ArticleNucleic acids research2003
Thermodynamic calculations and statistical correlations for oligo-probes design.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Thermodynamic Determinants in Antibody-Free Nucleic Acid Lateral Flow Assays (AF-NALFA): Lessons from Molecular Detection ofBiomolecules · 2025Article
- Article
- Sequence characteristics define trade-offs between on-target and genome-wide off-target hybridization of oligoprobes.PloS one · 2018Article
- Optimization of signal-to-noise ratio for efficient microarray probe design.Bioinformatics (Oxford, England) · 2016Article
- Native characterization of nucleic acid motif thermodynamics via non-covalent catalysis.Nature communications · 2016Article
- A revised design for microarray experiments to account for experimental noise and uncertainty of probe response.PloS one · 2014Article
- Physico-chemical foundations underpinning microarray and next-generation sequencing experiments.Nucleic acids research · 2013Review
- Intra-platform comparison of 25-mer and 60-mer oligonucleotide Nimblegen DNA microarrays.BMC research notes · 2013Article
- Protein expression dynamics during postnatal mouse brain development.Journal of experimental neuroscience · 2013Article
- The signature of maternal rearing in the methylome in rhesus macaque prefrontal cortex and T cells.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2012Article
- Optimized models for design of efficient miR30-based shRNAs.Frontiers in genetics · 2012Article
- The impact of quantitative optimization of hybridization conditions on gene expression analysis.BMC bioinformatics · 2011Article
- Shielding effect of monovalent and divalent cations on solid-phase DNA hybridization: surface plasmon resonance biosensor study.Nucleic acids research · 2010Article
- Nonparametric methods for the analysis of single-color pathogen microarrays.BMC bioinformatics · 2010Article
- Evaluating oligonucleotide properties for DNA microarray probe design.Nucleic acids research · 2010Article
- Antisense DNA parameters derived from next-nearest-neighbor analysis of experimental data.BMC bioinformatics · 2010Article
- G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration.BMC bioinformatics · 2010Article
- Hybridization thermodynamics of NimbleGen microarrays.BMC bioinformatics · 2010Article
- Article
- A model of base-call resolution on broad-spectrum pathogen detection resequencing DNA microarrays.Nucleic acids research · 2008Article
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6 authors.
Funding
Abstract
Optimization of probe design for array-based experiments requires improved predictability of oligonucleotide hybridization behavior. Currently, designing oligonucleotides capable of interacting efficiently and specifically with the relevant target is not a routine procedure. Multiple examples demonstrate that oligonucleotides targeting different regions of the same RNA differ in their hybridization ability. The present work shows how thermodynamic evaluations of oligo-target duplex or oligo self-structure stabilities can facilitate probe design. Statistical analysis of large sets of hybridization data reveals that thermodynamic evaluation of oligonucleotide properties can be used to avoid poor RNA binders. Thermodynamic criteria for the selection of 20 and 21mers, which, with high probability, interact efficiently and specifically with their targets, are suggested. The design of longer oligonucleotides can also be facilitated by the same calculations of DeltaG(o) (T) values for oligo-target duplex or oligo self-structure stabilities and similar selection schemes.
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