A nonanucleotide in which (-)-(7S,8R,9R,10S)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydroben zo alpha pyr ene (7-hydroxy group and epoxide oxygen are trans) is covalently bonded to the exocyclic N ...super(6)-amino group of deoxyadenosine through trans addition at C10 of the epoxide (10R adduct) has been synthesized. The modified oligonucleotide d(GGTCA*CGAG) was incorporated into the duplex d(GGTCA*CGAG)-d(CTCGGGACC), containing a dG mismatch opposite the modified base (dA*). Proton assignments for the solution structure of the duplex containing the 10R adduct were made using 2D TOCSY and NOESY NMR spectra. The complete hybrid relaxation matrix program, MORASS2.0, was used to generate NOESY distance constraints for iterative refinement using distance-restrained molecular dynamics calculations with AMBER4.0. The iteratively refined structure showed the hydrocarbon intercalated from the major groove immediately below the dC sub(4)-dG sub(15) base pair and oriented toward the 5'-end of the modified strand. The modified dA is in an anti configuration, with the dG of the GA mismatch turned out into the major groove. Chemical shifts of the hydrocarbon protons and unusual chemical shifts of sugar protons were accounted for by this orientation of the adduct. The information available currently provides the foundation for the rational explanation of observed benzo alpha pyrene (BaP) structures and predictions for other BaP dG and dA adducts.
The solution structure of a modified undecamer duplex containing (-)-(7R,8S,9R,10S)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzoa pyrene covalently bonded through trans ring opening at C10 of ...the epoxide by the N6-amino group of deoxyadenosine (dA) was studied. This diol epoxide 1 diastereomer has the benzylic 7-hydroxyl group and the epoxide oxygen cis. The modified nucleotide residue has R chirality at C10 of the hydrocarbon (10R adduct). The undecamer duplex d(C1G2G3T4C5A*6C7G8A9G10G11).d(C12C13T14C15G16T17G18A19C2 0C21G22) has a complementary T opposite the modified dA (dA*6 is the modified dA). Exchangeable and nonexchangeable proton assignments were made using 2D TOCSY, NOESY, and water/NOESY NMR spectroscopy. The hybrid complete relaxation matrix program MORASS was used to generate NOESY distance constraints for iterative refinement using distance-restrained molecular dynamics calculations. The refined structure showed the hydrocarbon intercalated from the major groove between dA*6-T17 and dC5-dG18 base pairs. The modified dA*6 was in the normal anti configuration and showed Watson-Crick base pairing to T17 opposite. The chemical shifts of the hydrocarbon protons and the unusual shifts of sugar protons were accounted for by the intercalated orientation of the hydrocarbon.
A nonanucleotide, d(G sub(1)G sub(2)T sub(3)C sub(4)BaPA sub(5)C sub(6)G sub(7)A sub(8)G sub(9)), in which (+)-(7R,8S,9S,10R)-7,8 -dihydroxy-9,10-epoxy -7,8,9,10-tetrahydrobenzoa pyrene (7-hydroxyl ...group and epoxide oxygen are trans) is covalently bonded to the exocyclic N super(6)-amino group of deoxyadenosine (dA sub(5)) through trans addition at C10 of the epoxide (to give a 10S adduct) has been synthesized. The solution structure of the duplex, d(G sub(1)G sub(2)T sub(3)C sub(4)BaPA sub(5)C sub(6)G sub(7)A sub(8)G sub(9)) - d(C sub(10)T sub(11)C sub(12)G sub(13)G sub(14)G sub(15)A sub(16)C sub(17)C sub(18)), containing a dG mismatch opposite the modified dA (designated 10S-BaPdA - dG 9-mer duplex) has been investigated using a combination of 1D and 2D (including COSY, PECOSY, TOCSY, NOESY, and indirect detection of super(1)H- super(31P) HETCOR) NMR spectroscopies. The NMR results together with restrained molecular dynamics/energy minimization calculations show that the modified dA sub(5) adopts a syn glycosidic torsion angle whereas all other nucleotide residues adopt anti glycosidic torsion angles. The sugar ring of dA sub(5) is in the C3'-endo conformation, and the sugar rings of the other residues are in the C2'-endo conformation. The hydrocarbon attached at dA sub(5) orients toward the 3' end of the modified strand (i.e., dC sub(6) direction) and intercalates between and parallel to bases of dG sub(13) and dG sub(14) of the complementary strand directly opposite dC sub(6) and dA sub(5), respectively. The edge of the hydrocarbon bearing H11 and H12 is positioned between the imino protons of dG sub(13) and dG sub(14) in the interior of the duplex, whereas H4 and H5 at the opposite edge are positioned near the sugar H1' and H2" protons of dG sub(13) and facing the exterior of the duplex. The mismatched AG base pair is stabilized by dA sub(syn)-dG sub(anti) base pairing in which the imino proton and the O super(6) of dG sub(14) are hydrogen bonded to N7-and the single N super(6)-amino proton, respectively, of the modified dA sub(5). The modified DNA duplex remains in a right-handed helix, which bends at the site of intercalation about 20 to 30 degree away from the helical axis and toward the direction of the modified strand.
