Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides

• Published in: RNA (Cambridge) 2013-11, Vol.19 (11), p.1474-1482
• Main Authors: Hudson, Graham A, Bloomingdale, Richard J, Znosko, Brent M
• Format: Article
• Language: English
• Subjects: Adenosine - chemistry; Adenosine - genetics; Algorithms; Base Pairing - genetics; Base Sequence; Hydrogen Bonding; Models, Chemical; Nucleic Acid Conformation; Nucleic Acid Denaturation; Oligoribonucleotides - chemistry; Oligoribonucleotides - genetics; Pseudouridine - chemistry; Pseudouridine - genetics; RNA - chemistry; RNA - genetics; Thermodynamics
• ISSN: 1355-8382; 1469-9001
• DOI: 10.1261/rna.039610.113

Pseudouridine (Ψ) is the most common noncanonical nucleotide present in naturally occurring RNA and serves a variety of roles in the cell, typically appearing where structural stability is crucial to function. Ψ residues are isomerized from native uridine residues by a class of highly conserved enzymes known as pseudouridine synthases. In order to quantify the thermodynamic impact of pseudouridylation on U-A base pairs, 24 oligoribonucleotides, 16 internal and eight terminal Ψ-A oligoribonucleotides, were thermodynamically characterized via optical melting experiments. The thermodynamic parameters derived from two-state fits were used to generate linearly independent parameters for use in secondary structure prediction algorithms using the nearest-neighbor model. On average, internally pseudouridylated duplexes were 1.7 kcal/mol more stable than their U-A counterparts, and terminally pseudouridylated duplexes were 1.0 kcal/mol more stable than their U-A equivalents. Due to the fact that Ψ-A pairs maintain the same Watson-Crick hydrogen bonding capabilities as the parent U-A pair in A-form RNA, the difference in stability due to pseudouridylation was attributed to two possible sources: the novel hydrogen bonding capabilities of the newly relocated imino group as well as the novel stacking interactions afforded by the electronic configuration of the Ψ residue. The newly derived nearest-neighbor parameters for Ψ-A base pairs may be used in conjunction with other nearest-neighbor parameters for accurately predicting the most likely secondary structure of A-form RNA containing Ψ-A base pairs.