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.     

Flow linear dichroism to probe binding of aromatic molecules and DNA to single-walled carbon nanotubes

Structures of carbon nanotube/ligand complexes were studied by flow linear dichroism (the differential absorption of light polarized parallel and perpendicular to the flow orientation direction) with the aim of establishing linear dichroism as a technique to study such systems. Anthracene, naphthalene, and DNA were chosen as ligands, and the potential for flow linear dichroism to probe ligands noncovalently (as well as covalently) bound to single-walled nanotubes is reported. Linear dichroism enables the determination of approximate orientations of the ligands on the carbon nanotubes.     

Single-walled carbon nanotubes chemiresistor aptasensors for small molecules: picomolar level detection of adenosine triphosphate

Here we report single walled-carbon nanotubes (SWNTs)-based chemiresistor aptasensors for highly sensitive and selective detection of weakly or uncharged molecules using the displacement format. As a proof-of-concept we demonstrate the detection of ATP, a small weakly charged molecule, by displacement of the ssDNA anti-ATP aptamer hybridized to a small capture oligonucleotide covalently attached on SWNTs, with picomolar sensitivity and selectivity over GTP.     

Recognition ability of DNA for carbon nanotubes correlates with their binding affinity

The ability to sort mixtures of carbon nanotubes (CNTs) based on chirality has recently been demonstrated using special short DNA sequences that recognize certain matching CNTs of specific chirality. In this work, we report on a study of the relationship between recognition sequences and the strength of their binding to the recognized CNT. We have chosen the (6,5) CNT and its corresponding DNA recognition sequences for investigation in this study. Binding strength is quantified by studying the kinetics of DNA replacement by a surfactant, which is monitored by following shifts in the absorption spectrum. We find that recognition ability correlates strongly with binding strength thus measured; addition or subtraction of just one base from the recognition sequence can enhance the kinetics of DNA displacement some 20-fold. The surfactant displaces DNA in two steps: a rapid first stage lasting less than a few seconds, followed by progressive removal lasting tens of minutes. The kinetics of the second stage is analyzed to extract activation energies. Fluorescence studies support the finding that the DNA sequence that recognizes the (6,5)-CNT forms a more stable hybrid than its close relatives.     

The binding of single-stranded DNA and PNA to single-walled carbon nanotubes probed by flow linear dichroism

The binding of single-stranded DNAs and a neutral DNA analogue (peptide nucleic acid, PNA) to single-walled carbon nanotubes in solution phase has been probed by absorbance spectroscopy and linear dichroism. The nanotubes are solubilised by aqueous sodium dodecyl sulfate, in which the nucleic acids also dissolve. The linear dichroism (LD) of the nanotubes, when subtracted from that due to the nanotubes/nucleic acid samples, gives the LD of the bound nucleic acid. The binding of the single-stranded DNA to the single-walled nanotubes is quite different from that previously observed for double-stranded DNA. It is likely that the nucleic acid bases lie flat on the nanotube surface with the backbone wrapping round the nanotube at an oblique angle in the region of 45 degrees . The net effect is like beads on a string. The base orientation with the single-stranded PNA is inverted with respect to that of the single-stranded DNA, as shown by their oppositely signed LD signals.     

Mass spectrometric studies on effects of counter ions of TMPyP4 on binding to human telomeric DNA and RNA G-quadruplexes