The solution structure of a modified undecamer duplex containing (-)-(7R,8S,9R,10S)-7,8-dihydroxy -9,10-epoxy-7,8,9,10-tetrahydrobenzoa pyrene covalently bonded through trans ring opening at C10 of ...the epoxide by the N super(6)-amino group of deoxyadenosine (dA) was studied. This diol epoxide 1 diastereomer has the benzylic 7-hydroxyl group and the epoxide oxygen cis. The modified nucleotide residue has R chirality at C10 of the hydrocarbon (10R adduct). The undecamer duplex d(C sub(1)G sub(2)G sub(3)T sub(4)C sub(5)A* sub(6) C sub(7)G sub(8)A sub(9)G sub(10)G sub(11)) - d(C sub(12)C sub(13)T sub(1 4)C sub(15) G sub(16)T sub(17)G sub(18)A sub(19) C sub(20)C sub(21)G sub(22)) has a complementary T opposite the modified dA (dA*6 is the modified dA). Exchangeable and nonexchangeable proton assignments were made using 2D TOCSY, NOESY, and water/NOESY NMR spectroscopy. The hybrid complete relaxation matrix program MORASS was used to generate NOESY distance constraints for iterative refinement using distance-restrained molecular dynamics calculations. The refined structure showed the hydrocarbon intercalated from the major groove between dA*6-T17 and dC5-dG18 base pairs. The modified dA*6 was in the normal anti configuration and showed Watson-Crick base pairing to T17 opposite. The chemical shifts of the hydrocarbon protons and the unusual shifts of sugar protons were accounted for by the intercalated orientation of the hydrocarbon.
This work provides a comparison of satellite retrievals of Saharan desert dust aerosol optical depth (AOD) during a strong dust event through March 2006. In this event, a large dust plume was ...transported over desert, vegetated, and ocean surfaces. The aim is to identify the differences between current datasets. The satellite instruments considered are AATSR, AIRS, MERIS, MISR, MODIS, OMI, POLDER, and SEVIRI. An interesting aspect is that the different algorithms make use of different instrument characteristics to obtain retrievals over bright surfaces. These include multi-angle approaches (MISR, AATSR), polarisation measurements (POLDER), single-view approaches using solar wavelengths (OMI, MODIS), and the thermal infrared spectral region (SEVIRI, AIRS). Differences between instruments, together with the comparison of different retrieval algorithms applied to measurements from the same instrument, provide a unique insight into the performance and characteristics of the various techniques employed. As well as the intercomparison between different satellite products, the AODs have also been compared to co-located AERONET data. Despite the fact that the agreement between satellite and AERONET AODs is reasonably good for all of the datasets, there are significant differences between them when compared to each other, especially over land. These differences are partially due to differences in the algorithms, such as assumptions about aerosol model and surface properties. However, in this comparison of spatially and temporally averaged data, it is important to note that differences in sampling, related to the actual footprint of each instrument on the heterogeneous aerosol field, cloud identification and the quality control flags of each dataset can be an important issue.
: We report here the identification and characterization of a novel human leucocyte antigen (HLA)‐DPB1 allele that was subsequently named HLA‐DPB1*0302 by the WHO Nomenclature Committee. ...HLA‐DPB1*0302 was identified in a single Sicilian individual by a combination of sequence‐specific primers, reverse line sequence‐specific oligonucleotide probing and DNA sequencing‐based typing. The DPB1*0302 allele is most similar to the DPB1*3101 allele, differing by a single mismatch at nucleotide position 301 (T to G).
This work provides a comparison of satellite retrievals of Saharan desert dust aerosol optical depth (AOD) during a strong dust event through March 2006. In this event, a large dust plume was ...transported over desert, vegetated, and ocean surfaces. The aim is to identify and understand the differences between current algorithms, and hence improve future retrieval algorithms. The satellite instruments considered are AATSR, AIRS, MERIS, MISR, MODIS, OMI, POLDER, and SEVIRI. An interesting aspect is that the different algorithms make use of different instrument characteristics to obtain retrievals over bright surfaces. These include multi-angle approaches (MISR, AATSR), polarisation measurements (POLDER), single-view approaches using solar wavelengths (OMI, MODIS), and the thermal infrared spectral region (SEVIRI, AIRS). Differences between instruments, together with the comparison of different retrieval algorithms applied to measurements from the same instrument, provide a unique insight into the performance and characteristics of the various techniques employed. As well as the intercomparison between different satellite products, the AODs have also been compared to co-located AERONET data. Despite the fact that the agreement between satellite and AERONET AODs is reasonably good for all of the datasets, there are significant differences between them when compared to each other, especially over land. These differences are partially due to differences in the algorithms, such as as20 sumptions about aerosol model and surface properties. However, in this comparison of spatially and temporally averaged data, at least as significant as these differences are sampling issues related to the actual footprint of each instrument on the heterogeneous aerosol field, cloud identification and the quality control flags of each dataset.
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