skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Mixed DNA/Oligo(ethylene glycol) Functionalized Gold Surface Improve DNA Hybridization in Complex Media

Abstract

Reliable, direct 'sample-to-answer' capture of nucleic acid targets from complex media would greatly improve existing capabilities of DNA microarrays and biosensors. This goal has proven elusive for many current nucleic acid detection technologies attempting to produce assay results directly from complex real-world samples, including food, tissue, and environmental materials. In this study, we have investigated mixed self-assembled thiolated single-strand DNA (ssDNA) monolayers containing a short thiolated oligo(ethylene glycol) (OEG) surface diluent on gold surfaces to improve the specific capture of DNA targets from complex media. Both surface composition and orientation of these mixed DNA monolayers were characterized with x-ray photoelectron spectroscopy (XPS) and near-edge x-ray absorption fine structure (NEXAFS). XPS results from sequentially adsorbed ssDNA/OEG monolayers on gold indicate that thiolated OEG diluent molecules first incorporate into the thiolated ssDNA monolayer and, upon longer OEG exposures, competitively displace adsorbed ssDNA molecules from the gold surface. NEXAFS polarization dependence results (followed by monitoring the N 1s{yields}{pi}* transition) indicate that adsorbed thiolated ssDNA nucleotide base-ring structures in the mixed ssDNA monolayers are oriented more parallel to the gold surface compared to DNA bases in pure ssDNA monolayers. This supports ssDNA oligomer reorientation towards a more upright position upon OEG mixed adlayer incorporation.more » DNA target hybridization on mixed ssDNA probe/OEG monolayers was monitored by surface plasmon resonance (SPR). Improvements in specific target capture for these ssDNA probe surfaces due to incorporation of the OEG diluent were demonstrated using two model biosensing assays, DNA target capture from complete bovine serum and from salmon genomic DNA mixtures. SPR results demonstrate that OEG incorporation into the ssDNA adlayer improves surface resistance to both nonspecific DNA and protein adsorption, facilitating detection of small DNA target sequences from these undiluted, unpurified complex biological mixtures unachievable with previously reported, analogous ssDNA/11-mercapto-1-undecanol monolayer surfaces« less

Authors:
; ; ;
Publication Date:
Research Org.:
Brookhaven National Laboratory (BNL) National Synchrotron Light Source
Sponsoring Org.:
Doe - Office Of Science
OSTI Identifier:
913963
Report Number(s):
BNL-78531-2007-JA
TRN: US0801435
DOE Contract Number:
DE-AC02-98CH10886
Resource Type:
Journal Article
Resource Relation:
Journal Name: Biointerphases; Journal Volume: 1
Country of Publication:
United States
Language:
English
Subject:
43 PARTICLE ACCELERATORS; DNA; DNA HYBRIDIZATION; ENVIRONMENTAL MATERIALS; FINE STRUCTURE; GOLD; HYBRIDIZATION; NUCLEIC ACIDS; X-RAY PHOTOELECTRON SPECTROSCOPY; NSLS; national synchrotron light source

