Assembly of complimentary naphthyl units in nucleotidomimetic foldamers

The large and complex architectures found in biomolecules not only are an amazing feat of molecular construction, but they also function to carry out all the processes necessary to sustain a living organism. For the organic chemist and biochemist that wish to mimic, improve or modify the structure and function of such natural molecular architectures, an understanding of non-covalent interactions in solution is necessary. In order to probe the particular inter- and intramolecular interactions involved in constructing higher order molecular architectures, the study of foldamers, small synthetic oligomers that adopt well-defined conformations in solution, has emerged. Our lab has been studying the particular interaction between complementary aromatic units, 1,4,5,8-naphthalenetetracarboxylic acid diimide (NDI) and 1,5-dialkoxynaphthalene (DAN) and their ability to drive the construction of aromatic foldamers in aqueous environments. Utilizing flexible peptide linked units of DAN and NDI, our lab has constructed a variety of unique folding assemblies. From the very first aromatic foldamer that folds into a pleated secondary structure in water to a heteroduplex system assembling oligo-DAN and oligo-NDI units in an intertwined fashion, the use of these complementary aromatic units has proven its versatility in foldamer assembly. Generally, this dissertation describes studies of the first NDI and DAN deoxyribonucleic acid oligonucleotides. While our previous foldamer assemblies utilized peptide linkers to string together DAN and NDI units, the work described herein draws inspiration from the sugar-phosphate backbone of DNA to assemble aromatic units. Chapter 2 describes the design and synthesis of 4,4’-dimethoxytrityl protected DAN and NDI phosphoramidites that can subsequently be incorporated into strands of natural DNA oligonucleotides using automated solid phase oligonucleotide synthesis. Chapter 3 investigates the insertion of a 3 base pair region of varying sequences of DAN and NDI into a 12-mer DNA oligonucleotide to explore the effect of DAN and NDI on duplex structure and stability. Chapter 4 describes the stability and structure of a 9-mer DNA oligonucleotide that incorporates two NDI-DAN-NDI triplet sequences either inserted into the interior of the duplex or appended at the terminal positions of the duplex. The NDI-DAN-NDI triplets appended to the terminal positions led to a profound increase in duplex stability (in comparison to internal positions), significantly beyond that seen with analogous sequences of G-C base pairs.Chemistr

The effect of temperature and salinity acclimation on the respiration rate of a marine polychaete, Serpula vermicularis L.

In January 1970, collections of Serpula vermicularis L. were obtained from Bray Point, Oregon, for the purpose of determining the effect of acclimation to salinity and temperature on its rate of respiration. The worms were removed from their tubes and acclimated to one of three salinities (28.8%₀, 31.1%₀, or 35.9%₀) and one of two temperatures (10°C or 15°C). Following a two-week acclimation period, measurements of the rates of respiration were made at 10°C, 15°C, 20°C, 25°C, and 30°C. The results of these measurements revealed that acclimation to salinity has no effect on the rate of respiration of Serpula vermicularis. This indicates that the serpulids had undergone complete compensation to these salinities. In comparing the rates of respiration of serpulids acclimated to different temperatures, it was found that the cold acclimated worms had higher rates of respiration than the warm acclimated worms at all experimental temperatures. The results of acclimation to temperature might be used to compare serpulids from different geographical areas. Perhaps such experiments would enable the researcher to gain insight into the variability of temperature regimes in different geographical locations by measuring the rates of respiration of serpulids collected in these areas

Subtle Recognition of 14-Base Pair DNA Sequences via Threading Polyintercalation

ABSTRACT: Small molecules that bind DNA in a sequence-specific manner could act as antibiotic, antiviral, or anticancer agents because of their potential ability to manipulate gene expression. Our laboratory has developed threading poly-intercalators based on 1,4,5,8-naphthalene diimide (NDI) units connected in a head-to-tail fashion by flexible peptide linkers. Previously, a threading tetraintercalator composed of alternating minor−major−minor groove-binding modules was shown to bind specifically to a 14 bp DNA sequence with a dissociation half-life of 16 days [Holman, G. G., et al. (2011) Nat. Chem. 3, 875−881]. Herein are described new NDI-based tetraintercalators with a different major groove-binding module and a reversed N to C directionality of one of the minor groove-binding modules. DNase I footprinting and kinetic analyses revealed that these new tetraintercalators are able to discriminate, by as much as 30-fold, 14 bp DNA binding sites that differ by 1 or 2 bp. Relative affinities were found to correlate strongly with dissociation rates, while overall C2 symmetry in the DNA-binding molecule appeared to contribute to enhanced association rates

NDI and DAN DNA: Nucleic Acid-Directed Assembly of NDI and DAN

Two novel DNA base surrogate phosphoramidites <b>1</b> and <b>2</b>, based upon relatively electron-rich 1,5-dialkoxynaphthalene (DAN) and relatively electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (NDI), respectively, were designed, synthesized, and incorporated into DNA oligonucleotide strands. The DAN and NDI artificial DNA bases were inserted within a three-base-pair region within the interior of a 12-mer oligonucleotide duplex in various sequential arrangements and investigated with CD spectroscopy and UV melting curve analysis. The CD spectra of the modified duplexes indicated B-form DNA topology. Melting curve analyses revealed trends in DNA duplex stability that correlate with the known association of DAN and NDI moieties in aqueous solution as well as the known favorable interactions between NDI and natural DNA base pairs. This demonstrates that DNA duplex stability and specificity can be driven by the electrostatic complementarity between DAN and NDI. In the most favorable case, an NDI–DAN–NDI arrangement in the middle of the DNA duplex was found to be approximately as stabilizing as three A–T base pairs

Subtle Recognition of 14-Base Pair DNA Sequences via Threading Polyintercalation

Small molecules that bind DNA in a sequence-specific manner could act as antibiotic, antiviral, or anticancer agents because of their potential ability to manipulate gene expression. Our laboratory has developed threading polyintercalators based on 1,4,5,8-naphthalene diimide (NDI) units connected in a head-to-tail fashion by flexible peptide linkers. Previously, a threading tetraintercalator composed of alternating minor–major–minor groove-binding modules was shown to bind specifically to a 14 bp DNA sequence with a dissociation half-life of 16 days [Holman, G. G., et al. (2011) <i>Nat. Chem. 3</i>, 875–881]. Herein are described new NDI-based tetraintercalators with a different major groove-binding module and a reversed N to C directionality of one of the minor groove-binding modules. DNase I footprinting and kinetic analyses revealed that these new tetraintercalators are able to discriminate, by as much as 30-fold, 14 bp DNA binding sites that differ by 1 or 2 bp. Relative affinities were found to correlate strongly with dissociation rates, while overall <i>C</i>₂ symmetry in the DNA-binding molecule appeared to contribute to enhanced association rates