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Molecules 2005, 10(2), 417-426; doi:10.3390/10020417

Investigation of DNA-protein Sequence-Specific Interactions with a ds-DNA Array

, , , ,  and *
Chien-Shiung Wu Laboratory, Department of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P.R. China
* Author to whom correspondence should be addressed.
Received: 2 April 2004 / Revised: 21 December 2004 / Accepted: 22 December 2004 / Published: 28 February 2005
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The sequence specific recognitions between DNAs and proteins play important roles in many biological functions. The use of double-stranded DNA arrays (ds-DNA arrays) for studying sequence specific recognition between DNAs and proteins is a promising method. Here we report the use of a ds-DNA probe with multi operation sites of restriction proteins in the middle sequence to investigate DNA-protein sequence-specific interactions including methylation. We arranged EcoR I site and Rsa I site on the same duplex DNA probe to fabricate ds-DNA arrays. We used the ds-DNA arrays to study DNA-restriction enzyme reactions before and after duplex DNA methylation under different probe concentration and reaction time conditions. Our results indicated that the ds-DNA arrays can be further biochemically modified and made accessible for interactions between DNAs and proteins in complex multi-step gene-regulation processes.
Keywords: ds-DNA array; restriction enzymes; methylase; DNA-protein interactions. ds-DNA array; restriction enzymes; methylase; DNA-protein interactions.
This is an open access article distributed under the Creative Commons Attribution License (CC BY) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Bai, Y.; Ge, Q.; Wang, J.; Li, T.; Liu, Q.; Lu, Z. Investigation of DNA-protein Sequence-Specific Interactions with a ds-DNA Array. Molecules 2005, 10, 417-426.

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