| AVS 54th International Symposium | |
| Biomaterial Interfaces | Wednesday Sessions |
| Session BI-WeA |
| Session: | Nucleic Acid Sequencing and Technology |
| Presenter: | D.Y. Petrovykh, University of Maryland, College Park, and Naval Research Laboratory |
| Authors: | D.Y. Petrovykh, University of Maryland, College Park, and Naval Research Laboratory A. Opdahl, University of Wisconsin L.J. Whitman, Naval Research Laboratory |
| Correspondent: | Click to Email |
DNA brushes with unique properties can be prepared using a new immobilization method that is based on the intrinsic affinity of blocks of adenine nucleotides for gold.1 Block-oligonucleotides are single-stranded DNA (ssDNA) with sequences that follow, for example, a d(Ak-Tm-Nn) pattern: a block of k adenine nucleotides [d(Ak)], followed by a block of m thymine nucleotides [d(Tm)], and a short sequence of n (arbitrary) nucleotides [d(Nn)]. Brushes formed by the d(Ak-Tm-Nn) block-oligonucleotides are particularly interesting, because they attach to gold via the d(A) blocks and present the d(N) "probe" sequence for hybridization with complementary nucleotides. We are quantitatively characterizing these DNA brushes before, after, and during the hybridization experiments using a combination of x-ray photoelectron spectroscopy (XPS) and surface plasmon resonance (SPR) imaging. Characterizing these systems presents several analytical challenges. First, unambiguous deconvolution of XPS spectral features is not possible for these chemically non-uniform brushes. Second, the low surface density of the d(N) probe sequences, which is required to maintain high hybridization efficiency, results in low XPS intensities. Finally, DNA hybridization is carried out in an aqueous environment, so comprehensive analysis of these experiments requires establishing quantitative correlations between the in situ SPR imaging and ex situ XPS measurements. We addressed these challenges by taking advantage of the high degree of control over the composition and grafting density of ssDNA brushes immobilized via adenine blocks. The resulting sets of samples having systematically varied properties allowed us to observe and quantify by both XPS and SPR the effects of the surface density of ssDNA probes on the resulting hybridization efficiencies. Developing such quantitative methods that combine results of in situ and ex situ analysis is critical for extending well-developed surface analysis techniques to complex biological surfaces and interfaces.
1Opdahl, et al., Proc. Natl. Acad. Sci. USA 104, 9 (2007).