Stability and Structure of Model DNA Triplexes and Quadruplexes and Their Interactions with Small Ligands

The major bovine milk protein β-lactoglobulin (β-LG), a member of the lipocalin superfamily, can bind a wide range of ligands and act as a transporter. In the present study, the combination of the hydrophobic molecule 2-(p-toluidino)-6-naphthalenesulfonic acid sodium salt (TNS) with β-LG was analyzed using fluorescence spectroscopy and AutoDock modeling to discern the major binding sites of the protein and to determine the capacity of other small ligands to bind with β-LG by utilizing TNS as a reference. The experimental data indicate that in a neutral pH environment, TNS is located in the hydrophobic domain of the protein, 2.5 nm away from the Trp19 residues of β-LG. The binding constant of the small molecule to β-LG is (3.30 ± 0.32) × 106 (mol L–1)−1. An interaction model between the ligand and β-LG was developed, and AutoDock modeling also demonstrates that the ligand is located in the central hydrophobic calyx of β-LG within the regions covered by the Förster radius of the Trp19–ligand pair. Although the interaction between the ligand and β-LG is affected by increasing ion strength, pH change, and heat treatment, the complex is maintained until the secondary structure of β-LG is destroyed. Additionally, the ligand binding stabilizes the folding of β-LG. The binding constants of sodium dodecyl sulfate (SDS) and sodium dodecylbenzene sulfonate (SDBS) to β-LG were obtained using competitive ligand binding measurements. With a sensitive fluorescence signal and stable complex, the ligand could be utilized as a reference to detect the binding of other small ligands to β-LG.

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DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies

Beilstein Journal of Organic Chemistry ◽

10.3762/bjoc.17.65 ◽

2021 ◽

Vol 17 ◽

pp. 749-761

Author(s):

Yongdong Su ◽

Maitsetseg Bayarjargal ◽

Tracy K Hale ◽

Vyacheslav V Filichev

Keyword(s):

Mouse Fibroblast ◽

Cell Uptake ◽

Dna Duplexes ◽

Nih3t3 Cells ◽

Dna Triplexes ◽

Snake Venom Phosphodiesterase ◽

Nuclease Digestion ◽

Dna Backbone ◽

Uptake Studies

Two phosphate modifications were introduced into the DNA backbone using the Staudinger reaction between the 3’,5’-dinucleoside β-cyanoethyl phosphite triester formed during DNA synthesis and sulfonyl azides, 4-(azidosulfonyl)-N,N,N-trimethylbutan-1-aminium iodide (N+ azide) or p-toluenesulfonyl (tosyl or Ts) azide, to provide either a zwitterionic phosphoramidate with N+ modification or a negatively charged phosphoramidate for Ts modification in the DNA sequence. The incorporation of these N+ and Ts modifications led to the formation of thermally stable parallel DNA triplexes, regardless of the number of modifications incorporated into the oligodeoxynucleotides (ONs). For both N+ and Ts-modified ONs, the antiparallel duplexes formed with complementary RNA were more stable than those formed with complementary DNA (except for ONs with modification in the middle of the sequence). Additionally, the incorporation of N+ modifications led to the formation of duplexes with a thermal stability that was less dependent on the ionic strength than native DNA duplexes. The thermodynamic analysis of the melting curves revealed that it is the reduction in unfavourable entropy, despite the decrease in favourable enthalpy, which is responsible for the stabilisation of duplexes with N+ modification. N+ONs also demonstrated greater resistance to nuclease digestion by snake venom phosphodiesterase I than the corresponding Ts-ONs. Cell uptake studies showed that Ts-ONs can enter the nucleus of mouse fibroblast NIH3T3 cells without any transfection reagent, whereas, N+ONs remain concentrated in vesicles within the cytoplasm. These results indicate that both N+ and Ts-modified ONs are promising for various in vivo applications.

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The binding of analogues of coralyne and related heterocyclics to DNA triplexes

Biochemistry and Cell Biology ◽

10.1139/o95-002 ◽

1995 ◽

Vol 73 (1-2) ◽

pp. 11-18 ◽

Cited By ~ 25

Author(s):

Laura J. P. Latimer ◽

Natasha Payton ◽

Gavin Forsyth ◽

Jeremy S. Lee

Keyword(s):

Thermal Denaturation ◽

Positive Charge ◽

Triplex Dna ◽

Alkyl Chains ◽

Dna Triplexes ◽

Weak Binding ◽

Related Alkaloid ◽

General Preference ◽

Nitrogen Ring ◽

Derivatives Of

Coralyne has been shown previously to bind well to both T∙A∙T- and C∙G∙C+-containing triplexes. Derivatives of coralyne were prepared and their binding to poly(dT)∙poly(dA)∙poly(dT) and poly[d(TC)]∙poly[d(GA)]∙poly[d(C+T)] was assessed from thermal denaturation profiles. A tetraethoxy derivative showed only weak binding to both types of triplex. Analogues with extended 8-alkyl chains showed good binding to poly(dT)∙poly(dA)∙poly(dT), but the preference for triplex poly[d(TC)]∙poly[d(GA)]∙poly[d(C+T)] was decreased compared with the duplex. Sanguinarine, a related alkaloid, bound well to poly(dT)∙poly(dA)∙poly(dT) but only weakly to the protonated triplex. It is hypothesized that the position of the protonated nitrogen ring is important for binding to poly[d(TC)]∙poly[d(GA)]∙poly[d(C+T)]. A series of other chromophores was studied and only those with a positive charge bound to triplexes. All of these bound well to poly(dT)∙poly(dA)∙poly(dT) but only weakly if at all to the duplex poly(dA)∙poly(dT). In contrast, most of them did not bind well to the triplex poly[d(TC)]∙poly[d(GA)]∙poly[d(C+T)] and those that did still showed a preference for duplex poly[d(TC)]∙poly[d(GA)]. In general, preference for triplex poly(dT)∙poly(dA)∙poly(dT) compared with the duplex is a common feature of intercalating drugs. On the other hand, specificity for protonated triplexes may be very difficult to achieve.Key words: triplex DNA, DNA-binding drugs, intercalation.

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