G-rich DNA sequences are able to fold into structures called G-quadruplexes. To obtain general trends in the influence of loop length on the structure and stability of G-quadruplex structures, we studied oligodeoxynucleotides with random bases in the loops. Sequences studied are dGGGW(i)GGGW(j)GGGW(k)GGG, with W = thymine or adenine with equal probability, and i, j, and k comprised between 1 and 4. All were studied by circular dichroism, native gel electrophoresis, UV-monitored thermal denaturation, and electrospray mass spectrometry, in the presence of 150 mM potassium, sodium, or ammonium cations. Parallel conformations are favored by sequences with short loops, but we also found that sequences with short loops form very stable multimeric quadruplexes, even at low strand concentration. Mass spectrometry reveals the formation of dimers and trimers. When the loop length increases, preferred quadruplex conformations tend to be more intramolecular and antiparallel. The nature of the cation also has an influence on the adopted structures, with K(+) inducing more parallel multimers than NH4(+) and Na(+). Structural possibilities are discussed for the new quadruplex higher-order assemblies.

DNA triplex and quadruplex structures have been successfully detected by electrospray mass spectrometry. Circular dichroism and UV-melting experiments show that these structures are stable in 150 mM ammonium acetate at pH = 7 for the quadruplexes and pH = 5.5 for the triplexes. The studied quadruplexes were the tetramer [d(TGGGGT)] 4 , the dimer [d(GGGGTTTTGGGG)] 2 , and the intramolecular folded strand dGGG(TTAGGG) 3 , which is an analog for the human telomeric sequence. The absence of sodium contamination allowed demonstration of the specific inclusion of n-1 ammonium cations in the quadruplex structures, n being the number of consecutive G-tetrads. We also detected the complexes between the quadruplexes and the quadruplex-specific drug mesoporphyrin IX. MS/MS spectra of [d(TGGGGT)] 4 and the complex with the drug are also reported. As the drug does not displace the ammonium cations, one can conclude that the drug binds at the exterior of the tetrads, and not between them. For the triplex structure, the ESI-MS spectra show the detection of the specific triplex, at m/z values typically higher than those typically observed for duplex species. Upon MS/MS the antigene strand, which is bound into the major groove of the duplex, separates from the triplex. This is the same dissociation pathway as in solution. To our knowledge this is the first report of a triplex DNA structure by electrospray mass spectrometry.

The never-ending race towards miniaturization of devices induced an intense research in the manufacturing processes of the components of those devices. However, the complexity of the process combined with high equipment costs makes the conventional lithographic techniques unfavorable for many researchers. Through years, nanosphere lithography (NSL) attracted growing interest due to its compatibility with wafer-scale processes as well as its potential to manufacture a wide variety of homogeneous one-, two-, or three-dimensional nanostructures. This method combines the advantages of both top-down and bottom-up approaches and is based on a two-step process: (1) the preparation of a colloidal crystal mask (CCM) made of nanospheres and (2) the deposition of the desired material through the mask. The mask is then removed and the layer keeps the ordered patterning of the mask interstices. Many groups have been working to improve the quality of the CCMs. Throughout this review, we compare the major deposition techniques to manufacture the CCMs (focusing on 2D polystyrene nanospheres lattices), with respect to their advantages and drawbacks. In traditional NSL, the pattern is usually limited to triangular structures. However, new strategies have been developed to build up more complex architectures and will also be discussed.

Cryptolepine hydrochloride is an indoloquinoline alkaloid isolated from the roots of Cryptolepis sanguinolenta. It is characterized by a multiplicity of host-mediated biological activities, including antibacterial, antiviral, and antimalarial properties. To date, the molecular basis for its diverse biological effects remains largely uncertain. Several lines of evidence strongly suggest that DNA might correspond to its principal cellular target. Consequently, we studied the strength and mode of binding to DNA of cryptolepine by means of absorption, fluorescence, circular, and linear dichroism, as well as by a relaxation assay using DNA topoisomerases. The results of various optical and gel electrophoresis techniques converge to reveal that the alkaloid binds tightly to DNA and behaves as a typical intercalating agent. In DNAase I footprinting experiments it was found that the drug interacts preferentially with GC-rich sequences and discriminates against homo-oligomeric runs of A and T. This study has also led to the discovery that cryptolepine is a potent topoisomerase II inhibitor and a promising antitumor agent. It stabilizes topoisomerase II-DNA covalent complexes and stimulates the cutting of DNA at a subset of preexisting topoisomerase II cleavage sites. Taking advantage of the fluorescence of the indoloquinoline chromophore, fluorescence microscopy was used to map cellular uptake of the drug. Cryptolepine easily crosses the cell membranes and accumulates selectively into the nuclei rather than in the cytoplasm of B16 melanoma cells. Quantitative analyses of DNA in cells after Feulgen reaction and image cytometry reveal that the drug blocks the cell cycle in G2/M phases. It is also shown that the alkaloid is more potent at inhibiting DNA synthesis rather than RNA and protein synthesis. Altogether, the results provide direct evidence that DNA is the primary target of cryptolepine and suggest that this alkaloid is a valid candidate for the development of tumor active compounds.