ArticleNucleic acids research2006
Position-dependent effects of locked nucleic acid (LNA) on DNA sequencing and PCR primers.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
24 citing papers in PubMed, 68 citations in OpenAlex.
- An Optimized RT-qPCR Protocol for Comprehensive Analysis of microRNAs and mRNAs inNon-coding RNA · 2026Article
- Advances in antisense oligonucleotide treatment for cancer.Japanese journal of clinical oncology · 2026Review
- Locked nucleic acid (LNA) based PCR approach for the diagnosis and screening of spinal muscular atrophy.The Indian journal of medical research · 2026Article
- Recombinase polymerase amplification for single nucleotide polymorphism-specific detection of βAnalytical biochemistry · 2025Article
- Parvalbumin Gene: A Valuable Marker for Pike Authentication and Allergen Risk Assessment.Journal of agricultural and food chemistry · 2024Article
- VESPA: an optimized protocol for accurate metabarcoding-based characterization of vertebrate eukaryotic endosymbiont and parasite assemblages.Nature communications · 2024Article
- LNA blockers for improved amplification selectivity.Scientific reports · 2023Article
- Vivid COVID-19 LAMP is an ultrasensitive, quadruplexed test using LNA-modified primers and a zinc ion and 5-Br-PAPS colorimetric detection system.Communications biology · 2023Article
- Current and Emerging Techniques for Diagnosis and MRD Detection in AML: A Comprehensive Narrative Review.Cancers · 2023Review
- Phosphate-Methylated Oligonucleotides as a Novel Primer for PCR and RT-PCR.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Surveillance of SARS-CoV-2 lineage B.1.1.7 in Slovakia using a novel, multiplexed RT-qPCR assay.Scientific reports · 2021Article
- Recent Advances in Oligonucleotide Therapeutics in Oncology.International journal of molecular sciences · 2021Review
- PANDAA intentionally violates conventional qPCR design to enable durable, mismatch-agnostic detection of highly polymorphic pathogens.Communications biology · 2021Article
- Improved Species-Level Clinical Identification of Enterobacteriaceae through Broad-RangeJournal of clinical microbiology · 2019Article
- Bridged Nucleic Acids Reloaded.Molecules (Basel, Switzerland) · 2019Review
- Point-of-Need DNA Testing for Detection of Foodborne Pathogenic Bacteria.Sensors (Basel, Switzerland) · 2019Review
- A highly sensitive 1-tube nested real-time RT-PCR assay using LNA-modified primers for detection of respiratory syncytial virus.Diagnostic microbiology and infectious disease · 2019Article
- LNA-modified isothermal oligonucleotide microarray for differentiating bacilli of similar origin.Journal of biosciences · 2014Article
- Application of Locked Nucleic Acid (LNA) oligonucleotide-PCR clamping technique to selectively PCR amplify the SSU rRNA genes of bacteria in investigating the plant-associated community structures.Microbes and environments · 2014Article
- An immature retroviral RNA genome resembles a kinetically trapped intermediate state.Journal of virology · 2014Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Genomes are becoming heavily annotated with important features. Analysis of these features often employs oligonucleotides that hybridize at defined locations. When the defined location lies in a poor sequence context, traditional design strategies may fail. Locked Nucleic Acid (LNA) can enhance oligonucleotide affinity and specificity. Though LNA has been used in many applications, formal design rules are still being defined. To further this effort we have investigated the effect of LNA on the performance of sequencing and PCR primers in AT-rich regions, where short primers yield poor sequencing reads or PCR yields. LNA was used in three positional patterns: near the 5' end (LNA-5'), near the 3' end (LNA-3') and distributed throughout (LNA-Even). Quantitative measures of sequencing read length (Phred Q30 count) and real-time PCR signal (cycle threshold, C(T)) were characterized using two-way ANOVA. LNA-5' increased the average Phred Q30 score by 60% and it was never observed to decrease performance. LNA-5' generated cycle thresholds in quantitative PCR that were comparable to high-yielding conventional primers. In contrast, LNA-3' and LNA-Even did not improve read lengths or C(T). ANOVA demonstrated the statistical significance of these results and identified significant interaction between the positional design rule and primer sequence.
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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.