A comparative study on human telomeric DNA G-quadruplex binding of meso-5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4) between its two salt forms, i.e., tetratosylate and tetrachloride, was conducted by using ESI-TOF-MS, UV-melting measurement, and molecular modeling methods. Besides cation TMPyP4, the tosyl anion was found to bind to human telomeric DNA G-quadruplex with multiple binding stoichiometries from 1:1 to 3:1 observed in ESI-TOF-MS spectra, indicating that the stabilization activity of TMPyP4 tetratosylate on G-quadruplex is derived from a synergetic effect of both TMPyP4 cation and tosyl anion. A molecular modeling study suggests that a tosyl anion fills up the vacant space between TMPyP4 cation and DNA G-quadruplex and thus stabilizes the complex by 3.8 kcal/mol. Therefore, it is estimated that TMPyP4 tetratosylate’s activity might not reflect the real effect of TMPyP4 cation in some bioassays related to G-quadruplex stabilization. This was verified by the results of less binding affinity of TMPyP4 tetrachloride with DNA G-quadruplex obtained from ESI-TOF-MS measurement, and of 2.27 °C less thermal stabilization of TMPyP4 tetrachloride for DNA G-quadruplex, compared to its tetratosylate under the same conditions. Our study demonstrated the influence of counter ions of TMPyP4 on G-quadruplex binding, which sheds light on the proper usage of TMPyP4 salt in the chemical and biological research associated with G-quadruplex binding. Subsequently, the binding of TMPyP4 tetrachloride to human telomeric RNA G-quadruplexes was studied with ESI-TOF-MS technique. The binding constants of TMPyP4 with human telomeric G-quadruplexes indicated that TMPyP4 binds to human telomeric RNA G-quadruplex one order of magnitude stronger than DNA counterpart. This is a comprehensive mass spectrometric report on binding study of TMPyP4 with human telomeric DNA/RNA G-quadruplexes.

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DNA-bleomycin interaction: Nucleotide sequence-specific binding and cleavage of DNA by bleomycin

Biosynthetic intermediates and synthetic analogues of bleomycin (BLM) have been investigated for their metal binding, dioxygen activation, and DNA cleavage. Molecular O₂ was activated by the Fe(II) complex of a synthetic model ligand. Nucleotide sequence specificities in DNA cleavage by the BLM-Fe(II) and deglyco-BLM-Fe(II) complexes were almost identical. It has been shown that (1) the β-aminoalanine-pyrimidine-β-hydroxyhistidine portion of BLM is essential for the metal binding and dioxygen activation and (2) the bithiazole moiety contributes to the specific binding to guanine base of DNA.     

DNA mediated assembly of single walled carbon nanotubes: role of DNA linkers and annealing

With the high demand for nanoelectronic devices, extensive research has focused on the use of single walled carbon nanotubes (CNTs) due to their high electron carrier mobility, large tensile strength, and single nanometer dimensions. Despite their promise, however, their applicability has been greatly hindered by the inherent difficulties of both separating nanotubes of different chiralities and diameters and positioning them from metallic tubes and positioning them in a precise location on a surface. In recent years, single stranded DNA (ssDNA) has been identified as a potential solution for both of these problems since DNA can be used to both separate the different types of CNTs as well as direct their organization. We demonstrate here the first principles on how to guide CNT assembly directly on surfaces from solution by specific DNA hybridization. It was found that the specific DNA sequence used to disperse the carbon nanotubes greatly influences the adsorption and specificity of nanotube binding to the surface. Furthermore, we demonstrate here that thermal annealing can correct misaligned tubes or incorrect binding. These studies provide an excellent foundation for employing two-dimensional DNA templates for CNT organization for nanoelectronic logic and memory based applications. Furthermore, using a single biomaterial to both sort and place CNTs in minimal steps would greatly help the throughput, manufacturability, and cost of such devices.     

Induction of a remarkable conformational change in a human telomeric sequence by the binding of naphthyridine dimer: inhibition of the elongation of a telomeric repeat by telomerase

The binding of a dimeric form of the 2-amino-1,8-naphthyridine derivative (naphthyridine dimer) to a human telomeric sequence, TTAGGG, was investigated by UV melting, CD spectra, and CSI-MS measurements. Both the 9-mer d(TTAGGGTTA) and the 15-mer d(TTAGGGTTAGGGTTA) showed apparent melting temperatures (T(m)) of 45.6 and 63.6 degrees C, respectively, in the presence of naphthyridine dimer (30 microM) in sodium cacodylate buffer (50 mM, pH 7.0) containing 100 mM NaCl. The CD spectra at 235 and 255 nm of the 9-mer increased in intensity accompanied with strong induced CDs at 285 and 340 nm upon complex formation with naphthyridine dimer. UV titration of the binding of naphthyridine dimer to the 9-mer at 320 nm showed a hypochromism of the spectra. A Scatchard plot of the data showed the presence of multiple binding sites with different association constants. Cold spray ionization mass spectrometry of the complex between naphthyridine dimer and the 9-mer clearly showed that one to three molecules of the ligand bound to the dimer duplex of the 9-mer. Telomeric repeat elongation assay showed that the binding of naphthyridine dimer to the telomeric sequence inhibits the elongation of the sequence by telomerase.     

