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Dongen, M.J.P. van; Doreleijers, Jurgen F.; Marel, Gijs A. van der; Boom, Jacques H. van; Hilbers, C. W.; Wijmenga, Sybren S.

doi:10.1038/12313

Cited by 16 publications

(2 citation statements)

References 36 publications

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“…The intramolecular triplex has also been reported to have an effect on the transcriptional regulation and replication in vivo [25–27]. H-DNA, found in Escherichia coli and eukaryotic cells [28–30], is found in promoter regions and around recombination hot spots [31]. Therefore, it likely plays a regulatory role in gene expression [32], recombination [33], and in transcription of human viruses [34].…”

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Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices

Kumar

Došen‐Mićović

et al. 2010

Biochimie

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Calorimetric and fluorescence techniques were used to characterize the binding of aminoglycosides-neomycin, paromomycin, and ribostamycin, with 5′-dA12-x-dT12-x-dT12-3′ intramolecular DNA triplex (x = hexaethylene glycol) and poly(dA).2poly(dT) triplex. Our results demonstrate the following features: (1) UV thermal analysis reveals that the Tm for triplex decreases with increasing pH value in the presence of neomycin, while the Tm for the duplex remains unchanged. (2) The binding affinity of neomycin decreases with increased pH, although there is an increase in observed binding enthalpy. (3) ITC studies conducted in two buffers (sodium cacodylate and MOPS) yield the number of protonated drug amino groups (Δn) as 0.29 and 0.40 for neomycin and paromomycin interaction with 5′-dA12-x-dT12-x-dT12-3′, respectively. (4) The specific heat capacity change (ΔCp) determined by ITC studies is negative, with more negative values at lower salt concentrations. From 100 mM to 250 mM KCl, the ΔCp ranges from −402 to −60 cal/(mol K) for neomycin. At pH 5.5, a more positive ΔCp is observed, with a value of −98 cal/(mol K) at 100 mM KCl. ΔCp is not significantly affected by ionic strength. (5) Salt dependence studies reveal that there are at least three amino groups of neomycin participating in the electrostatic interactions with the triplex. (6) FID studies using thiazole orange were used to derive the AC50 (aminoglycoside concentration needed to displace 50% of the dye from the triplex) values. Neomycin shows a seven fold higher affinity than paromomycin and eleven fold higher affinity than ribostamycin at pH 6.8. (7) Modeling studies, consistent with UV and ITC results, show the importance of an additional positive charge in triplex recognition by neomycin. The modeling and thermodynamic studies indicate that neomycin binding to the DNA triplex depends upon significant contributions from charge as well as shape complementarity of the drug to the DNA triplex Watson–Hoogsteen groove.

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confidence: 99%

Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices

Kumar

Došen‐Mićović

et al. 2010

Biochimie

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“…The glycosidic torsion angles [χ(S)] for all non-terminal residues were found in the range of -110 to -129_ (±10_/20_) (Table 1) at both 25 and 40_C. The nucleotide conformation is also partly described by the dihedral angle γ (O5′-C5′-C4′-C3′) (45). The g + rotamer could readily be distinguished from the gor t rotamers because in the g + state, the J 4′5′ and J 4′5′′ couplings are both small (∼3 Hz), whereas one coupling is large (∼12 Hz) in the other two rotamers.…”

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Solution Structure of the ATF-2 Recognition Site and Its Interaction with the ATF-2 Peptide

Conte¹,

Lane²,

Bloomberg

1997

Nucleic Acids Research

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The effect of leucine zipper proteins binding to the DNA recognition site is controversial. Results from crystallography, gel and solution methods have led to opposite conclusions about the conformation of the DNA in the complex. The role of the DNA binding site in the recognition process and in the gene induction mediated by transcription factors needs to be investigated further. In this article the self-complementary 16 bp oligodeoxynucleotide (CATGTGACGTCACATG)2, which contains the cAMP response element recognised by numerous transcription factors of the leucine zipper family, has been examined free from proteins and in its interaction with the mammalian activating transcription factor 2. The recognition process has been investigated by circular dichroism analysis, which has revealed conformational changes in both DNA and protein upon binding. The solution structure of the 16mer, important in order to define the effects induced by binding of leucine zipper proteins and the intrisic bending properties of DNA, has been determined from NMR data using direct refinement against NOE intensities, analysis of scalar coupling constants and restrained molecular dynamics calculations. Final structures starting from the A and B forms of DNA agreed to a pairwise root mean square deviation (r.m.s.d.) of 1.04 +/- 0.3 A (0.7 +/- 0.2 A to the average) for all atoms. The terminal base pairs were less well determined, and the pairwise deviation of the 12 core bp was 0.83 +/- 0.27 A (0.55 +/- 0.19 A to the average). The final structures are within the B-family with an average helical twist of 36+/-2 degrees. No significant intrinsic DNA bend is shown in the activating transcription factor regulatory site. However, there are substantial deviations from the canonical B-DNA (r.m.s.d. = 3.6 A) in the core of the molecule, associated with relatively large base inclinations.

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2012

NMR of Biomolecules

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Cited by 16 publications

References 36 publications

Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices

Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices

Solution Structure of the ATF-2 Recognition Site and Its Interaction with the ATF-2 Peptide

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