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Structure, dynamics, and thermodynamics of mismatched DNA oligonucleotide duplexes d(CCCAGGG)_2 and d(CCCTGGG)_2

Arnold, Frances H. and Wolk, Steven and Cruz, Phillip and Tinoco, Ignacio, Jr. (1987) Structure, dynamics, and thermodynamics of mismatched DNA oligonucleotide duplexes d(CCCAGGG)_2 and d(CCCTGGG)_2. Biochemistry, 26 (13). pp. 4068-4075. ISSN 0006-2960. https://resolver.caltech.edu/CaltechAUTHORS:20180822-111107897

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Abstract

The structures and hydrogen exchange properties of the mismatched DNA oligonucleotide duplexes d(CCCAGGG)_2 and d(CCCTGGG)_2 have been studied by high-resolution nuclear magnetic resonance. Both the adenine-adenine and thymine-thymine mismatches are intercalated in the duplexes. The structures of these self-complementary duplexes are symmetric, with the two strands in equivalent positions. The evidence indicates that these mismatches are not stably hydrogen bonded. The mismatched bases in both duplexes are in the anti conformation. The mismatched thymine nucleotide in d(CCCTGGG)_2 is intercalated in the duplex with very little distortion of the bases or sugar-phosphate backbone. In contrast, the bases of the adenine-adenine mismatch in d(CCCAGGG)_2 must tilt and push apart to reduce the overlap of the amino groups. The thermodynamic data show that the mismatch is less destabilizing than the mismatch when flanked by CG base pairs in this sequence, in contrast to their approximately equal stabilities when flanked by base pairs in the sequence d(CAAAXAAAG-CTTTYTTTG) where X and Y = A, C, G, and T [Aboul-ela, F., Koh, D., & Tinoco, I., Jr. (1985) Nucleic Acids Res. 13, 4811], Although the mechanism cannot be determined conclusively from the limited data obtained, exchange of the imino protons with solvent in these destabilized heteroduplexes appears to occur by a cooperative mechanism in which half the helix dissociates.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1021/bi00387a049DOIArticle
ORCID:
AuthorORCID
Arnold, Frances H.0000-0002-4027-364X
Alternate Title:Structure, dynamics, and thermodynamics of mismatched DNA oligonucleotide duplexes d(CCCAGGG)2 and d(CCCTGGG)2
Additional Information:© 1987 American Chemical Society. Received October 23, 1986; Revised Manuscript Received February 20, 1987. This work was supported by National Institutes of Health Grant GM 10840 and by the U.S. Department of Energy Office of Energy Research, under Contract AT03-82-ER60090.
Funders:
Funding AgencyGrant Number
NIHGM 10840
Department of Energy (DOE)AT03-82-ER60090
Issue or Number:13
Record Number:CaltechAUTHORS:20180822-111107897
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20180822-111107897
Official Citation:Structure, dynamics, and thermodynamics of mismatched DNA oligonucleotide duplexes d(CCCAGGG)2 and d(CCCTGGG)2 Frances H. Arnold, Steven Wolk, Phillip Cruz, and Ignacio Tinoco, Jr. Biochemistry 1987 26 (13), 4068-4075 DOI: 10.1021/bi00387a049
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:89032
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:22 Aug 2018 20:35
Last Modified:02 Nov 2019 17:16

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