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Independent control of grafting density and conformation of single-stranded DNA brushes

Opdahl, Aric, Petrovykh, Dmitri Y., Kimura-Suda, Hiromi, Tarlov, Michael J., Whitman, Lloyd J.
Proceedings of the National Academy of Sciences of the United States of America 2007 v.104 no.1 pp. 9-14
Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, adenine, adenine nucleotides, biotechnology, gold, nanotechnology, nucleic acid hybridization, quantitative analysis, single-stranded DNA, thiols, thymine
We describe self-assembly of ssDNA brushes that exploits the intrinsic affinity of adenine nucleotides (dA) for gold surfaces. The grafting density and conformation of these brushes is deterministically controlled by the length of the anchoring dA sequences, even in the presence of thymine nucleotides (dT). We produce and characterize brushes of model block-oligonucleotides, d(Tm-An), with systematically varied lengths m and n of the thymine and adenine blocks [denoted d(Tm) and d(An), respectively]. The hairpin conformation, dominant for self-complementary d(Tm-An) oligos in solution, is disrupted by the high preferential affinity of dA for gold surfaces. As a result, the d(Tm-An) oligos adsorb as a brush of d(T) strands immobilized via the d(A) blocks. Quantitative analysis by FTIR spectroscopy and x-ray photoelectron spectroscopy (XPS) reveals a unique feature of DNA immobilization via d(A) blocks: The surface density of dA nucleotides is close to saturation and is nearly independent of d(A) block length. Accordingly, the lateral spacing (grafting density) of the d(T) blocks is determined by the length of the d(A) blocks. The d(T) blocks extend away from the surface in a brush-like conformation at a lateral spacing 2-3 times larger (a grafting density 5-10 times lower) than in analogous films immobilized via standard thiol linkers. This combination of brush-like conformation and low saturation grafting density is expected to increase the efficiency of DNA hybridization at surfaces. Therefore, immobilization via d(A) blocks offers a method of producing DNA brushes with controlled properties for applications in biotechnology and nanotechnology.