DNA–DNA kissing complexes as a new tool for the assembly of DNA nanostructures

Kissing-loop annealing of nucleic acids occurs in nature in several viruses and in prokaryotic replication, among other circumstances. Nucleobases of two nucleic acid strands (loops) interact with each other, although the two strands cannot wrap around each other completely because of the adjacent double-stranded regions (stems). In this study, we exploited DNA kissing-loop interaction for nanotechnological application. We functionalized the vertices of DNA tetrahedrons with DNA stem-loop sequences. The complementary loop sequence design allowed the hybridization of different tetrahedrons via kissing-loop interaction, which might be further exploited for nanotechnology applications like cargo transport and logical elements. Importantly, we were able to manipulate the stability of those kissing-loop complexes based on the choice and concentration of cations, the temperature and the number of complementary loops per tetrahedron either at the same or at different vertices. Moreover, variations in loop sequences allowed the characterization of necessary sequences within the loop as well as additional stability control of the kissing complexes. Therefore, the properties of the presented nanostructures make them an important tool for DNA nanotechnology.     

Stability and isomerization of complexes formed by metal ions and cytosine isomers in aqueous phase

We present a systematic study of the stability of the formation of complexes produced by four metal ions (M^+/2+) and 14 cytosine isomers (C_n). This work predicts theoretically that predominant product complexes are associated with higher-energy C₄M^+/2+ and C₅M^+/2+ rather than the most stable C₁M^+/2+. The prediction resolves successfully several experimental facts puzzling two research groups. Meanwhile, in-depth studies further reveal that direct isomerization of C₁?C₄ is almost impossible, and also that the isomerization induced by either metalation or hydration, or by a combination of the two unfavorable. It is the single water molecule locating between the H1(?N1) and O2 of the cytosine that plays the dual roles of being a bridge and an activator that consequently improves the isomerization greatly. Moreover, the cooperation of divalent metal ion and such a monohydration actually leads to an energy-free C₁←C₄ isomerization in the gas phase. Henceforth, we are able to propose schemes inhibiting the free C₁←C₄ isomerization, based purely on extended hydration at the divalent metal ion.

Patterning protein complexes on DNA nanostructures using a GFP nanobody

DNA nanostructures have become an important and powerful tool for studying protein function over the last 5 years. One of the challenges, though, has been the development of universal methods for patterning protein complexes on DNA nanostructures. Herein, we present a new approach for labeling DNA nanostructures by functionalizing them with a GFP nanobody. We demonstrate the ability to precisely control protein attachment via our nanobody linker using two enzymatic model systems, namely adenylyl cyclase activity and myosin motility. Finally, we test the power of this attachment method by patterning unpurified, endogenously expressed Arp2/3 protein complex from cell lysate. By bridging DNA nanostructures with a fluorescent protein ubiquitous throughout cell and developmental biology and protein biochemistry, this approach significantly streamlines the application of DNA nanostructures as a programmable scaffold in biological studies.     

Characterization of a new class of DNA delivery complexes formed by the local anesthetic bupivacaine

Bupivacaine, a local anesthetic and cationic amphiphile, forms stable liposomal-like structures upon direct mixing with plasmid DNA in aqueous solutions. These structures are on the order of 50-70 nm as determined by scanning electron microscopy, and are homogeneous populations as analyzed by density gradient centrifugation. The DNA within these structures is protected from nuclease degradation and UV-induced damage in vitro. Bupivacaine:DNA complexes have a negative zeta potential (surface charge), homogeneous nature, and an ability to rapidly assemble in aqueous solutions. Bupivacaine:DNA complexes, as well as similar complexes of DNA with other local anesthetics, have the potential to be a novel class of DNA delivery agents for gene therapy and DNA vaccines.     

Ferrocenesuccinate-bridged lanthanide polymeric complexes: Syntheses, structures and properties

One-dimensional lanthanide-ferrocenesuccinate polymeric complexes [M(η²-FcCOC₂H₄COO)(μ₂-η²-FcCOC₂H₄COO)₂(H₂O)₂]_n (Fc = (η⁵-C₅H₄)Fe(η⁵-C₅H₄), M = Pr, 1; Ce, 2; La, 3) have been synthesized and structurally characterized by single-crystal X-ray crystallography. The three polymers are isomorphous, in which each Ln(III) ion is 10-coordinated and connects with two water molecules and eight oxygen atoms from ferrocenesuccinate units in two kinds of coordination modes: bidentate-chelating mode and tridentate-bridging mode. The variable-temperature magnetic susceptibility in the temperature range 5-300 K for 1 and 2 shows that both of them display weak antiferromagnetic interaction. In addition, the redox and fluorescent properties have been investigated. The redox properties are different from the previous results of transition metal compounds containing ferrocenyl systems. Compared with sodium ferrocenesuccinate, polymers 1 and 3, the fluorescent intensities of 2 are markedly enhanced in the solid state.     

