NEXAFS characterization of DNA components and molecular-orientation of surface-bound DNA oligomers

Samuel, Newton T.; Lee, Chi Ying; Gamble, Lara J.; Fischer, Daniel A.; Castner, David G.

doi:10.1016/j.elspec.2006.04.004

Cited by 61 publications

(106 citation statements)

References 54 publications

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“…But even taking into account this flexibility, a very strong positive peak would arise in the difference NEXAFS spectra from a film in which the DNA strands are parallel to the surface (nucleobases would then be predominantly oriented perpendicular to the substrate), and a very strong negative peak would be seen when all DNA molecules are oriented perpendicular to the surface (the nucleobases would then be predominantly oriented parallel to the substrate) [15,17,38]. In the case of ideal L-shape diblock-oligonucleotides [24,36], we would therefore expect to see a very strong positive peak from the parallel surface-binding adenine block and a very strong negative peak from the perpendicular sensing thymine block.…”

Section: Resultsmentioning

confidence: 99%

Thymine/adenine diblock-oligonucleotide monolayers and hybrid brushes on gold: a spectroscopic study

Howell¹,

Hamoudi²,

Zharnikov

2013

Biointerphases

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Background: The establishment of spectroscopic analysis techniques for complex, surface-bound biological systems is an important step toward the further application of these powerful experimental tools to new questions in biology and medicine. Methods: We use a combination of the complementary spectroscopic techniques of X-ray photoelectron spectroscopy, Infrared reflection-absorption spectroscopy, and near-edge x-ray absorption fine structure spectroscopy to monitor the composition and molecular orientation in adenine/thymine diblock oligonucleotide films and their hybridized brushes on gold.

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Section: Resultsmentioning

confidence: 99%

Thymine/adenine diblock-oligonucleotide monolayers and hybrid brushes on gold: a spectroscopic study

Howell¹,

Hamoudi²,

Zharnikov

2013

Biointerphases

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show abstract

“…However, in the intermediate and outer regions of the organomineral interface ( Fig. 2i-l) these transitions could also be the results of the C 1s-π* C_C and C 1s-σ* C\N transitions of amide-C in pyrrole side ring structures (C_C\N) of microbial amino acids and nucleobases and the C 1s-π* C_N transition of C = Nx species of organic matter originating from non-pyrogenic C sources (Table 1; Kaznacheyev et al, 2002;Samuel et al, 2006;Solomon et al, 2009). The C absorption bands that emerged near 287.5 eV ( Fig.…”

Section: Nano-scale Cluster Analysis Of C From the Organomineral Intementioning

confidence: 97%

Micro- and nano-environments of C sequestration in soil: A multi-elemental STXM–NEXAFS assessment of black C and organomineral associations

Solomon

Lehmann

Wang

et al. 2012

Science of The Total Environment

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“…Details of the instrumentation and data processing procedure have been previously reported. 38,39 For the NEXAFS spectra the angle is defined as the angle between the incident X-ray beam and the sample surface. The incident beam normal to the surface is defined as 90° while a glancing incident beam is 20° from the surface plane.…”

Section: Nexafs Analysismentioning

confidence: 99%

XPS, TOF-SIMS, NEXAFS, and SPR Characterization of Nitrilotriacetic Acid-Terminated Self-Assembled Monolayers for Controllable Immobilization of Proteins

2008

Self Cite

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For immobilization of proteins onto surfaces in a specific and controlled manner it is important to start with a well-defined surface that contains specific binding sites surrounded by a nonfouling background. For immobilizing histidine-tagged (his-tagged) proteins, surfaces containing nitrilotriacetic acid (NTA) headgroups and oligo(ethylene glycol) (OEG) moieties are a widely used model system. The surface composition, structure and reactivity of mixed NTA/OEG selfassembled monolayers (SAMs) on Au substrates were characterized in detail using x-ray photoelectron spectroscopy (XPS), near-edge x-ray absorption fine structure spectroscopy (NEXAFS), time-of-flight secondary ion mass spectrometry (ToF-SIMS) and surface plasmon resonance (SPR) biosensoring. XPS results for sequential adsorption of NTA thiols followed by OEG thiols showed that OEG molecules were incorporated into an incompletely formed NTA monolayer until a complete mixed SAM was formed. The surface concentration of NTA headgroups was estimated to be 0.9-1.3 molecule/nm 2 in the mixed NTA/OEG monolayers, compared to 1.9 molecule/nm 2 in pure NTA monolayers. Angle-dependent XPS indicated NTA headgroups were slightly reoriented toward an upright position after OEG incorporation and polarization-dependent NEXAFS results indicated increased ordering of the alkane chains of the molecules. Nitrogen-containing and OEG-related secondary ion fragments from the ToF-SIMS experiments confirmed the presence of NTA headgroups and OEG moieties in the monolayers. A multivariate peak intensity ratio was developed for estimating the relative NTA concentration in the outermost (10 Ǻ) of the monolayers. SPR measurements of a his-tagged, humanized antilysozyme variable fragment (HuLys Fv) immobilized onto Ni(II)-treated mixed NTA/OEG and pure NTA monolayers demonstrated the reversible, site-specific immobilization of his-tagged HuLys Fv (108 -205 ng/cm 2 ) with dissociation rates (k off ) between 1.0x10 −4 and 2.1x10 −5 s −1 , both depending on the NTA surface concentration and orientation. The monolayers without Ni(II) treatment exhibited low nonspecific adsorption of his-tagged HuLys Fv ( < 2ng/cm 2 ).

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NEXAFS characterization of DNA components and molecular-orientation of surface-bound DNA oligomers

Cited by 61 publications

References 54 publications

Thymine/adenine diblock-oligonucleotide monolayers and hybrid brushes on gold: a spectroscopic study

Thymine/adenine diblock-oligonucleotide monolayers and hybrid brushes on gold: a spectroscopic study

Micro- and nano-environments of C sequestration in soil: A multi-elemental STXM–NEXAFS assessment of black C and organomineral associations

XPS, TOF-SIMS, NEXAFS, and SPR Characterization of Nitrilotriacetic Acid-Terminated Self-Assembled Monolayers for Controllable Immobilization of Proteins

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