Sequence Dependent Ultrafast Electron Transfer of Nile Blue in Oligonucleotides |
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Authors: | Rajib Kumar Mitra Sudarson Sekhar Sinha Swati Maiti Samir Kumar Pal |
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Institution: | (1) Unit for Nano-Science and Technology, Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt Lake, Kolkata, 700098, India |
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Abstract: | In this contribution we report studies on the nature of binding of nile blue (NB), a well known DNA intercalating drug, with
three synthetic DNA oligonucleotides, (CGCAAATTTGCG)2, (GCGCGCGCGCGC)2 and (ATATATATATAT)2. The nature of fluorescence quenching of the ligand upon complexation with the DNAs has been studied using steady state and
picosecond-resolved optical spectroscopic techniques. The geometrical restriction on the probe in the DNA microenvironment
is measured using picosecond-resolved rotational anisotropy measurements. Our experiments identify both non-specific electrostatic
and intercalative modes of interaction of the probe with the DNAs at lower and higher DNA concentrations, respectively. This
dual nature of binding is also confirmed through gel electrophoresis experiments. The nature of electron transfer (ET) reaction
of GC base pairs with intercalated NB has also been explored. Competitive binding study reveals that binding affinity of the
probe is higher with SDS micelles than with the DNAs within its structural integrity in presence of the micelles, as evidenced
from circular dichroism (CD) measurements. The complex rigidity of NB with various DNAs and its fluorescence quenching with
DNAs elucidate a strong recognition mechanism between NB and DNA. |
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Keywords: | Nile blue Oligomers Electron transfer Picosecond dynamics |
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