Real-Time Detection of Nucleic Acid Interactions by Total Internal Reflection Fluorescence

Hp, Lehr; Reimann, Manja; Brandenburg, Albrecht; Sulz, Gerd; Klapproth, H

doi:10.1021/ac0206519

Cited by 76 publications

(50 citation statements)

References 22 publications

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“…33 For comparison, a typical fluorescence-based assay is limited by background to a detection limit of 1 pM for DNA hybridization adsorption. 31,34,35 In addition, at a target concentration of 1 pM the surface signal is limited by both adsorption kinetics (eq 5) and diffusion to the surface.…”

Section: A Langmuir Adsorption and Desorption Kineticsmentioning

confidence: 99%

Creating Advanced Multifunctional Biosensors with Surface Enzymatic Transformations

2006

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This article summarizes our recent work on the coupling of surface enzyme chemistry and bioaffinity interactions on biopolymer microarrays for the creation of multiplexed biosensors with enhanced selectivity and sensitivity. The surface sensitive techniques of surface plasmon resonance imaging (SPRI) and surface plasmon fluorescence spectroscopy (SPFS) are used to detect the surface enzymatic transformations in real time. Three specific examples of novel coupled surface bioaffinity/ surface enzymatic processes are demonstrated: (i) a surface enzymatic amplification method utilizing the enzyme ribonuclease H (RNase H) in conjunction with RNA microarrays that permits the ultrasensitive direct detection of genomic DNA at a concentration of 1 fM without labeling or PCR amplification, (ii) the use of RNA-DNA ligation chemistry to create renewable RNA microarrays from single stranded DNA microarrays, and (iii) the application of T7 RNA polymerase for the onchip replication of RNA from double stranded DNA microarray elements. In addition, a simple yet powerful theoretical framework that includes the contributions of both enzyme adsorption and surface enzyme kinetics is used to quantitate surface enzyme reactivity. This model is successfully applied to SPRI and SPFS measurements of surface hydrolysis reactions of RNase H and Exonuclease III (Exo III) on oligonucleotide microarrays.

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Section: A Langmuir Adsorption and Desorption Kineticsmentioning

confidence: 99%

Creating Advanced Multifunctional Biosensors with Surface Enzymatic Transformations

2006

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“…These sensors have been created to detect a wide variety of materials. Some of the more important uses of this technology have been to detect 2,4-dinitrotoluene, 1 pesticides, 2 pathogens, 3 nucleic acids, 4 gases, 5 and disease markers such as the HER2 breast cancer marker. 6 These sensors function by measuring the interaction of the evanescent field, a non-propagating near field optical wave, with the target.…”

Section: Introductionmentioning

confidence: 99%

Total internal reflection photoacoustic spectroscopy for the detection of β-hematin

et al. 2012

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Abstract. Evanescent field sensing methods are currently used to detect many different types of disease markers and biologically important chemicals such as the HER2 breast cancer receptor. Hinoue et al. used Total Internal Reflection Photoacoustic Spectroscopy (TIRPAS) as a method of using the evanescent field to detect an optically opaque dye at a sample interface. Although their methods were successful at detecting dyes, the results at that time did not show a very practical spectroscopic technique, which was due to the less than typical sensitivity of TIRPAS as a spectroscopy modality given the low power (∼1 to 2 W) lasers being used. Contrarily, we have used an Nd:YAG laser with a five nanosecond pulse that gives peak power of 1 MW coupled with the TIRPAS system to increase the sensitivity of this technique for biological material sensing. All efforts were focused on the eventual detection of the optically absorbing material, hemozoin, which is created as a byproduct of a malarial infection in blood. We used an optically analogous material, β-hematin, to determine the potential for detection in the TIRPAS system. In addition, four properties which control the sensitivity were investigated to increase understanding about the sensor's function as a biosensing method.

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“…The chips were placed in a chip reader consisting of a laser, a flow cell chamber, and a charge-coupled-device (CCD) camera ( Fig. 2) (21). In the flow cell, the hybridization progress of the molecules can be observed from the liquid phase to the immobilized oligonucleotides on a transducer surface.…”

Section: Methodsmentioning

confidence: 99%

Performance of a Polymer-Based DNA Chip Platform in Detection and Genotyping of Human Papillomavirus in Clinical Samples

et al. 2009

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Human papillomavirus (HPV) plays a key role in the development of cervical and laryngeal cancers. The aim of our study was to compare the performance of a new hydrogel-based HPV genotyping biochip assay (Biochip) to a commercially available and CE-marked conventional PCR followed by reverse hybridization (GenID-PCR). One hundred twenty-three samples were available for the study. Of these samples, 101/123 were gynecological swabs, 8/123 were swabs or biopsy samples of genital warts, 7/123 were biopsy samples of otorhinolaryngeal lesions, 5/123 were samples of skin warts, and 2/123 were samples of orolabial abnormalities. These molecular methods for HPV genotyping showed comparable sensitivity and specificity. However, 19/123 of the results were discrepant. Specifically, Biochip showed better performance in the detection of multiple infections, especially when more than one high-risk genotype was present. Due to the different probe configurations used in the two assays, GenID-PCR achieves only group-specific detection of many HPV genotypes, whereas Biochip allows for specific identification. Overall, the newly developed HPV chip system (Biochip) proved to be a suitable tool for HPV detection and genotyping; it also proved to be superior for establishing HPV genotyping methods.Persistent infection with human papillomavirus (HPV) is now well known to play the key role in the development of cervical carcinoma, which is the second most common malignancy in women worldwide. Certain HPV genotypes have been shown to be associated with a high risk for carcinogenesis. HPV type 16 (HPV-16) and HPV-18 are responsible for more than 70% of cervical carcinomas, whereas other high-risk genotypes (HPV-31, -33, -45, -52, -58, and others) are found less frequently (34,38,39).Due to the high negative predictive value of a negative HPV test result combined with negative cytology results, it is expected that, in the future, DNA testing will complement cytology in routine gynecological screening, thus enabling the development of a more cost-efficient screening program with expanded intervals between patient visits (11). For women with low-grade squamous intraepithelial lesions or atypical squamous cells of undetermined significance, HPV testing is an important requirement for triage strategies (3, 32). Since a significant proportion of HPV infections, including high-risk genotypes HPV-16 and -18, are cleared within several months by the immune system, single detection of HPV DNA alone is not sufficient to predict cancer development, especially in younger women (5). Consequently, the ability to genotype at least the most common high-risk HPV strains, i.e., and -18, in order to distinguish persistent infections with the same genotype from subsequent infections with other HPV genotypes is an important feature of modern HPV assays (16,33).In the last 2 years, we have seen a breakthrough in the prevention of HPV infections. Much of the progress is the result of immunological studies that have paved the way for development of the first effe...

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Real-Time Detection of Nucleic Acid Interactions by Total Internal Reflection Fluorescence

Cited by 76 publications

References 22 publications

Creating Advanced Multifunctional Biosensors with Surface Enzymatic Transformations

Creating Advanced Multifunctional Biosensors with Surface Enzymatic Transformations

Total internal reflection photoacoustic spectroscopy for the detection of β-hematin

Performance of a Polymer-Based DNA Chip Platform in Detection and Genotyping of Human Papillomavirus in Clinical Samples

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