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Methylene blue binding to DNA with alternating GC base sequence: Continuum treatment of salt effects

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Title Methylene blue binding to DNA with alternating GC base sequence: Continuum treatment of salt effects
 
Creator Rohs, Remo
Sklenar, Heinz
 
Description 1-6
Methylene blue (MB), an efficient singlet
oxygen generating photoactive dye, binds to DNA and allows photosensitized reactions
to be used for sequence-specific cleavage of the DNA backbone. Intercalation
and groove binding are possible binding modes of the dye, depending on base
sequences and environmental conditions. In a recent modeling study of methylene
blue binding to a double stranded DNA decamer with an alternating GC sequence,
six structural models for intercalation structures and for minor and major
groove binding have been obtained. By estimating the binding energies
(including electrostatic reaction field contributions of a salt-free aqueous
solvent), symmetric intercalation at the 5'-CpG-3' and 5'GpC-3' steps was found
as the predominant binding mode, followed by a slightly weaker binding of the
dye in the minor groove. In this study, the stability of the modeled structures
has been analysed as a function of salt concentration. The results of finite
difference numerical solutions of the non-linear Poisson-Boltzmann equation
show that the stabilizing effect of salt is larger for free DNA than for the
modeled MB-DNA complexes. Accordingly, the estimated binding energies decrease
with increasing ionic strength. A slightly higher stabilization of the groove
binding complexes results in comparable binding energies for symmetric
intercalation and minor groove binding at high salt concentration. Both results
are in qualitative agreement with experimental data.
 
Date 2013-07-16T05:17:31Z
2013-07-16T05:17:31Z
2001-04
 
Type Article
 
Identifier 0975-0959 (Online); 0301-1208 (Print)
http://hdl.handle.net/123456789/19790
 
Language en_US
 
Rights CC Attribution-Noncommercial-No Derivative Works 2.5 India
 
Publisher NISCAIR-CSIR, India
 
Source IJBB Vol.38(1-2) [February-April 2001]