Journal article
Stability and Mismatch Discrimination of Locked Nucleic Acid-DNA Duplexes
Biochemistry (Easton), Vol.50(43), pp.9352-9367
11/01/2011
DOI: 10.1021/bi200904e
PMCID: PMC3201676
PMID: 21928795
Abstract
Locked nucleic acids (LNA; symbols of bases, +A, +C, +G, and +T) are introduced into chemically synthesized oligonucleotides to increase duplex stability and specificity. To understand these effects, we have determined thermodynamic parameters of consecutive LNA nucleotides. We present guidelines for the design of LNA oligonucleotides and introduce free online software that predicts the stability of any LNA duplex oligomer. Thermodynamic analysis shows that the single strand-duplex transition is characterized by a favorable enthalpic change and by an unfavorable loss of entropy. A single LNA modification confines the local conformation of nucleotides, causing a smaller, less unfavorable entropic loss when the single strand is restricted to the rigid duplex structure. Additional LNAs adjacent to the initial modification appear to enhance stacking and H-bonding interactions because they increase the enthalpic contributions to duplex stabilization. New nearest-neighbor parameters correctly forecast the positive and negative effects of LNAs on mismatch discrimination. Specificity is enhanced in a majority of sequences and is dependent on mismatch type and adjacent base pairs; the largest discriminatory boost occurs for the central +C.C mismatch within the +T+C+C sequence and the +A.G mismatch within the +T+A+G sequence. LNAs do not affect specificity in some sequences and even impair it for many +G.T and +C.A. mismatches. The level of mismatch discrimination decreases the most for the central +G.T mismatch within the +G+G+C sequence and the +C.A mismatch within the +G+C+G sequence. We hypothesize that these discrimination changes are not unique features of LNAs but originate from the shift of the duplex conformation from B-form to A-form.
Details
- Title: Subtitle
- Stability and Mismatch Discrimination of Locked Nucleic Acid-DNA Duplexes
- Creators
- Richard Owczarzy - Integrated DNA TechnologiesYong You - Integrated DNA TechnologiesChristopher L. Groth - Integrated DNA TechnologiesAndrey V. Tataurov - Integrated DNA Technologies
- Resource Type
- Journal article
- Publication Details
- Biochemistry (Easton), Vol.50(43), pp.9352-9367
- DOI
- 10.1021/bi200904e
- PMID
- 21928795
- PMCID
- PMC3201676
- NLM abbreviation
- Biochemistry
- ISSN
- 0006-2960
- eISSN
- 1520-4995
- Publisher
- Amer Chemical Soc
- Number of pages
- 16
- Grant note
- R43GM081959 / National Institute of General Medical Sciences; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of General Medical Sciences (NIGMS)
- Language
- English
- Date published
- 11/01/2011
- Academic Unit
- Neurology
- Record Identifier
- 9984303015902771
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