Enhancement of the Binding Ability of a Ligand for Nucleobase Recognition by Introducing a Methyl Group

RIKEN, Вако, Saitama, Japan
Analytical Sciences (Impact Factor: 1.39). 03/2006; 22(2):201-3. DOI: 10.2116/analsci.22.201
Source: PubMed


The recognition ability of pteridine derivatives for nucleobases opposite an abasic (AP) site in an oligodeoxynucleotide (ODN) duplex is enhanced by using a propylene residue (Spacer-C3) as an AP site. The recognition ability is further enhanced both by attaching methyl groups to a fluorescent ligand and by measuring the fluorescence response at 5 degrees C; 6.2 x 10(6) M(-1) of the binding constant is attained between 2-amino-6,7-dimethyl-4-hydroxypteridine and guanine opposite the AP site in water.

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    • "Although the AP site can be targeted by non-fluorescent small molecules including binder/insertor heterodimer [5], [7]–[9], metalloinsertor [6], [10], redox probe [11], nitroxide spin label [12], and DNA base analog [13], fluorescent small molecules have received much attention due to simplicity and cost saving in the detection technologies. In this aspect, some fluorophores were found to be effective such as environment polarity-sensitive naphthalene derivative [14] as well as the organic probes possessing hydrogen bond moieties that are complementary to the bases opposite the AP site, including naphthyridine [15], [16], pyrazine [17], lumazine [18], pteridine [19], [20] and flavin [21] derivatives. However, due to formation of the static DNA complexes, excited state electron transfer, and the other intricate processes, fluorescence quenching was usually observed [15]–[21]. "
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    ABSTRACT: Small molecules that can specifically bind to a DNA abasic site (AP site) have received much attention due to their importance in DNA lesion identification, drug discovery, and sensor design. Herein, the AP site binding behavior of sanguinarine (SG), a natural alkaloid, was investigated. In aqueous solution, SG has a short-wavelength alkanolamine emission band and a long-wavelength iminium emission band. At pH 8.3, SG experiences a fluorescence quenching for both bands upon binding to fully matched DNAs without the AP site, while the presence of the AP site induces a strong SG binding and the observed fluorescence enhancement for the iminium band are highly dependent on the nucleobases flanking the AP site, while the alkanolamine band is always quenched. The bases opposite the AP site also exert some modifications on the SG's emission behavior. It was found that the observed quenching for DNAs with Gs and Cs flanking the AP site is most likely caused by electron transfer between the AP site-bound excited-state SG and the nearby Gs. However, the flanking As and Ts that are not easily oxidized favor the enhanced emission. This AP site-selective enhancement of SG fluorescence accompanies a band conversion in the dominate emission from the alkanolamine to iminium band thus with a large emission shift of about 170 nm. Absorption spectra, steady-state and transient-state fluorescence, DNA melting, and electrolyte experiments confirm that the AP site binding of SG occurs and the stacking interaction with the nearby base pairs is likely to prevent the converted SG iminium form from contacting with water that is thus emissive when the AP site neighbors are bases other than guanines. We expect that this fluorophore would be developed as a promising AP site binder having a large emission shift.
    PLoS ONE 11/2012; 7(11):e48251. DOI:10.1371/journal.pone.0048251 · 3.23 Impact Factor
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    • "The simplest explanation is that the methyl increases polarisability, allowing for more favourable van der Waals interactions with neighbouring bases [45]; when the neighbour is also methylated , the induced dipole-induced dipole attractions would become even larger. Based on this methyl effect, Dai et al. [49] investigated the DNA binding ability of ligands with and without methyl substitution and found the enhanced binding affinity with methyl substituted ligands. So in our case, it seems reasonable to assume that the two methyl substitutions (i.e. "
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    ABSTRACT: Acridine group of dyes are well known in the field of development of probes for nucleic acid structure and conformational determination because of their relevance in the development of novel chemotherapeutic agents, footprinting agents and for gene manipulation in biotechnology and medicine. Here, we report the interaction of 9-N,N-dimethylaniline decahydroacridinedione (DMAADD), a new class of dye molecule with calf thymus DNA (CT-DNA) which has been studied extensively by means of traditional experimental and theoretical techniques. The changes in the base stacking of CT-DNA upon the binding of DMAADD are reflected in the circular dichroic (CD) spectral studies. Competitive binding study shows that the enhanced emission intensity of ethidium bromide (EB) in presence of DNA was quenched by the addition of DMAADD indicating that it displaces EB from its binding site in DNA and the apparent binding constant has been estimated to be (3.3+/-0.2)x10(5) M(-1). This competitive binding study and further fluorescence experiments reveal that DMAADD is a moderate binder of CT-DNA, while viscosity measurements show that the mode of binding is partial intercalation. Generally, one would expect increase in the melting temperature (T(m)) of DNA in presence of intercalators. Interestingly, an unusual decrease in melting temperature (DeltaT(m) of -4+/-0.2 degrees C) of DNA by the addition of DMAADD was observed. From our knowledge such a decreasing trend in melting point was not reported before for all the possible modes of binding. Molecular modeling gave the pictorial view of the binding model which clearly shows that of the various mode of binding, the dye prefers the major groove binding to the sites rich in GC residues and to the sites rich in AT residues it prefers intercalation mode of binding either through major or minor groove with the inclusion of the N,N-dimethylaniline (DMA) group inside the double helix which has been stacked in between the bases, under physiological relevant pH of 7.5.
    Biochimica et Biophysica Acta 01/2007; 1760(12):1794-801. DOI:10.1016/j.bbagen.2006.08.011 · 4.66 Impact Factor
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    ABSTRACT: A new class of abasic site-binding fluorescence ligands, Naph-NBD in which 7-nitrobenzo-2-oxa-1,3-diazole (NBD) is connected to 2-amino-7-methyl-1,8-naphthyridine (Naph) by a propylene linker, is presented for the ratiometric assay for SNPs typing. In solutions buffered to pH 7.0 (1 = 0.11 M, at 5 degrees C), Naph-NBD is found to selectively recognize pyrimidine bases over purine bases opposite the abasic site in DNA duplexes (K-11/M-1: T, 8.1 X 10(6); C, 2.5 x 10(6); G, 0.33 X 10(6); A, 0.27 x 10(6)). The binding of Naph-NBD is accompanied by significant quenching of the fluorescence from the naphthyridine moiety (lambda(max,) 409 nm), while the emission from the NBD (lambda(max), 544 nm) is relatively unaffected. Such a fluorescence response of Naph-NBD allows the emission ratio detection of pyrimidine/purine transversion.
    Analytical Sciences 02/2006; 22(2):195-197. DOI:10.2116/analsci.22.195 · 1.39 Impact Factor
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