Structure Of Human Telomeric DNA Research Articles

Introduction of Ketamine as a G‐Quadruplex‐Binding Ligand Using Platinum Nanoparticle Modified Carbon Paste Electrode

AbstractWe designed an electrochemical platform by modifying a carbon paste electrode (CPE) with platinum nanoparticles to study the interaction between ketamine and the G‐quadruplex structure of human telomeric DNA (G4HTD). The drug ketamine (Kt) was used as the model ligand and its ability for stabilizing the G‐quadruplex structure was examined. The modified CPE (NPtCPE) was characterized by differential pulse voltammetry (DPV) and atomic force microscopy (AFM). The interaction of Kt with G4HTD was studied by DPV and the DPV current decreased with increasing Kt concentration. The results from UV‐vis and circular dichroism (CD) spectroscopy showed a prominent intercalation mode between G4HTD and Kt.

The crystal structure of human telomeric DNA complexed with berberine: an interesting case of stacked ligand to G-tetrad ratio higher than 1:1

The first crystal structure of human telomeric DNA in complex with the natural alkaloid berberine, produced by different plant families and used in folk medicine for millennia, was solved by X-ray diffraction method. The G-quadruplex unit features all-parallel strands. The overall folding assumed by DNA is the same found in previously reported crystal structures. Similarly to previously reported structures the ligand molecules were found to be stacked onto the external 5′ and 3′-end G-tetrads. However, the present crystal structure highlighted for the first time, the presence of two berberine molecules in the two binding sites, directly interacting with each tetrad. As a consequence, our structural data point out a 2:1 ligand to G-tetrad molar ratio, which has never been reported before in a telomeric intramolecular quadruplex structure.

Structure of Human Telomeric DNA in Crowded Solution

G-quadruplex structures formed by DNA at the human telomeres are attractive anticancer targets. Human telomeric sequences can adopt a diverse range of intramolecular G-quadruplex conformations: a parallel-stranded conformation was observed in the crystalline state, while at least four other forms were seen in K(+) solution, raising the question of which conformation is favored in crowded cellular environment. Here, we report the first NMR structure of a human telomeric G-quadruplex in crowded solution. We show that four different G-quadruplex conformations are converted to a propeller-type parallel-stranded G-quadruplex in K(+)-containing crowded solution due to water depletion. This study also reveals the formation of a new higher-order G-quadruplex structure under molecular crowding conditions. Our molecular dynamics simulations of solvent distribution provide insights at molecular level on the formation of parallel-stranded G-quadruplex in environment depleted of water. These results regarding human telomeric DNA can be extended to oncogenic promoters and other genomic G-rich sequences.

Single‐Walled Carbon Nanotubes Binding to Human Telomeric i‐Motif DNA Under Molecular‐Crowding Conditions: More Water Molecules Released

The natural occurrence of the human telomeric G-quadruplex or i-motif in vivo has not been demonstrated and the biological effects of the induction of these structures need to be clarified. Intracellular environments are highly crowded with various biomolecules and in vitro studies under molecular-crowding conditions will provide important information on how biomolecules behave in cells. Here we report that cell-mimic crowding can increase i-motif stability at acid pH and cause dehydration. However, crowding can not induce i-motif formation at physiological pH. Intriguingly, single-walled carbon nanotubes (SWNTs) can drive i-motif formation under cell-mimic crowding conditions and cause more water to be released. To our knowledge, there is no report to show how SWNTs can influence DNA under cell-mimic crowding conditions. Our results indicate that SWNTs may have the potential to modulate the structure of human telomeric DNA in vivo, like DNA B-A transitions and B-Z changes on SWNTs in live cells, which demonstrates potential for drug design and cancer therapy.

Structure of a human telomeric DNA sequence stabilized by 8‐bromoguanosine substitutions, as determined by NMR in a K+ solution

The structure of human telomeric DNA is controversial; it depends upon the sequence contexts and the methodologies used to determine it. The solution structure in the presence of K(+) is particularly interesting, but the structure is yet to be elucidated, due to possible conformational heterogeneity. Here, a unique strategy is applied to stabilize one such structure in a K(+) solution by substituting guanosines with 8-bromoguanosines at proper positions. The resulting spectra are cleaner and led to determination of the structure at a high atomic resolution. This demonstrates that the application of 8-bromoguanosine is a powerful tool to overcome the difficulty of nucleic acid structure determination arising from conformational heterogeneity. The obtained structure is a mixed-parallel/antiparallel quadruplex. The structure of telomeric DNA was recently reported in another study, in which stabilization was brought about by mutation and resultant additional interactions [Luu KN, Phan AT, Kuryavyi V, Lacroix L & Patel DJ (2006) Structure of the human telomere in K(+) solution: an intramolecular (3+1) G-quadruplex scaffold. J Am Chem Soc 128, 9963-9970]. The structure of the guanine tracts was similar between the two. However, a difference was seen for loops connecting guanine tracts, which may play a role in the higher order arrangement of telomeres. Our structure can be utilized to design a small molecule which stabilizes the quadruplex. This type of molecule is supposed to inhibit a telomerase and thus is expected to be a candidate anticancer drug.

The new models of the human telomere DNA in K+ solution revealed by NMR analysis assisted by the incorporation of 8-bromoguanines

The structure of human telomeric DNA has been controversial: the solution structure in the presence of Na(+) has been reported to be antiparallel basket-type quadruplex by NMR, while the crystal structure in the presence of K(+) has been reported to be parallel propeller-type quadruplex. The solution structure in the presence of K(+) has drawn intense interest, as the intracellular K(+) concentration is higher than that of Na(+), but the structure is still open to address. Recently Sugiyama et al. has suggested that the DNA exists as a mixture of mixed-parallel/antiparallel quadruplex and antiparallel chair-type quadruplex on the basis of the combination of a series of 8-bromoguanine mutations and CD analysis. Here, we have started NMR analysis of the DNAs with the mutations to evaluate the proposed model. So far, NMR analysis is qualitatively consistent with the proposal. The structure determination is in progress to evaluate the model at atomic resolution.

Structure of the Human Telomere in K+Solution: An Intramolecular (3 + 1) G-Quadruplex Scaffold

We present the intramolecular G-quadruplex structure of human telomeric DNA in physiologically relevant K(+) solution. This G-quadruplex, whose (3 + 1) topology differs from folds reported previously in Na(+) solution and in a K(+)-containing crystal, involves the following: one anti.syn.syn.syn and two syn.anti.anti.anti G-tetrads; one double-chain reversal and two edgewise loops; three G-tracts oriented in one direction and the fourth in the opposite direction. The topological characteristics of this (3 + 1) G-quadruplex scaffold should provide a unique platform for structure-based anticancer drug design targeted to human telomeric DNA.