ArticleNucleic acids research2001
Parallel multiplex thermodynamic analysis of coaxial base stacking in DNA duplexes by oligodeoxyribonucleotide microchips.
Article in Nucleic acids research, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 72 citations in OpenAlex.
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- Leveraging Steric Moieties for Kinetic Control of DNA Strand Displacement Reactions.Journal of the American Chemical Society · 2023Article
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- BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE.Biomaterials science · 2014Article
- On the biophysics and kinetics of toehold-mediated DNA strand displacement.Nucleic acids research · 2013Article
- End-to-end attraction of duplex DNA.Nucleic acids research · 2012Article
- Label-free high-throughput microRNA expression profiling from total RNA.Nucleic acids research · 2011Article
- Tailoring DNA structure to increase target hybridization kinetics on surfaces.Journal of the American Chemical Society · 2010Article
- Base-stacking and base-pairing contributions into thermal stability of the DNA double helix.Nucleic acids research · 2006Article
- Evaluation of gel-pad oligonucleotide microarray technology by using artificial neural networks.Applied and environmental microbiology · 2005Article
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- Low density DNA microarray for detection of most frequent TP53 missense point mutations.BMC biotechnology · 2005Article
- DNA analysis with multiplex microarray-enhanced PCR.Nucleic acids research · 2005Article
- Dissociation analysis in polymerase chain reaction and 1X SSC buffer as a prerequisite for selection of 13mer microarray probe sets with uniform hybridization behavior.Molecular biotechnology · 2005Article
- DNA microarrays with stem-loop DNA probes: preparation and applications.Nucleic acids research · 2001Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Parallel thermodynamic analysis of the coaxial stacking effect of two bases localized in one strand of DNA duplexes has been performed. Oligonucleotides were immobilized in an array of three-dimensional polyacrylamide gel pads of microchips (MAGIChips'). The stacking effect was studied for all combinations of two bases and assessed by measuring the increase in melting temperature and in the free energy of duplexes formed by 5mers stacked to microchip-immobilized 10mers. For any given interface, the effect was studied for perfectly paired bases, as well as terminal mismatches, single base overlaps, single and double gaps, and modified terminal bases. Thermodynamic parameters of contiguous stacking determined by using microchips closely correlated with data obtained in solution. The extension of immobilized oligonucleotides with 5,6-dihydroxyuridine, a urea derivative of deoxyribose, or by phosphate, decreased the stacking effect moderately, while extension with FITC or Texas Red virtually eliminated stacking. The extension of the immobilized oligonucleotides with either acridine or 5-nitroindole increased stacking to mispaired bases and in some GC-rich interfaces. The measurements of stacking parameters were performed in different melting buffers. Although melting temperatures of AT- and GC-rich oligonucleotides in 5 M tetramethylammonium chloride were equalized, the energy of stacking interaction was significantly diminished.
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