ArticleBiochemistry2011
Stability and mismatch discrimination of locked nucleic acid-DNA duplexes.
Article in Biochemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed, 163 citations in OpenAlex.
- Alternative probe chemistries for single-molecule analysis of long noncoding RNA.The Journal of biological chemistry · 2026Article
- Review
- Alternative probe chemistries for single-molecule analysis of long non-coding RNA.bioRxiv : the preprint server for biology · 2026Article
- Locked nucleic acid probes enable enzyme-free photoelectrochemical detection of double-stranded DNA cancer biomarkers.Mikrochimica acta · 2026Article
- Review
- Designing nucleic acid-based therapeutics for cancer treatment: Updates on the state of the art.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Review
- Position-Dependent Stabilization of DNA/RNA Duplexes by Site-Specific Incorporation of LNA Nucleosides.Journal of nucleic acids · 2026Article
- Antisense oligonucleotide-based switches for conditional translation of synthetic mRNA.Molecular therapy. Nucleic acids · 2025Article
- Recombinase polymerase amplification for single nucleotide polymorphism-specific detection of βAnalytical biochemistry · 2025Article
- Mismatch-Assisted Toehold Exchange Cascades for Magnetic Nanoparticle-based Nucleic Acid Diagnostics.JACS Au · 2025Article
- Topological Switch-OFF and β-Galactosidase-Triggered Switch-ON of Cyclic Antisense Oligonucleotides via CuAAC for Controlled RNA Cleavage.Bioconjugate chemistry · 2025Article
- Compartmentalized Suspension Array for the Isothermal, Digital, and Multiplex Detection of microRNAs.Journal of the American Chemical Society · 2025Article
- Multiplexed, universal probe-based rare variant detection with USE-PCR.Scientific reports · 2025Article
- DNA-Guided Self-Assembly of Carbon Nanotubes and Quantum Dots.ACS applied optical materials · 2025Article
- Efficiency of genome editing using modified single-stranded oligodeoxyribonucleotides in human cells.Scientific reports · 2025Article
- Thermodynamic control of mismatch discrimination for extensive splicing regulation of PKM pre-mRNA.RNA (New York, N.Y.) · 2025Article
- Advances in nucleic acid probe-based detection of gene point mutations: a review.Frontiers in chemistry · 2025Review
- Temporal evolution of insecticide resistance and bionomics in Anopheles funestus, a key malaria vector in Uganda.Scientific reports · 2024Article
- Sequence-Specific Free Energy Changes in DNA/RNA Induced by a Single LNA-T Modification in Antisense Oligonucleotides.International journal of molecular sciences · 2024Article
- Blocking uncertain mispriming errors of PCR.Biophysical journal · 2024Article
16 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.