Distamycin-NA: A DNA analog with an aromatic heterocyclic polyamide backbone. Part 2. Solid-phase synthesis of distamycin-NAs containing the nucleobase uracil: Unexpected solvent participation in the coupling step

10.1002/hlca.19980810512.abs The synthesis of the Fmoc-protected amino acid 2 is presented. First attempts of amide-bond formation to the homodimer 4 in solution showed only poor coupling yields indicative for the low reactivity of the amino and carboxy groups in the building blocks 1 and 2, respectively (Scheme 1). Best coupling yields were found using dicyclohexylcarbodiimide (DCC) without any additive. The oligomerization of building block 2 adopting the Fmoc ((9H-fluoren-9-ylmethoxy)carbonyl) solid-phase synthesis yielded a mixture of N-terminal-modified distamycin-NA derivatives. By combined HPLC and MALDI-TOF-MS analysis, the N-terminal functional groups could be identified as acetamide and N,N-dimethylformamidine functions, arising from coupling of the N-terminus of the growing chain with residual AcOH or DCC-activated solvent DMF. An improved preparation of building block 2 and coupling protocol led to the prevention of the N-terminal acetylation. However, ‘amidination’ could not be circumvented. A thus isolated tetramer of 2, containing a lysine unit at the C-terminus and a N,N-dimethylformamidine-modified N-terminus, not unexpectedly, showed no complementary base pairing to DNA and RNA, as determined by standard UV-melting-curve analysis.

MeV ion beam lithography of biocompatible halogenated Parylenes using aperture masks

Parylenes are poly(p-xylylene) polymers that are widely used as moisture barriers and in biomedicine because of their good biocompatibility. We have investigated MeV ion beam lithography using 16O+ ions for writing defined patterns in Parylene-C, which is evaluated as a coating material for the Cochlear Implant (CI) electrode array, a neuroprosthesis to treat some forms of deafness. Parylene-C and -F on silicon and glass substrates as well as 50 μm thick PTFE were irradiated to different fluences (1×1013-1×10161×1013-1×1016 1 MeV 16O+ ions cm−2) through aperture masks under high vacuum and a low pressure (<10−3 mbar) oxygen atmosphere. Biocompatibility of the irradiated and unirradiated surfaces was tested by cell-counting to determine the proliferation of murine spiral ganglion cells. The results reveal that an oxygen ion beam can be used to pattern Parylene-C and -F without using a liquid solvent developer in a similar manner to PTFE but with a ∼25× smaller removal rate. Biocompatibility tests showed no difference in cell adhesion between irradiated and unirradiated areas or ion fluence dependence. Coating the Parylene surface with an adhesion-promoting protein mixture had a much greater effect on cell proliferation.

(Table 1) Composition of paraffin hydrocarbons at DSDP Site 56-434

Geochemical investigation of 18 samples of sediments from Site 434 involved determining the content of organic carbon, of bitumoid A (The chloroform A-chl and alcohol-benzene A-alb extracts) and its various fractions, and of individual hydrocarbons as well as the structural group composition of resins. We identified certain samples that differed sharply from the rest by their increased bitumen content and relatively low molecular hydrocarbons and by the fact that their resinous components were more neutral and aliphatic in composition. The distribution of bitumoid and its components seems to reflect migration processes in operation during the early stages of the transformation of organic matter.

Organic petrography and extractable hydrocarbons of sediments at DSDP Leg 58 Holes

The quantity, type, and maturity of organic matter of Quaternary and Tertiary sediments from the Philippine Sea (DSDP Leg 58; Sites 442-446) were determined. Hydrocarbons in lipid extracts were analyzed by capillary-column gas chromatography. Kerogen concentrates were investigated by microscopy for vitrinite reflectance values and maceral composition. In the Shikoku Basin sediments (Sites 442, 443, and 444), organic carbon values range between 0.03 and 0.44 per cent. The higher values in the younger sediments are interpreted as an indication of increasing deposition of eroded organic particles during the past 4 m.y. Microscopic analyses revealed a dominance of reworked organic matter. Primary material could not be distinguished readily; thus, no maturation trend could be established. Extract yields were low. TV-alkane distributions mostly show maxima at n-C29 and n-C31 and high odd-over-even predominances, typical of material which originated in terrigenous higher plants. The organic-carbon values of sediments of the Daito Ridge and Basin region (Sites 444 and 445) range from less than 0.01 to 0.05 per cent. TV-alkanes exhibit varying marine and terrigenous influences. Some carbonate-rich samples show a pronounced even-over-odd predominance. At least the older sediments contained less recycled organic matter than the Shikoku Basin samples. The maturity, where measurable, was low. None of the Philippine Sea samples indicates a significant hydrocarbon-generation potential.

