Application of probes having 2′-deoxyinosine for typing of single nucleotide polymorphisms (SNPs) using DNA microarray

Kinoshita, Hideki; Ishiwata, Shigemasa; Tsuji, Yoshihiro; Dejima, Makiko; Yano, Kazuyoshi; Takase, Ichiro; Karube, Isao

doi:10.1016/j.aca.2005.12.009

Cited by 5 publications

(10 citation statements)

References 18 publications

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“…This implied that the conventional washing step could not effectively remove the nonspecifically bound targets, leading to inaccurate differentiation of the matched from mismatched sequences. Probe 2 containing two deoxyinosines was designed as Kinoshita et al reported . By use of probe 2, targets 1 and 2 gave strong fluorescent signals while targets 3 and 4 gave relatively weak fluorescent signals.…”

Section: Resultsmentioning

confidence: 99%

“…However, Kinoshita et al reported probes that two bases adjacent to the SNPs site were substituted by the deoxyinosines were used. The fluorescence intensity ratio of the mismatch to the match was 0.2–0.5 . The fluorescent intensity of mismatched probes was too high to successfully differentiate the mismatch, which might result in differentiation confusion.…”

Section: Introductionmentioning

confidence: 98%

“…In 2006, Kinoshita et al proposed that oligonucleotide probes containing deoxyinosines can be applied to genotype multialleles on a chip. The results indicated that the hybridization accuracy was enhanced.…”

Section: Introductionmentioning

confidence: 99%

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Effect of oligonucleotide probes substituted by deoxyinosines on the specificity of SNP detection on the DNA microarray

Qian

Liu

et al. 2014

Electrophoresis

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One of the main factors that can affect the quality of microarray results is the microarray hybridization specificity. The key factor that affects hybridization specificity is the design of the probes. In this paper, we described a novel oligonucleotide probe containing deoxyinosines aimed at improving DNA hybridization specificity. We compared different probes to determine the distance between deoxyinosine base and SNPs site and the number of deoxyinosine bases. The new probe sequences contained two set of deoxyinosines (each set had two deoxyinosines), in which the interval between SNP site and each set of deoxyinosines was two bases. The new probes could obtain the highest hybridization specificity. The experimental results showed that probes containing deoxyinosines hybridized effectively to the perfectly matched target and improved the hybridization specificity of DNA microarray. By including a simple washing step after hybridization, these probes could distinguish matched targets from single-base-mismatched sequences perfectly. For the probes containing deoxyinosines, the fluorescence intensity of a match sequence was more than eight times stronger than that of a mismatch. However, the intensity ratio was only 1.3 times or less for the probes without deoxyinosines. Finally, using hybridization of the PCR product microarrays, we successfully genotyped SNP of 140 samples using these new labeled probes. Our results show that this is a useful new strategy for modifying oligonucleotide probes for use in DNA microarray analysis.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 98%

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Effect of oligonucleotide probes substituted by deoxyinosines on the specificity of SNP detection on the DNA microarray

Qian

Liu

et al. 2014

Electrophoresis

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“…They are free of pin-holes, adhere strongly to a wide range of materials, and are chemically and mechanically stable. (19) A number of bioanalytical applications of PPFs for the modifications of sensor areas have been reported, (20,21) such as immunoassays, (22,23) single nucleotide polymorphisms (SNPs) typings, (24,25) amperometric biosensors, (26)(27)(28) capillary electrophoresis, (29) and protein patterning. (30) One of the remarkable features of PPFs is that protein molecules can be immobilized in PPFs without any loss of activity from direct exposure to plasma.…”

Section: Introductionmentioning

confidence: 99%

“…(30) One of the remarkable features of PPFs is that protein molecules can be immobilized in PPFs without any loss of activity from direct exposure to plasma. We have demonstrated that streptavidin (24,25,31) -and antibody (23) -embedded PPFs deposited on glass slides using hexamethyldisiloxane (HMDS) as a monomer can function as receptors for biotinylated DNA in DNA arrays and for antigens in protein chips, respectively.…”

Section: Introductionmentioning

confidence: 99%

Fluorescence Enhancement of Immunoassay Using Multilayered Glass Substrates Modified with Plasma-Polymerized Films

2015

Sensors and Materials

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The plasma polymerization technique, which enables deposition of thin and pinhole free films, was employed to fabricate multilayered substrates for fluorescencebased sensitive immunoassay. A glass slide was modified with a 200-nm-thick Ag layer as a metal mirror and further coated with plasma-polymerized films (PPFs) up to 120 nm thick as the optical interference layers. Cy3-labeled antibody was spotted on the resulting multilayered substrate and the fluorescence image was observed. The Cy3 fluorescence was highly enhanced on the multilayered substrate compared with that observed on the area without PPFs. The maximum fluorescence intensity was obtained when PPF thickness was 63 nm, showing a 30-fold enhancement of fluorescence compared with that obtained from the unmodified substrate. The multilayered substrates with PPF on which multiple proteins were immobilized were further utilized to perform immunoassays, resulting in specific and highly enhanced fluorescence detection.

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Plasma‐Polymerized Films for Biochip Design

Muguruma¹

2010

Plasma Processes & Polymers

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Developments in plasma‐polymerized films used for the design of chip‐based biosensors, commonly referred to as biochips, are described. Plasma‐polymerized films are suitable for the design of an interface between biological components and physical transducers, which are the two well‐known main parts of biochips. The roles and advantages of plasma‐polymerized films in biochip design are highlighted. Mainly, plasma‐polymerized films can play an important role in the control and manipulation of biological components on different spatial regions (patterning), while retaining their activity. In addition, dry‐process‐based plasma‐polymerization are compatible with biochip fabrication processes.

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Application of probes having 2′-deoxyinosine for typing of single nucleotide polymorphisms (SNPs) using DNA microarray

Cited by 5 publications

References 18 publications

Effect of oligonucleotide probes substituted by deoxyinosines on the specificity of SNP detection on the DNA microarray

Effect of oligonucleotide probes substituted by deoxyinosines on the specificity of SNP detection on the DNA microarray

Fluorescence Enhancement of Immunoassay Using Multilayered Glass Substrates Modified with Plasma-Polymerized Films

Plasma‐Polymerized Films for Biochip Design

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