Wendi M. David

Threshold dissociation energies of protonated amine/polyether complexes in a quadrupole ion trap.

Electrospray ionization mass spectrometry (ESI-MS) is increasingly used to probe the nature of noncovalent complexes; however, assessing the relevance of gas-phase results to structures of complexes in solution requires knowledge of the types of interactions that are maintained in a solventless environment and how these might compare to key interactions in solution. This study addresses the factors impacting the strength of hydrogen bonding noncovalent interactions in the gas phase. Hydrogen bonded complexes consisting of ammonium ions bound to polydentate ethers are transported to the gas phase with ESI, and energy-variable collisional activated dissociation (CAD) is used to map the relative dissociation energies. The measured relative dissociation energies are correlated with the gas-phase basicities and steric factors of the amine and polyether constituents. To develop correlations between hydrogen bonding strength and structural features of the donor and acceptor molecules, a variety of amines with different gas-phase basicities and structures were selected, including primary, secondary, and tertiary amines, as well as those that are bidentate to promote intramolecular hydrogen bonding. The acceptor molecules are polydentate ethers, such as 18-crown-6. Four primary factors influence the observed dissociation energies of the polyether/ammonium ion complexes: the gas-phase basicities of the polyether and amine, steric effects of the amines, conformational flexibility of the polyethers, and the inhibition of intramolecular hydrogen bonds of the guest ammonium ions in the resulting ammonium/polyether noncovalent complexes.

Simian virus 40 large T-antigen G-quadruplex DNA helicase inhibition by G-quadruplex DNA-interactive agents.

On the basis of growing evidence for G-quadruplex DNA structures in genomic DNA and the presumed need to resolve these structures for DNA replication, the G-quadruplex DNA unwinding ability of a prototypical replicative helicase, SV40 large T-antigen (T-ag), was investigated. Here, we demonstrate that this G-quadruplex helicase activity is robust and comparable to the duplex helicase activity of T-ag. Analysis of the SV40 genome demonstrates the presence of sequences that may form intramolecular G-quadruplexes, which are the presumed natural substrates for the G-quadruplex helicase activity of T-ag. A number of G-quadruplex-interactive agents as well as new perylene diimide (PDI) derivatives have been investigated as inhibitors of both the G-quadruplex and the duplex DNA helicase activities of T-ag. A unique subset of these G-quadruplex-interactive agents inhibits the G-quadruplex DNA unwinding activity of T-ag, relative to those reported to inhibit G-quadruplex DNA unwinding by RecQ-family helicases. We also find that certain PDIs are both potent and selective inhibitors of the G-quadruplex DNA helicase activity of T-ag. Surface plasmon resonance and fluorescence spectroscopic G-quadruplex DNA binding studies of these T-ag G-quadruplex helicase inhibitors have been carried out, demonstrating the importance of attributes in addition to binding affinity for G-quadruplex DNA that may be important for inhibition. The identification of potent and selective inhibitors of the G-quadruplex helicase activity of T-ag provides tools for probing the specific role of this activity in SV40 replication.

Synthesis of a heterocyclic aza-enediyne and its DNA-cleavage properties.

The benzimidazolium salt 2, incorporating an aza-enediyne moiety, has been prepared and is shown to be a very effective DNA-cleavage agent under mild physiological conditions. Its mechanism of action is currently under investigation but may involve the generation of a diradical intermediate. DNA alkylation, or both.

N-propargyl-2-alkynylbenzothiazolium aza-enediynes: role of the 2-alkynylbenzothiazolium functionality in DNA cleavage.

The 2-alkynylbenzothiazolium salts 3a-d incorporating an N-propargyl moiety have been prepared as aza-enediyne analogues. While these aza-enediynes are shown to be modest DNA cleavage agents, DNA cleavage was also observed with the N-methyl-2-alkynylbenzothiazolium salt 4, which lacks the aza-enediyne moiety. The structural requirements for DNA cleavage, and the correlation of DNA cleavage efficiency with the propensity of these compounds to undergo nucleophilic addition by methanol support a proposed DNA cleavage mechanism involving DNA alkylation by appropriate 2-alkynyl-substituted benzothiazolium salts.

Self-assembling Dimeric and Trimeric Aggregates Based on Solvophobic and Charge-pairing Interactions

Self-assembly processes based on shape complementarity and noncovalent binding interactions are widely recognized as a fundamental principle in nature. Besides charge pairing and hydrogen bonding, hydrophobic interactions play a crucial role in water. Here we report the self-assembly of structurally simple monomers to yield defined dimeric and trimeric aggregates in highly polar media, based on ionic and solvophobic interactions. NMR, mass spectrometry and curve fitting were used to characterize these supramolecular assemblies in water–methanol solutions.