Mimicking the Structure and Function of DNA: Insights into DNA Stability and Replication

The physical and chemical factors that allow DNA to perform its functions in the cell have been studied for several decades. Recent advances in the synthesis and manipulation of DNA have allowed this field to move ahead especially rapidly during the past fifteen years. One of the most common chemical approaches to the study of interactions involving DNA has been the use of DNA base analogues in which functional groups are added, deleted, blocked, or rearranged. Here we describe a different strategy, in which the polar natural DNA bases are replaced by nonpolar aromatic molecules of the same size and shape. This allows the evaluation of polar interactions (such as hydrogen bonding) with little or no interference from steric effects. We have used these nonpolar nucleoside isosteres as probes of noncovalent interactions such as DNA base pairing and protein - DNA recognition. We have found that, while base-pairing selectivity does depend on Watson - Crick hydrogen bonding in the natural pairs, it is possible to design new bases that pair selectively and stably in the absence of hydrogen bonds. In addition, studies have been carried out with DNA polymerase enzymes to investigate the importance of Watson - Crick hydrogen bonding in enzymatic DNA replication. Surprisingly, this hydrogen bonding is not necessary for efficient enzymatic synthesis of a base pair, and significant levels of selectivity can arise from steric effects alone. These results may have significant impact both on the study of basic biomolecular interactions and in the design of new, functionally active biomolecules.     

Oligodeoxyfluorosides: Strong Sequence Dependence of Fluorescence Emission

We describe the properties of a series of oligomeric polyfluorophores assembled on the DNA backbone. The 11 oligomers (oligodeoxyfluorosides, ODFs), 4-7 monomers in length, were composed of only two fluorescent monomers and a spacer in varied sequences, and were designed to test how fluorescent nucleobases can interact electronically to yield complexity in fluorescence emission. The monomer fluorophores were deoxyribosides of pyrene and perylene, which emit light in violet and blue wavelengths, respectively. The experiments show that simple variation in sequence and spacing can dramatically change fluorescence, yielding emission maxima ranging from 380 to 557 nm and visible colors from violet to orange-red. Fluorescence lifetime data, excitation spectra, and absorption data point to a number of multi-fluorophore electronic interactions, including pyrene-pyrene and perylene-perylene excimers, pyrene-perylene exciplexes, as well as monomer dye emissions, contributing to the final spectral outcomes. Thus, two simple fluorophores can be readily combined to give emissions over much of the visible spectrum, all requiring only a single excitation. The results demonstrate that fluorescent nucleobases in oligomeric form can act cooperatively as electronic units, and that fluorophore sequence in such oligomers is as important as fluorophore composition in determining fluorescence properties.     

Imaging of RNA in bacteria with self-ligating quenched probes

We report on the application of a new class of oligonucleotide reporter probes, QUAL probes, that "light up" when a nucleophilic phosphorothioate probe binds adjacent to a dabsyl-quenched probe. These self-ligating DNA probes were used for sequence-specific detection of 16S rRNA in Escherichia coli cells. Strong fluorescence was observed only when the phosphorothioate and quenched dabsyl probes bind side-by-side on a 16S rRNA target. The results demonstrate the use of QUAL probes to detect specific RNA sequences in bacterial cells without enzymes and without washing steps.     

Solution structure of xDNA: a paired genetic helix with increased diameter

We describe the structure in aqueous solution of an extended-size DNA-like duplex with base pairs that are approximately 2.4 A longer than those of DNA. Deoxy-lin-benzoadenosine (dxA) was employed as a dA analogue to form hydrogen-bonded base pairs with dT. The 10mer self-complementary extended oligodeoxynucleotide 5'-d(xATxAxATxATTxAT) forms a much more thermodynamically stable duplex than the corresponding DNA sequence, 5'-d(ATAATATTAT). NMR studies show that this extended DNA (xDNA) retains many features of natural B-form DNA, but with a few structural alterations due to its increased helical diameter. The results give insight into the structural plasticity of the natural DNA backbone and lend insight into the evolutionary origins of the natural base pairs. Finally, this structural study confirms the hypothesis that extended nucleobase analogues can form stable DNA-like structures, suggesting that alternative genetic systems might be viable for storage and transfer of genetic information.     

Artificial Genetic Sets Composed of Size‐Expanded Base Pairs

We describe in this Minireview the synthesis, properties, and applications of artificial genetic sets built from base pairs that are larger than the natural Watson–Crick architecture. Such designed systems are being explored by several research groups to investigate basic chemical questions regarding the functions of the genetic information storage systems and thus of the origin and evolution of life. For example, is the terrestrial DNA structure the only viable one, or can other architectures function as well? Working outside the constraints of purine–pyrimidine geometry provides more chemical flexibility in design, and the added size confers useful properties such as high binding affinity and helix stability as well as fluorescence. These features are useful for the investigation of fundamental biochemical questions as well as in the development of new biotechnological, biomedical, and nanostructural tools and methods.     

Morphological regimes of poly(ε-caprolactone)/octaisobutyl polyhedral oligosilsesquioxane composite films in relation to film composition and thickness

The morphological evolution of poly(ε-caprolactone) (PCL)/octaisobutyl polyhedral oligomeric silsesquioxane (IBUPOSS) films was analyzed using scanning electron microscopy (SEM) and polarized optical microscopy (POM). The morphologies of the blend films with PCL/IBUPOSS mass ratios of 95:5 to 50:50 were discussed according to decomposition mechanism in relation to film composition and thickness. In addition to the morphological regime for films with lower IBUPOSS loadings, in which the growth of PCL spherulites was nearly independent on the presence of fine IBUPOSS aggregates, two new morphological regimes were observed for the films with higher IBUPOSS loadings: (1) thicker blend films exhibited a rich dynamics, giving rise to a trilayer structure and (2) the decomposition of thinner films was induced by the kinetically controlled growth of IBUPOSS aggregates. By varying the thickness and the composition of the blend films, the current study provides important new insight into the rich phase behavior of nanoparticle-filled polymer films.     

Libraries of composite polyfluors built from fluorescent deoxyribosides

We report on a new class of water-soluble fluorescent molecules (polyfluors) that are composed of multiple individual fluorophores assembled on a DNA-like backbone. Four fluorophore deoxyribosides were synthesized, and these individual molecules were assembled into oligofluor strings on a DNA synthesizer. A library of 256 tetrafluors was generated by split and pool methods on polystyrene beads. Images of the library under a fluorescence microscope revealed at least 40-50 different hues and intensities. Selected tetrafluors were resynthesized in pure form in solution and displayed properties, such as large Stokes shifts, that individual fluorophores do not have.     

ON THE CONVERGENCE OF THE PARABOLIC APPROXIMATION OF A CONSERVATION LAW IN SEVERAL SPACE DIMENSIONS

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