Ruthenium-caged antisense morpholinos for regulating gene expression in zebrafish embryos

Photochemical approaches afford high spatiotemporal control over molecular structure and function, for broad applications in materials and biological science. Here, we present the first example of a visible light responsive ruthenium-based photolinker, Ru(bipyridine)₂(3-ethynylpyridine)₂ (RuBEP), which was reacted stoichiometrically with a 25mer DNA or morpholino (MO) oligonucleotide functionalized with 3′ and 5′ terminal azides, via Cu(i)-mediated [3+2] Huisgen cycloaddition reactions. RuBEP-caged circular morpholinos (Ru-MOs) targeting two early developmental zebrafish genes, chordin and notail, were synthesized and tested in vivo. One-cell-stage zebrafish embryos microinjected with Ru-MO and incubated in the dark for 24 h developed normally, consistent with caging, whereas irradiation at 450 nm dissociated one 3-ethynylpyridine ligand (Φ = 0.33) and uncaged the MO to achieve gene knockdown. As demonstrated, Ru photolinkers provide a versatile method for controlling structure and function of biopolymers.     

Dications of benzylidenefluorene and diphenylmethylidene fluorene: the relationship between magnetic and energetic measures of antiaromaticity

Oxidation of m- and p-substituted benzylidene fluorenes to antiaromatic dications was attempted by electrochemical and chemical means. Electrochemical oxidation to dications was successful for benzylidene fluorenes with p-methoxy, p-methyl, p-fluoro, and unsubstituted phenyl rings in the 3-position; attempts to oxidize the m-substituted derivatives via electrochemistry were unsuccessful. Chemical oxidation with SbF(5)/SO(2)ClF gave the dication of 9-[(4-methoxyphenyl)methylene]-9H-fluorene cleanly; oxidation of all other substituted benzylidene fluorenes resulted in mixtures of products. The excellent linear relationship between the chemical shifts calculated by the GIAO method and the experimental shifts for the p-methoxy-substituted benzylidene fluorene dication suggests that the calculations satisfactorily reflect the magnetic properties of this dication and potentially those of the other dications studied. The redox potentials from electrochemical oxidation, a measure of the stability of the dications, showed a good linear relationship with another measure of stability, the calculated difference in energy between each dication and its neutral precursor. The dications of benzylidene fluorenes were less stable than the dications of diphenylmethylidene fluorenes; within each type of compound, dications with p-substituted phenyl rings were more stable than dications with m-substituted phenyl rings and dications with phenyl rings substituted with electron-donating groups were more stable than dications with phenyl rings substituted with electron-withdrawing groups. The antiaromaticity of the fluorenyl system was assessed through the nucleus-independent chemical shift (NICS) that was also calculated by the GIAO method. The plot of the NICS values per square area versus the calculated energy difference for the dications showed a moderate degree of linearity; the plot of NICS values per square area versus the oxidation potentials was less linear. Thus, a suggestive, but not conclusive, relationship between magnetic and energetic measures of antiaromaticity was observed.     

Efficient Krylov subspace methods for uncertainty quantification in large Bayesian linear inverse problems

Uncertainty quantification for linear inverse problems remains a challenging task, especially for problems with a very large number of unknown parameters (e.g., dynamic inverse problems) and for problems where computation of the square root and inverse of the prior covariance matrix are not feasible. This work exploits Krylov subspace methods to develop and analyze new techniques for large‐scale uncertainty quantification in inverse problems. In this work, we assume that generalized Golub‐Kahan‐based methods have been used to compute an estimate of the solution, and we describe efficient methods to explore the posterior distribution. In particular, we use the generalized Golub‐Kahan bidiagonalization to derive an approximation of the posterior covariance matrix, and we provide theoretical results that quantify the accuracy of the approximate posterior covariance matrix and of the resulting posterior distribution. Then, we describe efficient methods that use the approximation to compute measures of uncertainty, including the Kullback‐Liebler divergence. We present two methods that use the preconditioned Lanczos algorithm to efficiently generate samples from the posterior distribution. Numerical examples from dynamic photoacoustic tomography demonstrate the effectiveness of the described approaches.     

Sharp melting of polymer-DNA hybrids: an associative phase separation approach

An associative equilibrium theory describing the sharp melting behavior of polymer-DNA hybrids is developed. The theory considers linear polymers with attached DNAs on each polymer that serve as "stickers" and with a two-state model governing the DNA melting equilibrium. For three or more oligonucleotides on each polymer, solutions of polymer-DNA hybrids are found to undergo phase separation at sufficiently low temperatures. The dense phase dissolves as temperature increases, which leads to a sharp increase in the fraction of non-hybridized DNA near the phase transition temperature, in agreement with experimental absorbance profiles at 260 nm. The melting temperature is predicted to have the same dependence on salt concentration as a solution of unattached DNAs and be weakly sensitive to the concentration of DNA in solution. The melting temperature is predicted to be higher than that of unattached DNA in solution, with the magnitude of the increase sensitive to the DNA hybridization cooperativity. The theoretical predictions are generally in good quantitative agreement with new experimental data (also presented here), which show the effect of the polymer-DNA hybrid length and salt concentration on the melting profiles.     

Multifunctional polymeric nanoparticles from diverse bioactive agents

We present a rational approach for assembling diverse bioactive agents, such as DNA, proteins, and drug molecules, into core-shell multifunctional polymeric nanoparticles (PNPs) that can be internalized in human breast cancer cells. Using ring-opening metathesis polymerization (ROMP), block copolymers containing small-molecule drug segments (>50% w/w) and tosylated hexaethylene glycol segments were prepared and assembled into PNPs that allowed for the surface conjugation of single-stranded DNA sequences and/or tumor-targeting antibodies. The resulting antibody-functionalized particles were readily uptaken by breast cancer cells that overexpressed the corresponding antigens.