Nucleobase orientation and ordering in films of single-stranded DNA on gold |
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Authors: | Petrovykh Dmitri Y Pérez-Dieste V Opdahl Aric Kimura-Suda Hiromi Sullivan J M Tarlov Michael J Himpsel F J Whitman Lloyd J |
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Affiliation: | Physics Department, University of Maryland, College Park, MD 20742, USA. dmitri.petrovykh@nrl.navy.mil |
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Abstract: | We demonstrate how the orientation and ordering of DNA bases in ultrahigh vacuum (UHV) and ambient environments can be determined using complementary spectroscopic methods. Near-edge X-ray absorption fine structure (NEXAFS) with fluorescence detection, X-ray photoelectron (XPS), and Fourier transform infrared (FTIR) spectroscopies are used to quantify the coverage, chemical composition, orientation, and ordering of thymine bases in model self-assembled monolayers of thymine homo-oligonucleotides [oligo(dT)] on gold. We find that, in monolayers of thiol-modified oligo(dT), thymine bases tend to orient parallel to the Au substrate, and this preferential orientation is significantly more pronounced in monolayers of thiolated 5-mers compared to 25-mers. We interpret this preferential orientation as a signature of significant correlations (local ordering) between individual nuleobases, which offers a way to quantify and compare nucleobase interactions in films under both ambient and UHV conditions. |
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