Mismatch formation in solution and on DNA microarrays: how modified nucleosides can overcome shortcomings of imperfect hybridization caused by oligonucleotide composition and base pairing

DC FieldValueLanguage
dc.contributor.authorSeela, Frank
dc.contributor.authorBudow, Simone
dc.date.accessioned2021-12-23T16:05:35Z-
dc.date.available2021-12-23T16:05:35Z-
dc.date.issued2008
dc.identifier.issn1742206X
dc.identifier.urihttps://osnascholar.ub.uni-osnabrueck.de/handle/unios/7087-
dc.description.abstractThe DNA microarray technology is a well-established and widely used technology although it has several drawbacks. The accurate molecular recognition of the canonical nucleobases of probe and target is the basis for reliable results obtained from microarray hybridization experiments. However, the great. exibility of base pairs within the DNA molecule allows the formation of various secondary structures incorporating Watson-Crick base pairs as well as non-canonical base pair motifs, thus becoming a source of inaccuracy and inconsistence. The first part of this report provides an overview of unusual base pair motifs formed during molecular DNA interaction in solution highlighting selected secondary structures employing non-Watson-Crick base pairs. The same mispairing phenomena obtained in solution are expected to occur for immobilized probe molecules as well as for target oligonucleotides employed in microarray hybridization experiments the effect of base pairing and oligonucleotide composition on hybridization is considered. The incorporation of nucleoside derivatives as close shape mimics of the four canonical nucleosides into the probe and target oligonucleotides is discussed as a chemical tool to resolve unwanted mispairing. The second part focuses non-Watson-Crick base pairing during hybridization performed on microarrays. This is exemplified for the unusual stable dG.dA base pair.
dc.language.isoen
dc.publisherROYAL SOC CHEMISTRY
dc.relation.ispartofMOLECULAR BIOSYSTEMS
dc.subjectAROMATIC STACKING
dc.subjectB-DNA
dc.subjectBiochemistry & Molecular Biology
dc.subjectCENTER-DOT-A
dc.subjectCRYSTAL-STRUCTURE
dc.subjectDA-DT
dc.subjectDANGLING ENDS
dc.subjectG.A MISMATCH
dc.subjectNUCLEAR-MAGNETIC-RESONANCE
dc.subjectSTABILITY
dc.subjectTHERMODYNAMIC PARAMETERS
dc.titleMismatch formation in solution and on DNA microarrays: how modified nucleosides can overcome shortcomings of imperfect hybridization caused by oligonucleotide composition and base pairing
dc.typereview
dc.identifier.doi10.1039/b713259j
dc.identifier.isiISI:000253492200006
dc.description.volume4
dc.description.issue3
dc.description.startpage232
dc.description.endpage245
dc.identifier.eissn17422051
dc.publisher.placeTHOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND
dcterms.isPartOf.abbreviationMol. Biosyst.
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