Characterization of sorbed volatile hydrocarbons from the Peru margin

Bacterial and thermogenic hydrocarbons are present in the sorbed-gas fraction of Peru margin sediments. At Ocean Drilling Program (ODP) Sites 681, 682, 684, and 686, bacterial gases are restricted to the early diagenetic zones, where dissolved sulfate has been exhausted and methanogenesis occurs. Methane migrating into the sulfate zone at Sites 681, 684, 686, and possibly 682, has been consumed anaerobically by methanotrophs, maintaining the low concentrations and causing an isotope shift in d13C(CH4) to more positive values. Significant amounts of C2+ hydrocarbons occur at the shelf Sites 680/681, 684, and 686/687, where these hydrocarbons may be associated with hypersaline fluids. There is evidence at Site 679 that sorbed C2+ hydrocarbons may also have been transported by hypersaline fluids. This characteristic C2+ hydrocarbon signature in the sorbed-gas fractions of sediments at Site 679 is not reflected in data obtained using the conventional "free-," "canned-," or "headspace-gas" procedures. The molecular and isotope compositions of the sorbed-gas fraction indicate that this gas may have a thermogenic source and may have spilled over with the hypersaline fluids from the Salaverry Basin into the Lima Basin. These traces of thermogenic hydrocarbon gases are over-mature (about 1.5% Ro) and are discordant with the less-mature sediments in which they are found. This observation supports the migration of these hydrocarbons, possibly from continental sources. Sorbed-gas analyses may provide important geochemical information, in addition to that of the free-gases. Sorbed-gases are less sensitive to activities in the interstitial fluids, such as methanogenesis and methanotrophy, and may faithfully record the migration of hydrocarbons associated with hypersaline fluids.

Halocarbons in surface water from SWEDARP97/98

A number of parameters of biogeochemical interest were monitored along a north-southerly transect (S 43-S 63°) in the Atlantic Sector of the Southern Ocean from the 8th to the 20th of December 1997. Changes in total dissolved inorganic carbon (CT) and total alkalinity (AT) were mostly dependent on temperature and salinity until the ice edge was reached. After this point only a weak correlation was seen between these. Highest mean values of CT and AT were observed in the Winter Ice Edge (WIE) (2195 and 2319 µmol/kg, respectively). Lowest mean AT (2277 µmol/kg) was observed in the Sub-Antarctic Front (SAF), whereas lowest mean CT concentration (2068 µmol/kg) was associated with the Sub-Tropical Front (STF). The pH in situ varied between 8.060 and 8.156 where the highest values were observed in the southern part of the Antarctic Polar Front (APF) and in the Summer Ice Edge (SIE) Region . These peaks were associated with areas of high chlorophyll a (chl a) and tribromomethane values. In the other areas the pH in situ was mainly dependent on hydrography. Bacterial abundance decreased more than one order of magnitude when going from north to south. The decrease appeared to be strongly related to water temperature and there were no elevated abundances at frontal zones. Microphytoplankton dominated in the SAF and APF, whereas the nano- and picoplankton dominated outside these regions. Volatile halogenated compounds were found to vary both with regions, and with daylight. For the iodinated compounds, the highest concentrations were found north of the STF. Brominated hydrocarbons had high concentrations in the STF, but elevated concentrations were also found in the APF and SIE regions. No obvious correlation could be found between the occurrence of individual halocarbons and chl a. On some occasions trichloroethene and tribromomethane related to the presence of nano- and microplankton, respectively.

C1-C5 hydrocarbons from core gas pockets at DSDP Leg 56 Holes

C1-C5 hydrocarbons from DSDP Legs 56 and 57 sediment gas pockets were analyzed on board ship. Results suggest that the C2-C5 hydrocarbons accompanied biogenic methane and were generated at low temperatures - less than 50° C - either by microorganisms or by low-temperature chemical reactions. Neopentane, a rare constituent of petroleum, is the major C5 component (about 80%) in much of the sediment at Site 438. This compound, which appeared in smaller amounts at Sites 434, 439, 440, and 441, seems to correlate with either fractured or coarse-grained sediments. Scatter in C4 and C5 isomer ratios and generally good correlation between C3, C4 and C5 components suggest local sources for these molecules.