ArticleBMC bioinformatics2008
Position dependent mismatch discrimination on DNA microarrays - experiments and model.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed.
- Constant Temperature Electrochemical Biosensor for SNP Detection in Human Genomic DNA Based on DNA Melting Analysis.ACS sensors · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Transient states during the annealing of mismatched and bulged oligonucleotides.Nucleic acids research · 2024Article
- Molecular insight into how the position of an abasic site modifies DNA duplex stability and dynamics.Biophysical journal · 2024Article
- Low-Cost Platform for Multiplexed Electrochemical Melting Curve Analysis.ACS measurement science au · 2022Article
- Hamming Distance as a Concept in DNA Molecular Recognition.ACS omega · 2017Article
- Information Limited Oligonucleotide Amplification Assay for Affinity-Based, Parallel Detection Studies.PloS one · 2016Article
- Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays.PloS one · 2016Article
- Evaluation of a low-density hydrogel microarray technique for mycobacterial species identification.Journal of clinical microbiology · 2015Article
- Detection of genetic variations in coagulopathy-related genes using ramified rolling circle amplification.BioMed research international · 2014Article
- Resolving the polymorphism-in-probe problem is critical for correct interpretation of expression QTL studies.Nucleic acids research · 2013Article
- Physico-chemical foundations underpinning microarray and next-generation sequencing experiments.Nucleic acids research · 2013Review
- The illusion of specific capture: surface and solution studies of suboptimal oligonucleotide hybridization.BMC research notes · 2013Article
- Article
- Effect of LNA- and OMeN-modified oligonucleotide probes on the stability and discrimination of mismatched base pairs of duplexes.Journal of biosciences · 2012Article
- Stability of double-stranded oligonucleotide DNA with a bulged loop: a microarray study.BMC biophysics · 2011Article
- Fourteen-genome comparison identifies DNA markers for severe-disease-associated strains of Clostridium difficile.Journal of clinical microbiology · 2011Article
- Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes.BMC biotechnology · 2011Article
- Hybridization properties of long nucleic acid probes for detection of variable target sequences, and development of a hybridization prediction algorithm.Nucleic acids research · 2010Article
- Evaluating the performance of oligonucleotide microarrays for bacterial strains with increasing genetic divergence from the reference strain.Applied and environmental microbiology · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe propensity of oligonucleotide strands to form stable duplexes with complementary sequences is fundamental to a variety of biological and biotechnological processes as various as microRNA signalling, microarray hybridization and PCR. Yet our understanding of oligonucleotide hybridization, in particular in presence of surfaces, is rather limited. Here we use oligonucleotide microarrays made in-house by optically controlled DNA synthesis to produce probe sets comprising all possible single base mismatches and base bulges for each of 20 sequence motifs under study.
resultsWe observe that mismatch discrimination is mostly determined by the defect position (relative to the duplex ends) as well as by the sequence context. We investigate the thermodynamics of the oligonucleotide duplexes on the basis of double-ended molecular zipper. Theoretical predictions of defect positional influence as well as long range sequence influence agree well with the experimental results.
conclusionMolecular zipping at thermodynamic equilibrium explains the binding affinity of mismatched DNA duplexes on microarrays well. The position dependent nearest neighbor model (PDNN) can be inferred from it. Quantitative understanding of microarray experiments from first principles is in reach.
Indexed as
Identifiers
What OpenQuestion holds
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.