Mass spectrometric characterization of DNA microarrays as a function of primary ion species

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• 作者：S. Hellweg ; A. Jacob ; J.D. Hoheisel ; T. Grehl and H.F. Arlinghaus
• 刊名：Applied Surface Science
• 出版年：2006
• 出版时间：30 July 2006
• 年：2006
• 卷：252
• 期：19
• 页码：6742-6745
• 全文大小：324 K

文摘

Recent studies have shown TOF-SIMS to be an appropriate method for the detailed examination of the immobilization process of PNA and its ability to hybridize to unlabeled complementary DNA fragments. Unlabeled single-stranded DNA was hybridized to Si wafer 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. An unambiguous discrimination was achieved between complementary and non-complementary sequences.

In order to optimize detection parameters, different primary ions were applied, including monoatomic ions (Bi⁺) as well as cluster ions (Bi₂⁺, Bi₃⁺, Bi₄⁺, Bi₃⁺⁺, Bi₅⁺⁺), and secondary ion yield behavior and formation efficiencies were studied. It was found that cluster primary ions resulted in a significantly increased yield of DNA-correlated fragments, enabling higher signal intensities and better secondary ion efficiencies.

TOF-SIMS is undoubtedly a highly useful technique for identifying hybridized DNA on PNA biosensor chips. It is suitable for studying the complexity of the immobilization and hybridization processes and may provide a rapid method for DNA diagnostics. With the absence of the labeling procedure and the simultaneous increase of the phosphate signal as a result of increasing DNA sequence length, this technique comes to be especially useful for the direct analysis of genomic DNA.