Making “Sense” of DNA

Stokes, Grace Y.; Gibbs, Julianne M.; Boman, Faith C.; Stepp, Brian R.; Condie, Allison G.; Nguyen, SonBinh T.; Geiger, Franz M.

doi:10.1021/ja071848r

Cited by 85 publications

(158 citation statements)

References 23 publications

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“…Techniques such as X-ray photoelectron spectroscopy (XPS) [13,14], near-edge X-ray absorption fine structure (NEXAFS) spectroscopy [15][16][17][18], time-of-flight secondary ion mass spectrometry (ToF-SIMS) [19][20][21], sum-frequency-generation (SFG) spectroscopy [22,23], and infrared reflection-absorption spectroscopy (IRRAS) [24,25] can be used to determine composition, content, molecular orientation and hybridization behavior of DNA assemblies. Yet despite the large amounts of potential information obtainable through use of these methods, the interpretation of spectra from biological samples, including surface-bound DNA, can be difficult, often resulting in the restriction of the use of these techniques to simplified or relatively straightforward systems.…”

Section: Introductionmentioning

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: Introductionmentioning

confidence: 99%

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

Howell¹,

Hamoudi²,

Zharnikov

2013

Biointerphases

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“…This may lead to a tilted alignment of the ssDNA strands and a subsequent increased peak intensity of the carbonyl groups. This work adds SFG to the techniques currently available for the characterization of ssDNA films in solution, further building on the SFG results obtained by Stokes et al, who examined hybridization phenomena, 25 and Asanuma et al, who studied the deformation of ssDNA films upon exposure to cations. 27 These results allow for further exploration of their findings, as well as results generated by XPS, NEXAFS, and FTIR, in aqueous environments, and may also serve to begin bridging the gap between ex situ and in situ characterization of ssDNA films.…”

Section: Discussionmentioning

confidence: 95%

“…However, our spectra of T 5 -SH reveals features similar to previously published results examining films of ssDNA in air. 25,26 The methyl groups in the thymine bases give rise to inplane and out-of-plane antisymmetric CH 3 stretching vibrations located at 2968 cm −1 ͑r ip − ͒ and 2954 cm −1 ͑r op − ͒, respectively. 31 These peaks are distinguishable in all T 5 -SH spectra and the ratio between them reveals information about the orientation of the methyl groups: the in-plane vibration has an infrared transition dipole moment along the bond be- tween the methyl group and the thymine ring, whereas the out-of-plane infrared transition dipole moment is perpendicular to it.…”

Section: Methodsmentioning

confidence: 99%

“…[25][26][27] Other SFG experiments involving DNA have also been performed by Wurpel and co-workers, who used -phage DNA bound to a cationic lipid monolayer at the air-water interface to study screening effects of counterions by detecting water signals in the OD stretching region at different concentrations. 28 Here we present the first report of the characterization of model monolayers of immobilized ssDNA on gold in air, D 2 O, and phosphate buffer solution in both the CH stretch and amide I regions.…”

Section: Introductionmentioning

confidence: 99%

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Sum-frequency-generation spectroscopy of DNA films in air and aqueous environments

et al. 2008

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Understanding the organization and orientation of surface-immobilized single stranded DNA (ssDNA) in aqueous environments is essential for optimizing and further developing the technology based on oligonucleotide binding. Here the authors demonstrate how sum-frequency-generation (SFG) spectroscopy can be used to compare the structure and orientation of model monolayers of ssDNA on gold in air, D2O, and phosphate buffered saline (PBS) solution. Films of adenine and thymine homo-oligonucleotides showed significant conformational changes in air versus aqueous environments in the CH stretching region. The thymine films showed changes between D2O and PBS solution, whereas the SFG spectra of adenine films under these conditions were largely similar, suggesting that the thymine films undergo greater conformational changes than the adenine films. Examination of thymine films in the amide I vibrational region revealed that molecules in films of nonthiolated DNA were lying down on the gold surface whereas molecules in films of thiol-linked DNA were arranged in a brushlike structure. Comparison of SFG spectra in the amide I region for thiol-linked DNA films in air and D2O also revealed substantial conformational changes.

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“…The tensor was accessed by upconverting the p-polarized infrared light at the filter surface using visible light polarized either +45°o r −45°away from the surface normal and recording the p-polarized component of the vibrational SFG response [Oh-e et al, 2004]. Under this configuration, achiral and racemic systems exhibit no signal difference whereas systems consisting of mixtures of unequal amounts of stereoisomers respond strongly [Belkin et al, 2000;Stokes et al, 2007].…”

Section: Methodsmentioning

confidence: 99%

Stereochemical transfer to atmospheric aerosol particles accompanying the oxidation of biogenic volatile organic compounds

Ebben

Zorn

Lee

et al. 2011

Geophys. Res. Lett.

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Asymmetric emission profiles of the stereoisomers of plant‐derived volatile organic compounds vary with season, geography, plant type, and stress factors. After oxidation of these compounds in the atmosphere, the low‐vapor pressure products ultimately contribute strongly to the particle‐phase material of the atmosphere. In order to explore the possibility of stereochemical transfer to atmospheric aerosol particles during the oxidation of biogenic volatile organic compounds, second‐order coherent vibrational spectra were recorded of the particle‐phase organic material produced by the oxidation of different stereoisomeric mixes of α‐pinene. The spectra show that the stereochemical configurations are not scrambled but instead are transferred from the gas‐phase molecular precursors to the particle‐phase molecules. The spectra also show that oligomers formed in the particle phase have a handed superstructure that depends strongly and nonlinearly on the initial stereochemical composition of the precursors. Because the stereochemical mix of the precursors for a material can influence the physical and chemical properties of that material, our findings suggest that chirality is also important for such properties of plant‐derived aerosol particles.

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Making “Sense” of DNA

Cited by 85 publications

References 23 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

Sum-frequency-generation spectroscopy of DNA films in air and aqueous environments

Stereochemical transfer to atmospheric aerosol particles accompanying the oxidation of biogenic volatile organic compounds

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