AVS 51st International Symposium
    Biomaterial Interfaces Monday Sessions
       Session BI-MoP

Paper BI-MoP20
Analysis of Contaminants in Commercial Thiolated Single-stranded DNA Oligomers by XPS and ToF-SIMS

Monday, November 15, 2004, 5:00 pm, Room Exhibit Hall B

Session: Poster Session
Presenter: C.-Y. Lee, University of Washington
Authors: C.-Y. Lee, University of Washington
L.J. Gamble, University of Washington
D.G. Castner, University of Washington
Correspondent: Click to Email
Commercially produced thiolated single-stranded DNA (SH-DNA) molecules are used in a variety of biotechnology applications including biosensors and DNA microarrays. The diversity of techniques used by different vendors in the synthesis and treatment lead to a significant variation in the quality of SH-DNA. In this work, we used x-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) to perform a comparative study of the relative purity of commercially-available SH-DNA from several vendors. We find that thiol-terminated 16-base pair oligomers from two of the vendors, which were self-assembled as thin layers onto gold surfaces, contain excess carbon and sulfur. By using ToF-SIMS, several contaminants including poly(dimethylsiloxane) (PDMS), lipid molecules, and sulfur-containing molecules were identified by their molecular fragments. Preliminary ToF-SIMS data indicates that the excess sulfur arises from the reductant (dithiothreitol) used to purify the SH-DNA by some of the vendors. Time dependent studies of purified versus contaminated SH-DNA were performed to determine the effect of contamination on DNA surface assembly over time. XPS results of purified SH-DNA show increased P, N, O and C atomic percentages over a 24-hour time period, confirming increasing DNA surface coverage on the gold. In contrast, XPS results of contaminated SH-DNA show that C and O atomic percentages increased over time, but no increase was observed in the P and N. This indicates that, after the initial SH-DNA adsorption during the first five minutes, the excess material adsorbed for the rest of the 24 hours was due to contamination.