Base opening in RNA and DNA duplexes: Implication for RNA stability

Autor:	Yu Zong Chen, R. H. Griffey, V. Mohan
Rok vydání:	2000
Předmět:	Steric effects RNA Stability Oligoribonucleotides Base Sequence Chemistry Stereochemistry Guanine Nucleic Acid Heteroduplexes RNA Uracil DNA chemistry.chemical_compound Drug Stability Oligodeoxyribonucleotides Duplex (building) Nucleic Acid Conformation Thermodynamics Crystallization Cytosine
Zdroj:	Physical Review E. 61:5640-5645
ISSN:	1095-3787 1063-651X
DOI:	10.1103/physreve.61.5640
Popis:	The energetics of a low-energy single base opening in several RNA duplex crystal structures has been calculated and compared to DNA duplexes. Base opening in RNA appears to have an overall preference towards the major groove, similar to results previously reported for B-DNA. Movement of each of the adenine, uracil, and cytosine bases into the minor groove is blocked by a high-energy barrier due to severe close contact with neighboring bases. Guanine bases are able to open towards both grooves because of the unique orientation of the base that avoids steric clash along the opening pathway. RNA bases are found to have a substantially smaller major groove opening extent than that of their B-DNA counterparts. A comparison with base opening behavior of A-DNA duplexes suggests that this difference results from helix constraint associated with A-form backbone conformation. The reduced opening extent correlates with the RNA duplex stability and is consistent with observed slower imino proton exchange rates in RNA duplexes.
Databáze:	OpenAIRE
Externí odkaz:	https://explore.openaire.eu/search/publication?articleId=doi_dedup___::171c7633104f6b18259fe5c571c39f5e https://doi.org/10.1103/physreve.61.5640 Zobrazit plný text záznamu