title: Evidence of impurities in thiolated single-stranded DNA oligomers and their effect on DNA self-assembly on gold.
abstract: The diversity of techniques used in the synthesis, treatment, and purification of the single-stranded DNA oligomers containing a thiol anchor group (SH-ssDNA) has led to a significant variation in the purity of commercially available SH-ssDNA. In this work, we use X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) to study how the impurities present in commercially synthesized SH-ssDNA oligomers affected the structure of the resulting DNA films on Au. XPS results indicate that two of the purchased SH-ssDNA oligomers contain excess carbon and sulfur. The molecular fragmentation patterns obtained with ToF-SIMS were used to determine the identity of several contaminants in the DNA films, including poly(dimethylsiloxane) (PDMS), lipid molecules, and sulfur-containing molecules. In particular, the ToF-SIMS results determined that the excess sulfur detected by XPS was due to the presence of dithiothreitol, a reductant often used to cleave disulfide precursors. Furthermore, we found that the SH-ssDNA self-assembly process is affected by the presence of these contaminants. When relatively pure SH-ssDNA is used to prepare the DNA films, the P, N, O, and C atomic percentages were observed by XPS to increase over a 24-h time period. In contrast, surfaces prepared using SH-ssDNA containing higher levels of contaminants did not follow this trend. XPS result indicates that, after the initial SH-ssDNA adsorption, the remaining material incorporated into these films was due to contamination.
authors.affiliation: National ESCA and Surface Analysis Center for Biomedical Problems, Center for Nanotechnology and Department of Bioengineering Engineering, Box 351750, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Chi-Ying
authors.initials: CY
authors.lastname: Lee
authors.forename: Heather E
authors.initials: HE
authors.lastname: Canavan
authors.forename: Lara J
authors.initials: LJ
authors.lastname: Gamble
authors.forename: David G
authors.initials: DG
authors.lastname: Castner
mesh_terms: D004247:DNA / Q000737:chemistry*; D006046:Gold / Q000737:chemistry*; D015394:Molecular Structure; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry* / Q000302:isolation & purification; D012680:Sensitivity and Specificity; D018629:Spectrometry, Mass, Secondary Ion / Q000379:methods; D013052:Spectrometry, X-Ray Emission / Q000379:methods; D013438:Sulfhydryl Compounds / Q000737:chemistry*
chemical_list: D009841:Oligonucleotides; D013438:Sulfhydryl Compounds; D006046:Gold; D004247:DNA