Electron attachment to DNA single strands: gas phase and aqueous solution

The 2′-deoxyguanosine-3′,5′-diphosphate, 2′-deoxyadenosine-3′,5′-diphosphate, 2′-deoxycytidine-3′,5′-diphosphate and 2′-deoxythymidine-3′,5′-diphosphate systems are the smallest units of a DNA single strand. Exploring these comprehensive subunits with reliable density functional methods enables one to approach reasonable predictions of the properties of DNA single strands. With these models, DNA single strands are found to have a strong tendency to capture low-energy electrons. The vertical attachment energies (VEAs) predicted for 3′,5′-dTDP (0.17 eV) and 3′,5′-dGDP (0.14 eV) indicate that both the thymine-rich and the guanine-rich DNA single strands have the ability to capture electrons. The adiabatic electron affinities (AEAs) of the nucleotides considered here range from 0.22 to 0.52 eV and follow the order 3′,5′-dTDP > 3′,5′-dCDP > 3′,5′-dGDP > 3′,5′-dADP. A substantial increase in the AEA is observed compared to that of the corresponding nucleic acid bases and the corresponding nucleosides. Furthermore, aqueous solution simulations dramatically increase the electron attracting properties of the DNA single strands. The present investigation illustrates that in the gas phase, the excess electron is situated both on the nucleobase and on the phosphate moiety for DNA single strands. However, the distribution of the extra negative charge is uneven. The attached electron favors the base moiety for the pyrimidine, while it prefers the 3′-phosphate subunit for the purine DNA single strands. In contrast, the attached electron is tightly bound to the base fragment for the cytidine, thymidine and adenosine nucleotides, while it almost exclusively resides in the vicinity of the 3′-phosphate group for the guanosine nucleotides due to the solvent effects. The comparatively low vertical detachment energies (VDEs) predicted for 3′,5′-dADP⁻ (0.26 eV) and 3′,5′-dGDP⁻ (0.32 eV) indicate that electron detachment might compete with reactions having high activation barriers such as glycosidic bond breakage. However, the radical anions of the pyrimidine nucleotides with high VDE are expected to be electronically stable. Thus the base-centered radical anions of the pyrimidine nucleotides might be the possible intermediates for DNA single-strand breakage.     

Synthesis, thermal stability and photoluminescence of new cadmium sulfide/organic composite hollow sphere nanostructures

Novel cadmium sulfide/organic composite hollow spheres composed of sword-like nanorods were synthesized via a simple reaction between cadmium salts and thioglycolic acid (TGA) at room temperature. The products were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), selected area electron diffraction (SEAD) and Fourier transform infrared (FT-IR) spectra. Thermal stability of the organic composite was investigated. CdS/organic composite would decompose into pure wurtzite CdS through hydrothermal treatment. Effect of the cadmium source on the formation of the CdS/organic composite was investigated. Photoluminescence (PL) was used to study the optical properties of CdS/organic composite and pure CdS.     

The nature of the complexes formed between the Int protein and DNA

The λ Int protein interacts with DNA to form highly condensed complexes of a non-specific nature. Complexes formed with DNA carrying the bacterial attachment site or lacking any attachment site are dissociated by incubation with heparin or single-stranded DNA. Complexes formed with DNA carrying the phage attachment site are converted to simple complexes by these treatments, and the bound Int molecules are localized at the phage attachment site. Int is present in these complexes as an oligomer.     

Formation of DNA complexes with actinomycins in aqueous solutions and films

The mechanisms of DNA interaction with actinomycin D (AMD), 7-amino-actinomycin D (7-AAMD), and ethidium bromide (EtBr) were studied in aqueous solutions and in condensed state (films coating plates). The use of the methods of absorption (UV, IR, and visible spectral ranges) and fluorescence (steady-state, polarization, and phase-modulation) spectroscopy revealed that (1) the formation of DNA complexes with 7-AAMD in solution was not accompanied by energy transfer from photoexcited nucleotides to phenoxazone chromophore and (2) the mechanism of ligand incorporation was distinct from stacking. In the film of the DNA-7-AAMD complex, which simulated the native state in a biological cell, the efficiency of the energy transfer was high. This indicates that a stacking-type mechanism underlies actinomycin intercalation into DNA. In the presence of high concentrations of 7-AAMD in the film, DNA denatured and its double-helical structure, degraded. In the DNA-AMD complex, the native B-form of DNA molecule was conserved both in films and in solution.     

