Please use this identifier to cite or link to this item: https://scholarbank.nus.edu.sg/handle/10635/104738
Title: Base opening in RNA and DNA duplexes: Implication for RNA stability
Authors: Chen, Y.Z. 
Mohan, V.
Griffey, R.H.
Issue Date: May-2000
Citation: Chen, Y.Z.,Mohan, V.,Griffey, R.H. (2000-05). Base opening in RNA and DNA duplexes: Implication for RNA stability. Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics 61 (5 B) : 5640-5645. ScholarBank@NUS Repository.
Abstract: 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.
Source Title: Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics
URI: http://scholarbank.nus.edu.sg/handle/10635/104738
ISSN: 1063651X
Appears in Collections:Staff Publications

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