Formation of (3+1) G-quadruplexes with a long loop by human telomeric DNA spanning five or more repeats

Structural studies of human telomeric repeats represent an active field of research with potential applications toward the development of specific telomeric quadruplex-targeting drugs for anticancer treatment. To date, high-definition structures were limited to DNA sequences containing up to four GGGTTA repeats. Here we investigate the formation of G-quadruplexes in sequences spanning five to seven human telomeric repeats using NMR, UV, and CD spectroscopy. A (3+1) G-quadruplex with a long propeller loop was isolated from a five-repeat sequence utilizing a guanine-to-inosine substitution. A simple approach of selective site-specific labeling of guanine residues was devised to rigorously determine the folding topology of the oligonucleotide. The same scaffold could be extrapolated to six- and seven-repeat sequences. Our results suggest that long human telomeric sequences consisting of five or more GGGTTA repeats could adopt (3+1) G-quadruplex structures harboring one or more repeat(s) within a single loop. We report on the formation of a Watson-Crick duplex within the long propeller loop upon addition of the complementary strand, demonstrating that the long loop could serve as a new recognition motif.     

PNA C-C+ i-motif: superior stability of PNA TC8 tetraplexes compared to DNA TC8 tetraplexes at low pH

Study of self-assembly of PNA TC8 monitored by UV thermal transition at 295 nm indicates formation of a C-C+ tetraplex (i-motif) in acidic pH, with higher stability than the analogous dTC8.     

Synthesis and characterization of Ru(II)-DMSO-Cl-chalcone complexes: DNA binding, nuclease, and topoisomerase II inhibitory activity

The complexes of type cis-[Ru(S-DMSO)(3)(R-CO-CH═CH-R')Cl] (R = 2-hydroxyphenyl for all, R' = phenyl 1, naphthyl 2, anthracenyl 3, thiophene 4, 3-methyl thiophene 5) are synthesized and characterized using spectroscopic (IR, (1)H and (13)C NMR, and UV-vis) and single crystal X-ray diffraction techniques. Their crystal structures show the formation of both intermolecular and intramolecular H-bonding. The molecular assembly of complex 5 using secondary interactions provides a butterfly structure. The binding of complexes with calf thymus DNA is monitored using UV-vis spectral titrations. The binding interaction of complexes 1, 2, and 3 with DNA increases with increasing conjugation of aromatic rings. However, complexes 4 and 5 interact with DNA strongly. The emission from ethidium bromide (EB) bound DNA recorded in phosphate buffer solution (pH = 7.2) decreases by incremental addition of solution of the complexes. The complexes 4 and 5 (100 μM) bind with the minor groove of DNA and cleave double-stranded pBR322 DNA significantly even in the absence of an activator. In the presence of H(2)O(2), they cleave supercoiled DNA via oxidative pathway even at lower concentration (20 μM). Both complexes 4 and 5 inhibit topoisomerase II activity with IC(50) values of 18 and 13. These values suggest that 4 and 5 are potential topoisomerase II inhibitors as compared to some of known inhibitors like novobiocin and etoposide.     