Citation Formats

Lee,C., Gamble, L., Grainger, D., and Castner, D. Mixed DNA/Oligo(ethylene glycol) Functionalized Gold Surface Improve DNA Hybridization in Complex Media. United States: N. p., 2006. Web. doi:10.1116/1.2219110.
Lee,C., Gamble, L., Grainger, D., & Castner, D. Mixed DNA/Oligo(ethylene glycol) Functionalized Gold Surface Improve DNA Hybridization in Complex Media. United States. doi:10.1116/1.2219110.
Lee,C., Gamble, L., Grainger, D., and Castner, D. Sun . "Mixed DNA/Oligo(ethylene glycol) Functionalized Gold Surface Improve DNA Hybridization in Complex Media". United States. doi:10.1116/1.2219110.
@article{osti_913963,
title = {Mixed DNA/Oligo(ethylene glycol) Functionalized Gold Surface Improve DNA Hybridization in Complex Media},
author = {Lee,C. and Gamble, L. and Grainger, D. and Castner, D.},
abstractNote = {Reliable, direct 'sample-to-answer' capture of nucleic acid targets from complex media would greatly improve existing capabilities of DNA microarrays and biosensors. This goal has proven elusive for many current nucleic acid detection technologies attempting to produce assay results directly from complex real-world samples, including food, tissue, and environmental materials. In this study, we have investigated mixed self-assembled thiolated single-strand DNA (ssDNA) monolayers containing a short thiolated oligo(ethylene glycol) (OEG) surface diluent on gold surfaces to improve the specific capture of DNA targets from complex media. Both surface composition and orientation of these mixed DNA monolayers were characterized with x-ray photoelectron spectroscopy (XPS) and near-edge x-ray absorption fine structure (NEXAFS). XPS results from sequentially adsorbed ssDNA/OEG monolayers on gold indicate that thiolated OEG diluent molecules first incorporate into the thiolated ssDNA monolayer and, upon longer OEG exposures, competitively displace adsorbed ssDNA molecules from the gold surface. NEXAFS polarization dependence results (followed by monitoring the N 1s{yields}{pi}* transition) indicate that adsorbed thiolated ssDNA nucleotide base-ring structures in the mixed ssDNA monolayers are oriented more parallel to the gold surface compared to DNA bases in pure ssDNA monolayers. This supports ssDNA oligomer reorientation towards a more upright position upon OEG mixed adlayer incorporation. DNA target hybridization on mixed ssDNA probe/OEG monolayers was monitored by surface plasmon resonance (SPR). Improvements in specific target capture for these ssDNA probe surfaces due to incorporation of the OEG diluent were demonstrated using two model biosensing assays, DNA target capture from complete bovine serum and from salmon genomic DNA mixtures. SPR results demonstrate that OEG incorporation into the ssDNA adlayer improves surface resistance to both nonspecific DNA and protein adsorption, facilitating detection of small DNA target sequences from these undiluted, unpurified complex biological mixtures unachievable with previously reported, analogous ssDNA/11-mercapto-1-undecanol monolayer surfaces},
doi = {10.1116/1.2219110},
journal = {Biointerphases},
number = ,
volume = 1,
place = {United States},
year = {Sun Jan 01 00:00:00 EST 2006},
month = {Sun Jan 01 00:00:00 EST 2006}
}
  • The surface structure and DNA hybridization performance of thiolated single-strand DNA (HS-ssDNA) covalently attached to a maleimide-ethylene glycol disulfide (MEG) monolayer on gold have been investigated. Monolayer immobilization chemistry and surface coverage of reactive ssDNA probes were studied by X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry. Orientation of the ssDNA probes was determined by near-edge X-ray absorption fine structure (NEXAFS). Target DNA hybridization on the DNA-MEG probe surfaces was measured by surface plasmon resonance (SPR) to demonstrate the utility of these probe surfaces for detection of DNA targets from both purified target DNA samples and complex biological mixturesmore » such as blood serum. Data from complementary techniques showed that immobilized ssDNA density is strongly dependent on the spotted bulk DNA concentration and buffer ionic strength. Variation of the immobilized ssDNA density had a profound influence on the DNA probe orientation at the surface and subsequent target hybridization efficiency. With increasing surface probe density, NEXAFS polarization dependence results (followed by monitoring the N 1s {yields} {pi}* transition) indicate that the immobilized ssDNA molecules reorient toward a more upright position on the MEG monolayer. SPR assays of DNA targets from buffer and serum showed that DNA hybridization efficiency increased with decreasing surface probe density. However, target detection in serum was better on the 'high-density' probe surface than on the 'high-efficiency' probe surface. The amounts of target detected for both ssDNA surfaces were several orders of magnitude poorer in serum than in purified DNA samples due to nonspecific serum protein adsorption onto the sensing surface.« less
  • This paper describes the preparation of oligo(ethylene glycol)-terminated alkanethiols having structure HS-(CH{sub 2}){sub 11}(OCH{sub 2}CH{sub 2}){sub m}OH (m = 3-7) and their use in the formation of self-assembled monolayers (SAMs) on gold. A combination of experimental evidence derived from x-ray photoelectron spectroscopy (XPS), measurement of contact angles, and ellipsometry implies substantial disorder in the oligo(ethylene glycol)-containing segment. The order in the {minus}(CH{sub 2}){sub 11}-group is not defined by the available evidence. The SAMSs are moderately hydrophilic: {theta}{sub a}(H{sub 2}O) = 34-38; {theta}{sub r}(H{sub 2}O) = 22-25. A study of monolayers containing mixtures of HS(CH{sub 2}){sub 11}CH{sub 3} and HS(CH{sub 2}){submore » 11}(OCH{sub 2}CH{sub 2}){sub 6}OH suggest that the oligo(ethylene glycol) moieties are effective at preventing underlying methylene groups from influencing wetting by water. A limited study demonstrates that these oligo(ethylene glycol)-containing SAMs resist the adsorption of protein from solution and suggests that SAMs will be a useful model system for studying the adsorption of proteins onto organic surfaces.« less
  • No abstract prepared.
  • The attachment of linear poly(ethylene glycol)(PEG) molecules (MW = 2,000--5,000) to gold surfaces via orthopyridyl-disulfide (OPSS) terminal groups has been studied with X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (TOF-SIMS), and surface plasmon resonance (SPR). The molecules examined included a PEG molecule terminated with a methoxy group and derivatized with an OPSS group at the other end (M-PEG-OPSS), a PEG molecule derivatized with OPSS at both ends (PEG-(OPSS){sub 2}), and a PEG derivatized with an N-hydroxysuccinimide group at one end and an OPSS group at the other (NHS-PEG-OPSS). Exposure of gold to aqueous solutions of these resulted inmore » immobilization via gold - thiolate bonds from the OPSS disulfide groups. The resulting mixed PEG-/OPS-thiolate monolayers were not always in 1:1 ratio. Most of the PEG-(OPSS){sub 2} molecules formed gold-thiolate bonds at both ends, but some left a free, intact OPSS group. For biosensor applications, this or the free NHS groups in the NHS-PEG-OPSS films can be used to immobilize biomolecules with accessible cysteines or lysines via formation of disulfide bonds or amide bonds, respectively. The PEG films formed by M-PEG-OPSS and PEG-(OPSS){sub 2} resist the adsorption of albumin.« less
  • We report how the covalent attachment of short oligo (ethyleneglycol) chains to cobalt tris(bipyridine) complexes (I), tetrathiafulvalene (II), tetraphenylporphyrin (III), and ferrocenecarboxylate (IV) transforms these normally crystalline materials into room-temperature melts which freely dissolve electrolytes like LiClO{sub 4} to yield ionically conductive and is a novel electroactive molten salt. This paper describes a microelectrode-based voltammetric study of diffusion and electron transport phenomena in compounds I-IV in undiluted forms. 15 refs., 1 fig.