Expansion of the genetic alphabet has been a long time goal of chemical biology. A third DNA base pair that is stable and replicable would have a great number of practical applications and would also lay the foundation for a semi-synthetic organism. We have reported that DNA base pairs formed between deoxyribonucleotides with large aromatic, predominantly hydrophobic nucleobase analogs, such as propinyl isocarbostyril (dPICS), are stable and efficiently synthesized by DNA polymerases. However, once incorporated into the primer, these analogs inhibit continued primer elongation. More recently, we have found that DNA base pairs formed between nucleobase analogs that have minimal aromatic surface area in addition to little or no hydrogen-bonding potential, such as 3-fluoro benzene (d3FB), are synthesized and extended by DNA polymerases with greatly increased efficiency. Here we show that the rate of synthesis and extension of the self pair formed between two d3FB analogs is sufficient for in vitro DNA replication. To better understand the origins of efficient replication, we examined the structure of DNA duplexes containing either the d3FB or dPICS self pairs. We find that the large aromatic rings of dPICS pair in an intercalative manner within duplex DNA, while the d3FB nucleobases interact in an edge-on manner, much closer in structure to natural base pairs. We also synthesized duplexes containing the 5-methyl substituted derivatives of d3FB (d5Me3FB) paired opposite d3FB or the unsubstituted analog (dBEN). In all, the data suggest that structure, electrostatics and dynamics can all contribute to the extension of unnatural primer termini. The results also help explain the replication properties of many previously examined unnatural base pairs and should help design unnatural base pairs that are better replicated.

Volatile furandiones and aldehydes are significant atmospheric oxidation products of aromatic compounds. The mechanism of secondary organic aerosol formation by these compounds was probed using particle chamber observations and macroscale simulations of condensed phases. Growth of inorganic seed aerosol was monitored in the presence of humidity and high concentrations of 2,5-furandione (maleic anhydride), 3-methyl-2,5-furandione (citraconic anhydride), benzaldehyde, and trans-cinnamaldehyde. Particle growth commenced when the gas-phase saturation level of each organic compound and water vapor (relative to its pure liquid), when summed together, reached a threshold near one, implying the formation of a nearly ideal mixed organic/aqueous phase. However, these organics are immiscible with water at the high mole fractions that would be expected in such a phase. Highly acidic dicarboxylic acids produced by the reactions between furandiones and water were shown to rapidly acidify an aqueous phase, resulting in greatly increased benzaldehyde solubility. Thus, the uptake of these organics onto particles in the presence of humidity appears to be reaction-dependent. Finally, it is shown that dicarboxylic acids produced in these reactions recyclize back to furandiones when subjected to normal GC injector temperatures, which could cause large artifacts in gas/particle phase distribution measurements.

We used a facile, aqueous reaction coupled with gas chromatography–mass spectrometry (GC–MS), visible spectrophotometry, and high performance liquid chromatography (HPLC) to quantify the amounts of α-dicarbonyl compounds in wine samples. The aqueous reaction between an α-dicarbonyl compound and o-phenylenediamine yields a highly stable quinoxaline molecule with an absorbance maximum of 315 nm. GC–MS is used to identify each quinoxaline via mass. Likewise, owing to the similar absorption properties of the quinoxaline products, visible spectrometry is not useful for quantitation although it reveals the absorbance maximum to use for optical detection of the quinoxalines by HPLC. The analytical techniques used in this experiment complement each other since visible spectrophotometry is needed to determine the absorption wavelength, which is used for HPLC analysis; and HPLC is used for quantitation, while GC–MS is used to confirm the identities of the reaction products.

The conditions under which semivolatile organic gases condense were studied in a Teflon particle chamber by scanning mobility particle sizing (SMPS) of the resultant particles. Benzaldehyde, maleic and citraconic anhydrides, n-decane, trans-cinnamaldehyde, and citral were introduced in various combinations into a particle chamber containing either particle-free nitrogen or nitrogen with dry seed particles made out of sodium chloride, D-tartartic acid, ammonium sulfate, or 1,10-decanediol. No organic gas was allowed to reach its saturation point relative to the vapor pressure of its pure liquid in any experiment. In the absence of seed particles, organic aerosol particles formed by ternary nucleation when the sum of the individual organic saturation levels reached a threshold between 1.17 and 1.86. With seed particles present, particle sizes began to increase when the sum of organic saturation levels reached 1.0. This size increase corresponds to the establishment and activation of ternary organic layers on the "clean" seed particles, as predicted by absorption partitioning theory. The observed increases in particle volume depended on initial seed particle volume, indicating that either gas diffusion rates or chemical reactions were controlling the rate of uptake.