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Target concentration dependence of DNA melting temperature on oligonucleotide microarrays
Biotechnology progress, 2012-03, Vol.28 (2), p.556-566
Ozel, Ayse Bilge
Srivannavit, Onnop
Rouillard, Jean-Marie
Gulari, Erdogan
2012
Details
Autor(en) / Beteiligte
Ozel, Ayse Bilge
Srivannavit, Onnop
Rouillard, Jean-Marie
Gulari, Erdogan
Titel
Target concentration dependence of DNA melting temperature on oligonucleotide microarrays
Ist Teil von
Biotechnology progress, 2012-03, Vol.28 (2), p.556-566
Ort / Verlag
Hoboken: Wiley Subscription Services, Inc., A Wiley Company
Erscheinungsjahr
2012
Link zum Volltext
Quelle
MEDLINE
Beschreibungen/Notizen
The design of microarrays is currently based on studies focusing on DNA hybridization reaction in bulk solution. However, the presence of a surface to which the probe strand is attached can make the solution‐based approximations invalid, resulting in sub‐optimum hybridization conditions. To determine the effect of surfaces on DNA duplex formation, the authors studied the dependence of DNA melting temperature (Tm) on target concentration. An automated system was developed to capture the melting profiles of a 25‐mer perfect‐match probe–target pair initially hybridized at 23°C. Target concentrations ranged from 0.0165 to 15 nM with different probe amounts (0.03–0.82 pmol on a surface area of 1018 Å2), a constant probe density (5 × 1012 molecules/cm2) and spacer length (15 dT). The authors found that Tm for duplexes anchored to a surface is lower than in‐solution, and this difference increases with increasing target concentration. In a representative set, a target concentration increase from 0.5 to 15 nM with 0.82 pmol of probe on the surface resulted in a Tm decrease of 6°C when compared with a 4°C increase in solution. At very low target concentrations, a multi‐melting process was observed in low temperature domains of the curves. This was attributed to the presence of truncated or mismatch probes. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012
Sprache
Englisch
Identifikatoren
ISSN: 8756-7938
eISSN: 1520-6033
DOI: 10.1002/btpr.1505
Titel-ID: cdi_proquest_miscellaneous_993912096
Format
–
Schlagworte
Biological and medical sciences
,
Biotechnology
,
DNA hybridization thermodynamics
,
DNA melting temperature
,
Fundamental and applied biological sciences. Psychology
,
Nucleic Acid Denaturation
,
Nucleic Acid Hybridization
,
Oligonucleotide Array Sequence Analysis - instrumentation
,
oligonucleotide microarray
,
Oligonucleotides - chemistry
,
Oligonucleotides - genetics
,
target concentration
,
Temperature
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