Ellipsometric and Interferometric Characterization of DNA Probes Immobilized on a Combinatorial Array

Gray, David E.; Case-Green, Stephen C.; Fell, Tanja; Dobson, Peter J.; Southern, Edwin M.

doi:10.1021/la962139m

Cited by 95 publications

(70 citation statements)

References 27 publications

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“…Recently, advances have been made to characterize the structure of surface-bound DNA probes using such optical or contact methods as ellipsometry, optical reflectivity (7,8), neutron reflectivity (9), x-ray photoelectron spectroscopy (10), FRET (11,12), SPR (13,14), and AFM (15)(16)(17)(18). This previous work has helped in visualizing the structure of the surface-bound DNA depending on its density and surface charge.…”

mentioning

confidence: 99%

DNA conformation on surfaces measured by fluorescence self-interference

Moiseev¹,

Ünlü

Swan³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

105

103

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The conformation of DNA molecules tethered to the surface of a microarray may significantly affect the efficiency of hybridization. Although a number of methods have been applied to determine the structure of the DNA layer, they are not very sensitive to variations in the shape of DNA molecules. Here we describe the application of an interferometric technique called spectral selfinterference fluorescence microscopy to the precise measurement of the average location of a fluorescent label in a DNA layer relative to the surface and thus determine specific information on the conformation of the surface-bound DNA molecules. Using spectral self-interference fluorescence microscopy, we have estimated the shape of coiled single-stranded DNA, the average tilt of doublestranded DNA of different lengths, and the amount of hybridization. The data provide important proofs of concept for the capabilities of novel optical surface analytical methods of the molecular disposition of DNA on surfaces. The determination of DNA conformations on surfaces and hybridization behavior provide information required to move DNA interfacial applications forward and thus impact emerging clinical and biotechnological fields.hybridization ͉ microarray ͉ spectroscopy D NA array technology has become a widespread tool in biological research with applications in expression screening, sequencing, and drug discovery, all benefiting greatly by the highly paralleled detection of the technique. One of the defining characteristics of a DNA array is the availability of the single-stranded probes for hybridization with the target. Immobilized molecules located farther away from the solid support are closer to the solution state and are more accessible for contact with dissolved analytes. The surface, especially a hydrophobic one, acts as a shield for probes positioned close to it because of the associated steric factors and lack of diffusion of the bound molecules (1-5). Thus, knowing the physical structure of DNA probes may prove useful not only in the future development and fabrication of microarrays, but also in designing new applications (6).Recently, advances have been made to characterize the structure of surface-bound DNA probes using such optical or contact methods as ellipsometry, optical reflectivity (7, 8), neutron reflectivity (9), x-ray photoelectron spectroscopy (10), FRET (11,12), SPR (13,14), and AFM (15-18). This previous work has helped in visualizing the structure of the surface-bound DNA depending on its density and surface charge. However, most experimental techniques characterize the DNA layer as a single entity (for instance, parameterizing its thickness or density) without examining the specific positions of internal elements of the DNA chain. Spectral selfinterference fluorescence microscopy (SSFM) can measure the vertical position of a fluorescent label above an optically structured silicon chip. We show that locating the label attached to a certain position within a DNA chain provides insight into the shape of DNA molecules boun...

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mentioning

confidence: 99%

DNA conformation on surfaces measured by fluorescence self-interference

Moiseev¹,

Ünlü

Swan³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

105

103

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“…Related examples are classical interferometers (Mach-Zehnder 37 , Young 38 , Hartman 39 or Backscattering 40 instruments), surface plasmon resonance (SPR) technologies 4142 , 43 , 44 , 45 , with improvements enabling to detect changes in protein conformation (by coupled plasmon waveguide resonance CPWR 46 ) and enhanced sensitivity (by resonant microcavities -sphere, cylinder, ring or toroid shaped-that create a whispering gallery mode phenomenon, 47 54 , 55 (DPI) and optical fiber based biosensors 56 , 57 . Other label free techniques not based on evanescent field measures are ellipsometry 58 , 59 , atomic force microscopy 60 or photonic crystals 61 , 62 . Photonic 7 crystals posses a periodic dielectric structure within wavelength scale that enables them to be used as biosensors as any event disturbing the periodic structure (for instance, a biomolecule attached to its surface) will lead to a detectable defect mode.…”

Section: Methods For Detection Of Biointeractionsmentioning

confidence: 99%

Photopolymerization as a promising method to sense biorecognition events

Peris

Bañuls

Maquieira

et al. 2012

TrAC Trends in Analytical Chemistry

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ElsevierPeris Chanzá, EJ.; Bañuls Polo, M.; Maquieira Catala, Á.; Puchades, R. (2012 The present review summarizes the main topics related to the photopolymerization process focusing on its applications in biosensing chemistry. Among the variety of known polymeric substances, the wide spread usage of ethylene glycol derivatives in medical applications justifies their selection for this purpose. Fundamental aspects of photopolymerization are commented together with the nature and reactivity of the molecules involved, considering both a semi-empirical thermodynamic approach and the development of a kinetic model leaning on experimental values. An effort is made to sum up the most referred characterization techniques applied to figure out the composition of the formed products and to follow the reaction advance. Finally, initial and more recent photopolymerization examples and applications are presented as visiting card of this promising biosensing methodology.

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“…In addition, the increased mobility of the alkane-thiols that form the SAM on gold surfaces at higher temperature might also disrupt the previously highly ordered packing. 34 Similarly, the degradation of the modified silicon surface may start from the oxidation of silicon atoms on the surface, particularly under basic conditions, [35][36][37][38] resulting in subsequent hydrolysis and the loss of surface-bound DNA molecules. Methods to achieve greater stability for the gold and the silicon surfaces are currently under investigation.…”

Section: Chemical Stability To High-temperature Incubationmentioning

confidence: 99%

Invasive cleavage reactions on DNA‐modified diamond surfaces

Knickerbocker

Cai

et al. 2004

Biopolymers

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Recently developed DNA-modified diamond surfaces exhibit excellent chemical stability to high-temperature incubations in biological buffers. The stability of these surfaces is substantially greater than that of gold or silicon surfaces, using similar surface attachment chemistry. The DNA molecules attached to the diamond surfaces are accessible to enzymes and can be modified in surface enzymatic reactions. An important application of these surfaces is for surface invasive cleavage reactions, in which target DNA strands added to the solution may result in specific cleavage of surface-bound probe oligonucleotides, permitting analysis of single nucleotide polymorphisms (SNPs). Our previous work demonstrated the feasibility of performing such cleavage reactions on planar gold surfaces using PCR-amplified human genomic DNA as target. The sensitivity of detection in this earlier work was substantially limited by a lack of stability of the gold surface employed. In the present work, detection sensitivity is improved by a factor of approximately 100 (100 amole of DNA target compared with 10 fmole in the earlier work) by replacing the DNA-modified gold surface with a more stable DNA-modified diamond surface.

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Ellipsometric and Interferometric Characterization of DNA Probes Immobilized on a Combinatorial Array

Cited by 95 publications

References 27 publications

DNA conformation on surfaces measured by fluorescence self-interference

DNA conformation on surfaces measured by fluorescence self-interference

Photopolymerization as a promising method to sense biorecognition events

Invasive cleavage reactions on DNA‐modified diamond surfaces

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