Solubility of aminotriethylene glycol functionalized single wall carbon nanotubes: A density functional based tight binding molecular dynamics study

Pristine CNTs are exemplary hydrophobic solutes; properly functionalized CNTs can be seen as hydrophilic ones. The solubility of aminotriethylene glycol (ATG) functionalized single walled carbon nanotubes (fSWCNTs) were examined using density functional based tight binding method. According to the dynamics study, the ATG-fSWCNTs interaction energies (IE) and diffusion coefficients (D) are diameter dependent. As the diameter of the (n,0) tube is incrementally increased, a distinguishable pattern is observed, specifically the IE of the ATG-fSWCNT in water is quite higher for n that is an integral multiple of three (n = 9,12,15) while the D is lower due to its π bonding structures. In general, the metallic ATG functionalized nanotube possess a higher IE and a much lower D in aqueous media. © 2019 Wiley Periodicals, Inc.     

Mixed-ligand copper(II)-phenolate complexes: effect of coligand on enhanced DNA and protein binding, DNA cleavage, and anticancer activity

The copper(II) complex [Cu(tdp)(ClO4)].0.5H2O (1), where H(tdp) is the tetradentate ligand 2-[(2-(2-hydroxyethylamino)ethylimino)methyl]phenol, and the mixed ligand complexes [Cu(tdp)(diimine)]+ (2-5), where diimine is 2,2'-bipyridine (bpy) (2), 1,10-phenanthroline (phen) (3), 3,4,7,8-tetramethyl-1,10-phenanthroline (tmp) (4), and dipyrido-[3,2-d:2',3'-f]-quinoxaline (dpq) (5), have been isolated and characterized by analytical and spectral methods. Complexes 1 and [Cu(tdp)(phen)]ClO4 (3) have been structurally characterized, and their coordination geometries around copper(II) are described as distorted octahedral. The equatorially coordinated ethanolic oxygen in 1 is displaced to an axial position upon incorporating the strongly chelating phen, as in 3. The solution structures of all the complexes have been assessed to be square-based using electronic absorption and electron paramagnetic resonance (EPR) spectroscopy. The interaction of the complexes with calf thymus DNA (CT DNA) has been explored by using absorption, emission, and circular dichroic spectral and viscometric studies, and modes of DNA binding for the complexes have been proposed. Absorption spectral (Kb = 0.071 +/- 0.005 (2), 0.90 +/- 0.03 (3), 7.0 +/- 0.2 (4), 9.0 +/- 0.1 x 10(5) M(-1) (5)), emission spectral (Kapp = 4.6 (1), 7.8 (2), 10.0 (3), 12.5 (4), 25.0 x 10(5) M(-1) (5)), and viscosity measurements reveal that 5 interacts with DNA more strongly than the other complexes through partial intercalation of the extended planar ring of the coordinated dpq with the DNA base stack. Interestingly, only complex 4 causes a B to A conformational change upon binding DNA. All the complexes hydrolytically cleave pBR322 supercoiled DNA in 10% DMF/5 mM Tris-HCl/50 mM NaCl buffer at pH 7.1 in the absence of an activating agent, and the cleavage efficiency varies in the order 5 > 3 > 2 > 4 > 1 with 5 displaying the highest Kcat value (5.47 +/- 0.10 h(-1)). The same order of cleavage is observed for the oxidative cleavage of DNA in the presence of ascorbic acid as a reducing agent. Interestingly, of all the complexes, only 5 displays efficient photonuclease activity through double-strand DNA breaks upon irradiation with 365 nm light through a mechanistic pathway involving hydroxyl radicals. The protein binding ability of 1-5 has been also monitored by using the plasma protein bovine serum albumin (BSA), and 4 exhibits a protein binding higher than that of the other complexes. Further, the anticancer activity of the complexes on human cervical epidermoid carcinoma cell line (ME180) has been examined. Interestingly, the observed IC50 values reveal that complex 4, which effects conformational change on DNA and binds to BSA more strongly, exhibits a cytotoxicity higher than the other complexes. It also exhibits approximately 100 and 6 times more potency than cisplatin and mitomycin C for 24 and 48 h incubation times, respectively, suggesting that 4 can be explored further as a potential anticancer drug. Complexes 4 and 5 mediate the arrest of S and G2/M phases in the cell cycle progression at 24 h harvesting time, which progress into apoptosis.