DNA binding, DNA cleavage, and cytotoxicity studies of two new copper (II) complexes

The DNA binding behavior of [Cu(phen)(phen-dione)Cl]Cl (1) and [Cu(bpy)(phen-dione)Cl]Cl (2) was studied with a series of techniques including UV-vis absorption, circular dichroism spectroscopy, and viscometric methods. Cytotoxicity effect and DNA unwinding properties were also investigated. The results indicate that the Cu(II) complexes interact with calf-thymus DNA by both partially intercalative and hydrogen binding. These findings have been further substantiated by the determination of intrinsic binding constants spectrophotometrically, 12.5?×?10(5) and 5?×?10(5) for 1 and 2, respectively. Our findings suggest that the type of ligands and structure of complexes have marked effect on the binding affinity of complexes involving CT-DNA. Circular dichroism results show that complex 1 causes considerable increase in base stacking of DNA, whereas 2 decreases the base stacking, which is related to more extended aromatic area of 1,10-phenanthroline in 1 rather than bipyridine in 2. Slow decrease in DNA viscosity indicates partially intercalative binding in addition to hydrogen binding on the surface of DNA. The second binding mode was also confirmed by additional tests: interaction in denaturation condition and acidic pH. Also, these new complexes induced cleavage in pUC18 plasmid DNA as indicated in gel electrophoresis and showed excellent antitumor activity against K562 (human chronic myeloid leukemia) cells.     

Electron microscopy visualization of DNA-protein complexes formed by Ku and DNA ligase IV

The repair of DNA double-stranded breaks (DSBs) is essential for cell viability and genome stability. Aberrant repair of DSBs has been linked with cancer predisposition and aging. During the repair of DSBs by non-homologous end joining (NHEJ), DNA ends are brought together, processed and then joined. In eukaryotes, this repair pathway is initiated by the binding of the ring-shaped Ku heterodimer and completed by DNA ligase IV. The DNA ligase IV complex, DNA ligase IV/XRRC4 in humans and Dnl4/Lif1 in yeast, is recruited to DNA ends in vitro and in vivo by an interaction with Ku and, in yeast, Dnl4/Lif1 stabilizes the binding of yKu to in vivo DSBs. Here we have analyzed the interactions of these functionally conserved eukaryotic NHEJ factors with DNA by electron microscopy. As expected, the ring-shaped Ku complex bound stably and specifically to DNA ends at physiological salt concentrations. At a ratio of 1 Ku molecule per DNA end, the majority of DNA ends were occupied by a single Ku complex with no significant formation of linear DNA multimers or circular loops. Both Dnl4/Lif1 and DNA ligase IV/XRCC4 formed complexes with Ku-bound DNA ends, resulting in intra- and intermolecular DNA end bridging, even with non-ligatable DNA ends. Together, these studies, which provide the first visualization of the conserved complex formed by Ku and DNA ligase IV at juxtaposed DNA ends by electron microscopy, suggest that the DNA ligase IV complex mediates end-bridging by engaging two Ku-bound DNA ends.     

Organization and dynamics of the proteolipid complexes formed by annexin V and lipids in planar supported lipid bilayers

The consequences of the binding of annexin V on its lateral mobility and that of lipids were investigated by means of experimental and simulated FRAP experiments. Experiments were carried out on planar supported bilayers (PC/PS 9:1 mol/mol mixtures) in the presence of 1 mM CaCl2 in the subphase. The probes C12-NBD-PS and fluorescein-labeled annexin V were used and the data compared with that previously obtained for C12-NBD-PC [Saurel, O., Cézanne, L., Milon, A., Tocanne, J. F., & Demange, P. (1998) Biochemistry 37, 1403-1410]. At complete coverage of the lipid bilayer by the protein (Cannexin = 80 nM), the lateral mobility of C12-NBD-PC was reduced by 40% while C12-NBD-PS and bound annexin V molecules were nearly immobilized (D < 10(-)11 cm2/s). At moderate protein concentration (20 nM < Cannexin < 80 nM), best fitting of the lipid and protein probe recoveries was achieved with one single diffusion coefficient and a mobile fraction close to 100%, indicating homogeneous lipid and protein populations. In contrast, at low protein concentration (Cannexin < 20 nM), C12-NBD-PS showed a two-component diffusion. The slow PS population at Cannexin < 20 nM and the single PS population at Cannexin > 20 nM moved at the same rate that bound annexin V (mobile fraction close to 100%), indicating strong PS/protein interactions. With the aid of computer simulations of the lateral motion of PC molecules, based on the 2-D crystalline networks formed by annexin V in contact with the lipid bilayer, these FRAP results may be accounted for by considering a rather simple model of a proteolipidic complex consisting of an extended 2-D crystalline protein network facing the lipid bilayer and stabilized by strong interactions between annexin V and PS molecules. In this model, immobilization of annexin V and PS molecules originates from their mutual interactions. The slowing down of PC molecules is due to various obstacles to their lateral diffusion which can be described as: the four PS molecules bound to the protein, the tryptophan 187 which presumably interacts with the lipids at the level of their polar headgroups and probably the three other hydrophobic amino acid residues located on the AB calcium-binding loops of the protein.     

