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Суровая, А.Н.; Гроховский, С. Л.; Burkhardt, Gerhard; Fritzsche, H.; Zimmer, Ch.; Gurskii, G. V.

doi:10.1023/a:1020639917565

Cited by 6 publications

(6 citation statements)

References 18 publications

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“…Notably, the CD spectra of (T 2 AG 3 ) n ( n = 4–20) have isodichroic points in each experimental condition (Figure ). The isodichroic points in these CD spectra indicate that the structures of these telomeric DNAs generating the CD signal are the same with each other under each condition . In addition, under the dilute and molecular crowding conditions in the presence of Na + , the CD intensity at 293 nm has a linear relationship with the number of G-quadruplex units (Figures S1A and S1B of the Supporting Information, SI).…”

Section: Resultsmentioning

confidence: 75%

Beads-on-a-String Structure of Long Telomeric DNAs under Molecular Crowding Conditions

Nakano

et al. 2012

J. Am. Chem. Soc.

100

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The structure and stability of long telomeric DNAs, (T(2)AG(3))(n) (n = 4-20), were studied under dilute and molecular crowding conditions in the presence of Na(+) and K(+). Structural analysis showed that the long telomeric DNAs formed intramolecular G-quadruplexes under all conditions. In the presence of Na(+), the telomeric DNAs formed an antiparallel G-quadruplex under both dilute and molecular crowding conditions. However, in the presence of K(+), molecular crowding induced a conformational change from mixed to parallel. These results are consistent with numerous structural studies for G-quadruplex units under molecular crowding conditions. Thermodynamic analysis showed that G-quadruplexes under the molecular crowding conditions were obviously more stable than under dilute condition. Interestingly, this stabilization effect of molecular crowding was reduced for the longer telomeric DNAs, indicating that the G-quadruplex structure of long telomeric DNAs is not as stable under molecular crowding conditions, as implied from the large stabilization of isolated G-quadruplex units as previously reported. Moreover, a hydration study revealed that upon structure folding, the interior of a G-quadruplex unit was dehydrated, whereas the linker between two units was more hydrated. It is thus possible to propose that the linkers between G-quadruplex units are ordered structures but not random coils, which could have an important influence on the stability of the entire structure of long telomeric DNAs. These results are significant to elucidate the biological characteristics of telomeres, and can aid in the rational design of ligands and drugs targeting the telomere and related proteins.

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Section: Resultsmentioning

confidence: 75%

Beads-on-a-String Structure of Long Telomeric DNAs under Molecular Crowding Conditions

Nakano

et al. 2012

J. Am. Chem. Soc.

100

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“…They correspond to bis -netropsin binding predominantly in the monomeric form [6][7][8][9]. At ë / BP > 0.1, significant concentration-depending changes were observed in the CD spectra.…”

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confidence: 92%

“…We suggest that the dimeric complex is similar in structure to the trimeric complex between distamycin and DNA oligomer, in which two molecules of this antibiotic in the form of a sandwich are incorporated into a narrow DNA groove to span five to six AT base pairs [5]. We have shown previously that bis -netropsin I forms a complex with the self-complementary decamer 5'-CGTATATACG-3' (stoichiometric composition 2 : 1) and does not bind to this complex to form a pin [6].…”

mentioning

confidence: 99%

“…These antibiotics bind to the clusters of AT base pairs in a narrow DNA groove [1][2][3][4]. The simplest way to enhance the selectivity of this binding is to synthesize dimeric (oligomeric) analogues, in which at least two monomers are bound covalently with each other [2][3][4][6][7][8][9].…”

mentioning

confidence: 99%

“…Unbound bis -netropsins are optically inactive. After their binding to DNA, a CD band appears in the area of 300-360 nm, the amplitude and form of which depend on the level of binding and the type of the bis -netropsin-DNA complex [6,9]. The contribution of the nucleic acid to the CD amplitude in this spectral area may be neglected.…”

mentioning

confidence: 99%

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DNA-binding and antiviral activity of bis-netropsins containing clusters of lysine residues in the N-terminal region

Андронова

Гроховский

Surovaya

et al. 2004

Dokl Biochem Biophys

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DNA-Based Nanostructures: Changes of Mechanical Properties of DNA upon Ligand Binding

Nechipurenko

Grokhovsky

Gursky

et al. 2008

Nanomaterials for Application in Medicine and Biology

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The formation of DNA-based nanostructures involves the binding of different kinds of ligands to DNA as well as the interaction of DNA molecules with each other. Complex formation between ligand and DNA can alter physicochemical properties of the DNA molecule. In the present work, the accessibility of DNAligand complexes to cleavage by DNase I are considered, and the exact algorithms for analysis of diagrams of DNase I footprinting for ligand-DNA complexes are obtained. Changes of mechanical properties of the DNA upon ligand binding are also demonstrated by the cleavage patterns generated upon ultrasound irradiation of cis-platin-DNA complexes. Propagation of the mechanical perturbations along DNA in the presence of bound ligands is considered in terms of a string model with a heterogeneity corresponding to the position of a bound ligand on DNA. This model can reproduce qualitatively the cleavage patterns obtained upon ultrasound irradiation of cis-platin-DNA complexes.

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Cited by 6 publications

References 18 publications

Beads-on-a-String Structure of Long Telomeric DNAs under Molecular Crowding Conditions

Beads-on-a-String Structure of Long Telomeric DNAs under Molecular Crowding Conditions

DNA-binding and antiviral activity of bis-netropsins containing clusters of lysine residues in the N-terminal region

DNA-Based Nanostructures: Changes of Mechanical Properties of DNA upon Ligand Binding

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