Retarded electrophoretic mobility of W chromosome specific DNA fragment from chicken

In the study we report the unusually slow mobility of W chromosome specific DNA fragment. The primers designed to amplify a 481 bp DNA fragment of W chromosome of female chicken revealed its size on agarose gel electrophoresis to be 556 bp. The mobility of this fragment was still slower in polyacrylamide gel electrophoresis. This trend was observed in indigenous, exotic and Vanaraja varieties of chicken. This phenomenon of slow mobility of W chromosome specific DNA fragment was cross checked with the control DNA fragment of 256 bp. Delayed migration of PCR products was observed for other fragment of W chromosome repeat as well. Sequencing of PCR products revealed that the fragments were comprised of clusters of A (2–5) and T (2–5) sequences separated by (5–7) relatively G/C rich sequences. The anomalous behavior of slow migration of W chromosome specific fragments could be attributed to the occurrence of DNA curvatures because of the above mentioned sequence characteristics.