Binuclear monofunctional platinum(II) complexes formed by hexaazamacrocyclic bisdien ligands: Crystal structure, DNA binding and cytotoxicity studies

Two binuclear 3N-chelated monofunctional Pt^II complexes, [Pt₂L1Cl₂]Cl₂ (complex III) and [Pt₂L2Cl₂]Cl₂ (complex IV) [L1 = 3,6,9,16,19,22-hexaazatricyclo[22.2.2.2^11,14]-triaconta-11,13,24,26(1),27,29-hexaene, L2 = 3,6,9,17,20,23-hexaazatricyclo[23.3.1.1^11,15]-triaconta-1(29),11(30),12,14,25,27-hexaene] have been synthesized and structurally characterized. Structural determination revealed that each Pt^II center was coordinated by one chloride anion and three N atoms from each diethylenediamine motif. The Pt-Cl bonds in complex III are shorter than those found in complex IV. The rigid para- and meta-xylylene groups make the two complexes adopt a rigid boat-like conformation and a flexible twisted chair-like conformation, respectively. Moreover, complex III has higher tendency to bind with each other than complex IV. DNA binding studies demonstrated that complex IV could bind effectively with calf thymus DNA, possibly via platination of N7 of guanine residue, while no obvious DNA binding was observed for complex III. However, complex III displays a comparable cytotoxicity to cisplatin against HeLa cell line, while compound IV does not show any effective cell inhibition at low concentration. Therefore, the rigid spacers in complexes III and IV play a determining role in their anti-cancer activity and DNA binding ability.     

Protein phase behavior in aqueous solutions: crystallization, liquid-liquid phase separation, gels, and aggregates

The aggregates and gels commonly observed during protein crystallization have generally been considered disordered phases without further characterization. Here their physical nature is addressed by investigating protein salting-out in ammonium sulfate and sodium chloride for six proteins (ovalbumin, ribonuclease A, soybean trypsin inhibitor, lysozyme, and β-lactoglobulin A and B) at 4°C, 23°C, and 37°C. When interpreted within the framework of a theoretical phase diagram obtained for colloidal particles displaying short-range attractive interactions, the results show that the formation of aggregates can be interpreted theoretically in terms of a gas-liquid phase separation for aggregates that are amorphous or gel-like. A notable additional feature is the existence of a second aggregation line observed for both ovalbumin and ribonuclease A in ammonium sulfate, interpreted theoretically as the spinodal. Further investigation of ovalbumin and lysozyme reveals that the formation of aggregates can be interpreted, in light of theoretical results from mode-coupling theory, as a kinetically trapped state or a gel phase that occurs through the intermediate of a gas-liquid phase separation. Despite the limitations of simple theoretical models of short-range attractive interactions, such as their inability to reproduce the effect of temperature, they provide a framework useful to describe the main features of protein phase behavior.     

Sheet and chain polymeric transition metal complexes formed by N,N-o-phenylenedimethylenebis(pyridin-4-one)

The preparations are reported of the ‘extended reach’ ligand N,N^′-o-phenylene-dimethylenebis(pyridin-4-one) (o-XBP4) and of a range of its metal complexes with Mn(II), Co(II), Ni(II), Cu(II) and Zn(II), two of which have been shown by X-ray studies to have polymeric structures. In the compound [Mn(o-XBP4)(H₂O)₂(NO₃)](NO₃) the o-XBP4 ligands link ‘Mn(H₂O)₂(NO₃)’ units into chains which are then cross-linked into sheets by the bridging action of the coordinated nitrate. In [Cu(o-XBP4)(NO₃)₂] chains are also formed by the bridging action of the o-XBP4 ligands but here they simply pack trough-in-trough with no nitrate cross-linking. X-band EPR spectra are reported for these and the other Mn and Cu compounds as are relevant spectroscopic results for the other complexes.