Nucleic acids that contain multiple sequential guanines assemble into guanine quadruplexes (G-quadruplexes). Drugs that induce or stabilize G-quadruplexes are of interest because of their potential use as therapeutics. Previously, we reported on the interaction of the Cu(2+) derivative of 5,10,15,20-tetrakis(1-methyl-4-pyridyl)-21H,23H-porphine (CuTMpyP4), with the parallel-stranded G-quadruplexes formed by d(T(4)G( n )T(4)) (n = 4 or 8) (Keating and Szalai in Biochemistry 43:15891-15900, 2004). Here we present further characterization of this system using a series of guanine-rich oligonucleotides: d(T(4)G( n )T(4)) (n = 5-10). Absorption titrations of CuTMpyP4 with all d(T(4)G( n )G(4)) quadruplexes produce approximately the same bathochromicity (8.3 +/- 2 nm) and hypochromicity (46.2-48.6%) of the porphyrin Soret band. Induced emission spectra of CuTMpyP4 with d(T(4)G( n )T(4))(4) quadruplexes indicate that the porphyrin is protected from solvent. Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry revealed a maximum porphyrin to quadruplex stoichiometry of 2:1 for the shortest (n = 4) and longest (n = 10) quadruplexes. Electron paramagnetic resonance spectroscopy shows that bound CuTMpyP4 occupies magnetically noninteracting sites on the quadruplexes. Consistent with our previous model for d(T(4)G(4)T(4)), we propose that two CuTMpyP4 molecules are externally stacked at each end of the run of guanines in all d(T(4)G( n )T(4)) (n = 4-10) quadruplexes.

Fluorescence of unmodified oligonucleotides has not been exploited for guanine‐quadruplex (G‐quadruplex) characterization. We observe that G‐rich sequences fluoresce more strongly than duplex or single‐stranded DNA but much more weakly than fluorophores like fluorescein. This increase in the intrinsic fluorescence is not due to an increase in absorption at the excitation wavelength but rather to a change in the quantum yield. We show that unlabeled oligonucleotides that form G‐quadruplexes can be differentiated on the basis of their emission spectra from similar sequences that do not contain consecutive guanines. Intermolecular quadruplexes formed by the oligonucleotides 5′‐T4GnT4‐3′ (n = 4–10) display a nonlinear, but continuous, increase in emission intensity as the G content increases. The sequence 5′‐GGGT‐3′, which has been proposed to form a monomeric quadruplex and an interlocked quadruplex (Krishnan‐Ghosh et al. J Am Chem Soc 2004, 126, 11009), was compared with the similar sequence 5′‐TGGG‐3′, the structure of which has not been characterized. Both the maximum emission intensity and the spectral shape differ for these oligonucleotides as a function of sample preparation, indicating that different types of quadruplexes form for both sequences. Our work is the first to demonstrate that the suprastructure of G‐rich sequences can be probed using fluorescence signatures of unmodified oligonucleotides. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 841–850, 2009.This article was originally published online as an accepted preprint. The ”Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Perpendicular magnetic anisotropy (PMA) in transition metal thin films offers a pathway for enabling the interesting physics of nanomagnetism and developing a wide range of spintronics applications. We demonstrate a simple method to obtain Ni thin films with PMA by depositing them onto nanoporous anodic alumina membranes (NPAAMs), with different pore diameters varying in the range between 32 ± 2 and 93 ± 1 nm. Thus, several sets of Ni antidot arrays thin films have been fabricated with different hole diameters, 35 nm ≤ d ≤ 89 nm, and fixed interhole distances, D int , around 103 ± 2 nm but reducing the edge-to-edge separation between adjacent antidots, (W = D int − d), and in two different situations, by considering that W is well above or below the layer thickness, t, of the thin film. The crossover from the in-plane magnetization to out of plane magnetization in a ferromagnetic thin film has been achieved by modifying only the nanopore size of the patterned anodic alumina template and the experimental results were supported by micromagnetic simulations performed with Mumax 3 code. A dramatic change in the coercivity, H C , dependence with d and W parameters has been observed with a critical nanohole diameter, d c , at which the appearance of the perpendicular magnetization is observed. The decreasing of the inplane coercivity for samples with d > 75 nm is due to the weakened of the in-plane magnetic anisotropy and the rising of the out of plane component. The effective perpendicular magnetic anisotropy energy density for Ni antidot thin film with d = 90 nm and t = 20 nm is around 1.44 erg/cm 2 , larger than that obtained by traditional approaches for Ni films with PMA (0.03−0.2 erg/cm 2 ). These findings point toward antidot thin films as novel routes to engineer the magnetic behavior of ferromagnetic metal with large PMA, which might entail a milestone for future applications in bit patterned magneto-optic perpendicular recording media and spintronic devices.

We consider the numbers arising in the problem of normal ordering of expressions in boson creation a † and annihilation a operators ([a, a † ] = 1). We treat a general form of a boson string (a † ) rn a sn ...(a † ) r2 a s2 (a † ) r1 a s1 which is shown to be associated with generalizations of Stirling and Bell numbers. The recurrence relations and closed-form expressions (Dobiński-type formulas) are obtained for these quantities by both algebraic and combinatorial methods. By extensive use of methods of combinatorial analysis we prove the equivalence of the aforementioned problem to the enumeration of special families of graphs. This link provides a combinatorial interpretation of the numbers arising in this normal ordering problem.

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Design of novel multisegmented magnetic nanowires can pave the way for the next generation of data storage media and logical devices, magnonic crystals, or in magneto-plasmonics, among other energy conversion, recovery, and storage technological applications. In this work, we present a detailed study on the synthesis, morphology, structural, and magnetic properties of Ni, Co, and Ni-Co alloy and multisegmented Ni/Co nanowires modulated in composition, which were grown by template-assisted electrodeposition employing nanoporous anodic aluminum oxide as patterned templates. X-ray diffraction, and scanning and high-resolution transmission electron microscopies allowed for the structural, morphological, and compositional investigations of a few micrometers long and approximately 40 nm in diameter of pure Ni and Co single elements, together with multisegmented Ni/Co and alloyed Ni-Co nanowires. The vibrating sample magnetometry technique enabled us to extract the main characteristic magnetic parameters for these samples, thereby evaluating their different anisotropic magnetic behaviors and discuss them based on their morphological and structural features. These novel functional magnetic nanomaterials can serve as potential candidates for multibit magnetic systems in ultra-high-density magnetic data storage applications.

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We have fabricated a DNA-based nanofiber created by self-assembly of guanine quadruplex (Hoogsteen base pairing) and double-stranded DNA (Watson-Crick base pairing). When duplexes containing a long stretch of contiguous guanines and single-stranded overhangs are incubated in potassium-containing buffer, the preformed duplexes create high molecular weight species that contain quadruplexes. In addition to observation of these larger species by gel electrophoresis, solutions were analyzed by atomic force microscopy to reveal nanofibers. Analysis of the atomic force microscopy images indicates that fibers form with lengths ranging from 250 to 2,000 nm and heights from 0.45 to 4.0 nm. This work is a first step toward the creation of new structurally heterogeneous (quadruplex/duplex), yet controllable, DNA-based materials exhibiting novel properties suitable for a diverse array of nanotechnology applications.