, G . U, and nonbonded base pairs. Sequences ApGpApCpU (Tm = 26 degrees C) and ApGpCpCpU (Tm = 25 degrees C) were each found to...

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Bibliographic Details
Published in:Biochemistry (Easton) 1982-04, Vol.21 (9), p.2109-2117
Main Authors: Alkema, D, Hader, P A, Bell, R A, Neilson, T
Format: Article
Language:English
Subjects:
Base Composition
Base Sequence
Magnetic Resonance Spectroscopy
Nucleic Acid Conformation
Nucleic Acid Heteroduplexes
Oligoribonucleotides - chemical synthesis
RNA
Temperature
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Summary:A series of pentaribonucleotides, ApGpXpGpU (where X identical to A, G, C, or U), was synthesized to investigate the effects of flanking G . C pairs on internal Watson-Crick, G . U, and nonbonded base pairs. Sequences ApGpApCpU (Tm = 26 degrees C) and ApGpCpCpU (Tm = 25 degrees C) were each found to form a duplex with non-base-paired internal residues that stacked with the rest of the sequence but were not looped out. ApGpGpCpU also forms a duplex (Tm = 30 degrees C) but with dangling terminal nonbonded adenosines rather than internal nonbonded guanosines. ApGpUpCpU prefers a stacked single-strand conformation. In addition, contribution to duplex stability from an internal A . U or G . C base pair is enhanced by 6 degrees C when flanked by G . C base pairs as compared to A . U base pairs. G . C base pairs flanking an internal G . U base pair were found to be more tolerant to the altered conformation of a G . U pair and result in an increase to stability comparable with that found for an internal A . U base pair.
ISSN:0006-2960
DOI:10.1021/bi00538a020