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J. Phys. Chem. B 2000, 104, 2500-2505
Adsorption of DNA Bases onto a Semiconductor Surface: Evidence for Surface-Mediated Promotion and Detection of Complementary Base Pair Formation Kathleen Meeker and Arthur B. Ellis* Department of Chemistry, UniVersity of WisconsinsMadison, Madison, Wisconsin 53706 ReceiVed: NoVember 18, 1999
The adsorption of DNA basessadenine (A), thymine (T), guanine (G), and cytosine (C)sand base pairs onto single-crystal n-CdSe substrates has been studied in several solvents, using the band gap photoluminescence (PL) of the semiconductor as a probe. In methanol solution, all four bases cause similar, reversible PL quenching, consistent with their acting as Lewis acids toward the surface. The PL changes can be well fit by a dead-layer model, indicating that adsorption increases the depletion width of the semiconductor by ∼200300 Å. In DMSO solution, there is no PL response to individual bases. However, the complementary A-T and G-C base pairs yield a PL response, providing evidence that the surface can promote base pair formation. The A-T and C-G responses in DMSO correspond to depletion width increases of ∼100 and 200 Å and persist to ∼45 and 75 °C, respectively. Competition experiments reveal a preference for C-G binding at elevated temperatures. In chloroform solution, the PL response of C-G base pairs can be distinguished from those of C and G individually, whereas A, T, and A-T are experimentally indistinguishable. Electronic and hydrogen-bonding effects that may contribute to the PL responses are discussed.
Introduction Although hydrogen bonding is widely recognized as contributing to the stability of complementary DNA base pairssadenine (A) with thymine (T), and cytosine (C) with guanine (G)sthese interactions have been found to vary substantially among solvents.1 The interaction of DNA bases with surfaces can, in principle, provide additional insight into base pair formation, as the adsorbent provides a binding platform that competes with the solution environment for solute. In this paper, we use three solvents with different hydrogen bonding capabilitiessmethanol, dimethyl sulfoxide (DMSO), and chloroformsto explore the binding of DNA bases and base pairs to an emissive semiconducting CdSe substrate. The semiconductor provides an in situ probe of surface binding. A hypothetical interaction of hydrogenbonded A-T and G-C base pairs with a CdSe surface, shown in Scheme 1, illustrates the potential for the surface to influence base pair formation. Several prior studies involving adsorption of DNA base pairs onto surfaces have been motivated by biosensing applications. For example, thiolated single strands of DNA have been bound to gold surfaces, providing a platform with specificity for the complementary strand.2-4 Porous silicon and nanocrystalline CdS substrates were used to assess nucleic acid conformations through adsorption effects on optical properties.5,6 The luminescence of Ru(phen)32+ has been coupled with a quartz-crystal microbalance to monitor immobilization of DNA strands on metal-coated semiconductor substrates.7 In previous studies, we have demonstrated that the photoluminescence (PL) of single-crystal n-CdSe can serve as a probe of the chemical ambient, both in the vapor phase and in solution.8,9 The mechanism for these PL responses is hypothesized to be the formation of weak charge-transfer complexes between adsorbates and surface atoms, leading to reversible increases or decreases in the electric field thickness in the nearsurface depletion region of the semiconductor. This region that
is on the order of the depletion width is considered to be nonemissive, a “dead layer”, because photogenerated electronhole pairs are swept apart by the electric field and are unable to recombine. Changes in the electric field thickness arise from a shifting of electron density into surface electronic states or out of these states, reflecting adsorbate Lewis acidity or basicity, respectively, and defining a “luminescent litmus test”: Typically, Lewis acids quench the PL intensity while Lewis bases enhance it. For weakly bound adsorbates, PL changes are readily reversible and can potentially be used for on-line analyte detection. In this paper, we demonstrate that PL from CdSe substrates can be reversibly modulated by adsorption of A, T, G, C, and their complementary base pairs. The PL response varies substantially across the solvents methanol, DMSO, and CHCl3 and is well fit by the aforementioned dead-layer model. For at least one set of experimental conditions, base pair formation appears to be promoted by adsorption onto the CdSe substrate. Electronic and hydrogen-bonding effects that may contribute to the PL responses are discussed. Experimental Section Materials. Single-crystal, vapor-grown c-plates of n-CdSe, having a resistivity of ∼2 Ω‚cm, were obtained from Cleveland Crystals, Inc. After undergoing mechanical polishing with 5-µm alumina and being rinsed with refluxing methanol and heptane, the samples were etched in 1:15 (v/v) Br2/MeOH for 30 s, revealing the shiny Cd-rich (0001) face, which was illuminated in these PL experiments. Adenine (99%), thymine (99%), cytosine (99%), and guanine (>99%; SigmaUltra grade) were obtained from Sigma and used as received. The derivatives 9-ethylguanine, 9-ethyladenine, 1-methyladenine, 6-(methylamino)purine (N-methyladenine), 1-methylcytosine, 7-methylguanine, 1-methylguanine, and 2-(dimethylamino)-6-hydroxypurine (N2,N2-dimethylguanine) (98%) were obtained from
10.1021/jp9941099 CCC: $19.00 © 2000 American Chemical Society Published on Web 02/23/2000
Adsorption of DNA Bases
J. Phys. Chem. B, Vol. 104, No. 11, 2000 2501
SCHEME 1: Hypothetical Side View of Watson-Crick Base Pair Interactions with the (0001) CdSe Surfacea
a
Structures are not drawn to scale; base pairs are approximately 10 Å wide, and the distance between two cadmium atoms on the surface is approximately 4.3 Å. The smaller circles represent cadmium atoms and the larger circles, selenium atoms.
Sigma and used as received. Solutions were prepared from methanol (EM Science), which was distilled over Mg/I2; from chloroform (Aldrich, 99.8%), which was distilled over P2O5; and from dimethyl sulfoxide (Aldrich, HPLC grade), which was dried over molecular sieves (4-Å) and otherwise used as received. Solution Preparation. The DNA bases have similar solubilities in methanol, with the exception of G, which has a lower solubility than the others in all three solvents discussed here. Typically, solutions were heated and stirred to solvate the analytes fully, and stock solutions containing G were filtered through glass wool after appearing clear to the eye, to ensure that no particulates remained; solution concentrations, as monitored by UV-visible spectroscopy, were consistent with those expected.10 Apparatus and Optical Measurements. The CdSe sample was mounted on a glass rod between two Teflon spacers in a glass cell that permitted various solutions to be introduced and removed without altering the optical alignment. PL measurements were made using either a Coherent Innova model 90C 5.0-W Ar+ laser (458, 514 nm) or a Melles-Griot HeNe laser (633 nm). Data were collected with an Oriel Instaspec IV CCD detector and processed by a PC. The red band-edge PL of n-CdSe was monitored at the band maximum of 720 nm with filtering of exciting wavelengths; under the low-resolution conditions employed (∼1 nm), there was no change in the PL spectral distribution upon adsorption of any of the analytes studied. Electronic absorption spectra of the molecules used as adsorbates, obtained with a Hewlett-Packard HP89530A spectrometer, reveal negligible absorption (absorbance of
