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Z-->B transition in poly[d(G-m5C)2] induced by interaction with 4',6-diamidino-2-phenylindole
S K Kim1, S Eriksson, B Nordén
1Department of Physical Chemistry, Chalmers University of Technology, Gothenburg, Sweden.
Abstract:
The Z form of poly[d(G-m5C)2], in presence of Mg2+ ion, is found to be transformed into B form upon interaction with 4',6-diamidino-2-phenylindole (DAPI). The Z-->B transformation is complete at a mixing ratio of about 0.07 DAPI per DNA base pairs, i.e., each DAPI molecule may be related to the conversion of 6-7 base pairs. An interaction between DAPI and poly[d(G-m5C)2] in its Z form at low drug: DNA ratios is suggested from optical dichroism and time-resolved luminescence anisotropy results. The spectroscopic behaviour of DAPI indicates that the Z conformation of DNA does not provide normal binding sites for DAPI, such as groove or intercalation sites, but that the initial association may be of external nature.
Insights
The Z-form of poly[d(G-m5C)2] DNA converts to the B-form when interacting with 4
Area of Science:
- Molecular Biology
- Biophysics
- Genetics
Background:
- The Z-DNA conformation is an alternative left-handed double helix structure.
- Poly[d(G-m5C)2] is a synthetic DNA polymer known to adopt the Z-form in the presence of Mg2+.
- 4',6-diamidino-2-phenylindole (DAPI) is a fluorescent dye commonly used to stain DNA.
Purpose of the Study:
- To investigate the interaction between DAPI and the Z-form of poly[d(G-m5C)2].
- To determine if DAPI binding induces a conformational change in Z-DNA.
- To characterize the binding mode of DAPI to Z-DNA.
Main Methods:
- Spectroscopic analysis including optical dichroism.
- Time-resolved luminescence anisotropy measurements.
- Monitoring DNA conformational changes upon drug interaction.
Main Results:
- DAPI induces a complete Z-form to B-form DNA transformation in poly[d(G-m5C)2].
- The transformation occurs at a low drug-to-base pair ratio (0.07 DAPI per base pair).
- Spectroscopic data suggest an initial external association of DAPI with Z-DNA, not groove or intercalation.
Conclusions:
- DAPI binding disrupts the Z-DNA conformation, favoring the B-DNA form.
- The Z-DNA structure may not offer canonical binding sites for DAPI.
- This study reveals a novel DAPI-induced DNA conformational switch.