AVS 52nd International Symposium
    DNA Topical Conference Monday Sessions
       Session DN-MoP

Paper DN-MoP3
PNA Microarray Development and DNA Diagnosis with TOF-SIMS

Monday, October 31, 2005, 5:00 pm, Room Exhibit Hall C&D

Session: DNA Poster Session
Presenter: H.F. Arlinghaus, Westfälische Wilhelms-Universität Münster, Germany
Authors: H.F. Arlinghaus, Westfälische Wilhelms-Universität Münster, Germany
S. Hellweg, Westfälische Wilhelms-Universität Münster, Germany
T. Grehl, ION-TOF GmbH, Germany
E. Niehuis, ION-TOF GmbH, Germany
A. Jakob, Deutsches Krebsforschungszentrum Heidelberg, Germany
J. Hoheisel, Deutsches Krebsforschungszentrum Heidelberg, Germany
Correspondent: Click to Email
TOF-SIMS was used for the detailed examination of the immobilization process of PNA and its hybridization capability to unlabeled complementary DNA fragments. PNA sequences were immobilized onto SiO@sub 2@ and Au surfaces using different linking mechanisms. Unlabeled single-stranded DNA was hybridized to these biosensor chips containing both complementary and non-complementary immobilized PNA sequences. The hybridization of complementary DNA could readily be identified by detecting phosphate-containing molecules from the DNA backbone such as PO@sub 3@@super -@. The achieved discrimination between complementary and non-complementary sequences was very good. Further investigations were conducted regarding the influence of length and type of spacer molecules on the hybridization efficiency. The spacer molecule defines the distance between the PNA molecule and the biosensor chip surface. It was observed that a greater spacer length leads to higher hybridization efficiency. Using different primary ions, secondary ion yield behavior and fragmentation patterns were studied. This included monoatomic ions (Ar@super +@, Xe@super +@, Au@super +@, Bi@super +@) as well as polyatomic and cluster ions (SF@sub 5@@super +@, Au@sub x@@super +@, Bi@sub x@@super +@). It was found that using polyatomic and cluster primary ions resulted in a significantly increased yield of DNA-correlated fragments, resulting in higher signal intensities and better signal-to-noise ratios. It can be concluded that TOF-SIMS is undoubtedly a highly useful technique for identifying unlabeled hybridized DNA on PNA biosensor chips. It may provide a rapid method for DNA diagnostics and is suitable for studying the complexity of the immobilization and hybridization processes.