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

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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Abstract

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 3.0).

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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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