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.
Highlights
The regular duplex structure with canonical A–T and G–C is the common structure for DNA
Many DNA hairpin structures have been determined [7] and they are involved in the biological processes in both prokaryotic and eukaryotic cells [8]; these hairpins have been documented in replication origins [9,10]
We investigated an abnormal separation for DNA markers on microchip electrophoresis, and we searched for the reason standing behind this anomalous separation by studying the structure of the DNA markers, expecting that the formation of a mini-loop is the reason for it
Summary
The regular duplex structure with canonical A–T and G–C is the common structure for DNA. DNA can fold in several varieties of structures, and these structures have been observed, studied, and divided into several categories such as: hairpins, triplexes, and quadruplexes. These repeats can occur in the eukaryotic genome [1,2,3,4,5,6] and are called minisatellites. Capillary electrophoresis (CE) has played an important role for DNA analysis and genome sequencing. Microchip electrophoresis is an important tool in genomic and proteomic analysis which will result in a new class of drugs based on gene therapy and DNA diagnosis. We investigated an abnormal separation for DNA markers on microchip electrophoresis, and we searched for the reason standing behind this anomalous separation by studying the structure of the DNA markers, expecting that the formation of a mini-loop is the reason for it
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