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. 2016 May 26;84(3):507-513.
doi: 10.3390/scipharm84030507.

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

Mohammad Jabasini  1   2 , Ashraf Ewis  3 , Youichi Sato  4 , Yutaka Nakahori  5 , Yoshinobu Baba  6   7   8
Affiliations

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

Mohammad Jabasini et al. Sci Pharm. .

Abstract

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.

Keywords: DNA; anomalous separation; microchip electrophoresis.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The anomalous separation of sY592 (65 bp) and sY638 (64 bp) before modification.
Figure 2
Figure 2
Hairpin DNA structure which can be formed from (CTG)n, (CAG)n, (CCG)n, (CGG)n repeats.
Figure 3
Figure 3
Separation results of sY592 (65 bp) and 1-Modified sY638 (64 bp).
Figure 4
Figure 4
Separation results of the sY610 (61 bp) and 1-modified sY638 (64 bp).
See this image and copyright information in PMC

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