Range of Separation of Potential Tool for Bioseparation, Microchip Electrophoresis System, for DNA Polymorphisms on the Human Y-Chromosome

Jabasini, Mohammad; Xu, Feng; Dang, Fuquan; Shinka, Toshikatsu; Nakahori, Yutaka; Baba, Yoshinobu

doi:10.2116/analsci.19.175

Cited by 5 publications

(7 citation statements)

References 7 publications

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“…The inability to separate sY610 (61 bp) from any of the modified fragments of sY638 (64 bp) supports a previous study result that 5 bp is the minimum length difference for separating two DNA marker fragments on the microchip electrophoresis system [ 21 ].…”

Section: Resultssupporting

confidence: 84%

“…Accordingly, we can conclude that: The inability to separate sY610 (61 bp) from any of the modified fragments of sY638 (64 bp) supports a previous study result that 5 bp is the minimum length difference for separating two DNA marker fragments on the microchip electrophoresis system [ 21 ]. This anomalous separation can be a guiding example for the researcher in the separation field that if any research study resulted in separating two DNA markers with a very limited difference between the two DNA markers This result must not be accepted directly and should be deeply studied by taking into consideration that an anomalous DNA structure might be behind that.…”

Section: Resultssupporting

confidence: 82%

“…Thus DNA separation and analysis on microchip electrophoresis was subjected to several studies. Early studies focused on the validation of the microchip separation ability with special concerns including the separation time, the resolution of the separation on chip, the required volume of the sample, and the ability to separate standard markers as well as real samples [ 20 , 21 , 22 ]. The positive results obtained from these studies paved the way for a wide use of microchip electrophoresis in several DNA research studies.…”

Section: Resultsmentioning

confidence: 99%

“…In a previous work, we studied the range of separation for DNA on a chip and we could separate two DNA markers with a length difference of only 5 bp, in a DNA range less than 100 bp. All other attempts to separate any two DNA fragments with a difference lower than 5 base pairs proved to be impossible, so we concluded that the 5 bp difference in the fragment length is the minimum size difference that the microchip could separate [ 21 ]. Recently, we separated two DNA markers with 1 bp difference sY638 (64 bp) and sY592 (65 bp).…”

Section: Resultsmentioning

confidence: 99%

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Anomalous Separation of Small Y-Chromosomal DNA Fragments on Microchip Electrophoresis

et al. 2016

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We investigated an anomalous DNA separation where two DNA fragments from the human Y-chromosome sY638 (64 bp) and sY592 (65 bp), with only one base pair difference, were separated. This result is abnormal since in a previous study, we found that 5 bp was the minimum difference between two DNA fragments that the microchip electrophoresis system can separate. The formation of a mini-loop in the structure of the DNA fragment of sY638 (64 bp) was strongly expected to be the reason. To investigate this, we synthesized three modified DNA fragments for sY638 (64 bp), and the modifications were in two expected locations for possible mini-loop formation. Later, the separation between sY592 (65 bp) and the three modified fragments of sY638 (64 bp) was not possible. Thus, we conclude that the formation of a mini-loop in the structure of the DNA is the reason behind this anomalous separation.

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Section: Resultssupporting

confidence: 84%

Section: Resultssupporting

confidence: 82%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Anomalous Separation of Small Y-Chromosomal DNA Fragments on Microchip Electrophoresis

et al. 2016

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“…Microchip technology with its potential ability for the analysis of DNA markers could solve this problem, 11,12 by allowing the screening of several markers simultaneously with good separation and less sample consumption as well as obtaining reliable and reproducible electrophoresis separation. 13,14 This high-speed analysis of the microchip electrophoresis for the mutations and the markers on the human genes is very important for the high-speed diagnosis of genetic diseases.…”

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confidence: 99%

Ultrafast Diagnosis of the Genetic-related Disorders Using the Combined Technologies of Multiplex PCR and Multichannel Microchip Electrophoresis

Jabasini

Ewis

et al. 2005

ANAL. SCI.

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Screening of mixed poly(ethylene oxide) solutions for microchip separation of double-stranded DNA using an orthogonal design approach

Jabasini

Baba

2005

Electrophoresis

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We describe a quick and systematic optimization of molecular weights (MWs) and concentrations of a series of mixed poly(ethylene oxide) (PEO) matrices for separating specific double-stranded DNA fragments on polymethylmethacrylate-based microchips by using an orthogonal design (ORD) approach. The mixed matrices are composed of PEOs in four MW ranges (M(w) 8 x 10(6), 1 x 10(6), 4 x 10(5), and 1 x 10(5)) with varying concentration ratios. In the mixed solutions, PEO with an intermediate MW of 4 x 10(5) is found to be a dominant factor for separating small DNA fragment pairs (e.g., 82 and 88 bp), while PEO with a high MW of 8 x 10(6) plays an important role in separating intermediate and large fragments (e.g., 271 and 281 bp, 506 and 517 bp, 7 and 10 kbp). High-concentration PEO mixtures give better resolution for short fragments, while dilute PEO mixtures show better resolution for long fragments. The optimized matrices are suitable for high-resolution separation of multiplex polymerase chain reaction-amplified products and restriction digest fragments ranging in size from 20 bp to 40 kbp within 4 min at a constant field strength of 177 V/cm. The experimental results indicate the robustness and speediness of the ORD to screen the contribution of PEO MWs and to tune optimally the PEO concentration ratio of different MWs with reference to the performance of specific DNA fragments separated.

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Range of Separation of Potential Tool for Bioseparation, Microchip Electrophoresis System, for DNA Polymorphisms on the Human Y-Chromosome

Cited by 5 publications

References 7 publications

Anomalous Separation of Small Y-Chromosomal DNA Fragments on Microchip Electrophoresis

Anomalous Separation of Small Y-Chromosomal DNA Fragments on Microchip Electrophoresis

Ultrafast Diagnosis of the Genetic-related Disorders Using the Combined Technologies of Multiplex PCR and Multichannel Microchip Electrophoresis

Screening of mixed poly(ethylene oxide) solutions for microchip separation of double-stranded DNA using an orthogonal design approach

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