Probing the effect of minor groove interactions on the catalytic efficiency of DNAzymes 8–17 and 10–23

DNAzymes (Dz) 8–17 and 10–23 are two widely studied and well-characterized RNA-cleaving DNA catalysts. In an effort to further improve the understanding of the fragile interactions and dynamics of the enzymatic mechanism, this study examines the catalytic efficiency of minimally modified DNAzymes. Five single mutants of Dz8–17 and Dz10–23 were prepared by replacing the adenine residues in the corresponding catalytic cores with 3-deazaadenine units. Kinetic assays were used to assess the effect on the catalytic activity and thereby identify the importance of hydrogen bonding that arises from the N3 atoms. The results suggest that modifications at A15 and A15.0 of Dz8–17 have a significant influence and show a reduction in catalytic activity. Modification at each location in Dz10–23 results in a decrease of the observed rate constants, with A12 appearing to be the most affected with a reduction of ∼80% of kobs and ∼25% of the maximal cleavage rate compared to the wild-type DNAzyme. On the other hand, modification of A12 in Dz8–17 showed an ∼130% increase in kobs, thus unraveling a new potential site for the introduction of chemical modifications. A pH-profile analysis showed that the chemical cleavage step is rate-determining, regardless of the presence and/or location of the mutation. These findings point towards the importance of the N3-nitrogens of certain adenine nucleotides located within the catalytic cores of the DNAzymes for efficient catalytic activity and further suggest that they might directly partake in maintaining the appropriate tertiary structure. Therefore, it appears that minor groove interactions constitute an important feature of DNAzymes as well as ribozymes.

(Table 1.4) Ratios of petrogenic components in glassy and crystalline basalts from the north part of the Bougault anomaly, Mid-Atlantic Ridge 15°N

Structure and composition of sub-surface bottom sediments from the southwest Barents Sea have been under study. The study has revealed heterogeneity of sediment structure resulted from temporal irregularity and variability of sedimentation processes. The study of the heavy minerals from 0.1-0.01 mm grain size fraction has shown prevalence of green hornblende, epidote, garnet, and ilmenite in all types of sediments; these minerals are the basis of terrigenous-mineralogical province. At the same time in different areas local terrigenous-mineralogical associations have been identified. Clay mineral composition of in the sediments was quite uniform: biotite, chlorite, hydromica, smectite. Despite this, a number of features indicating initial stages of clay mineral transformation has been identified. Differences in material composition and structure of the studied sediments are associated with rapid change in paleogeographic situation on the land - ice cover melting on the Kola Peninsula and subsequent Holocene climatic situation.

Holocene sedimentation in the Strait of Otranto, Mediterranean Sea

An extensive radiograph study of 24 undisturbed, up to 206-cm long box and gravity cores from the western part of the Strait of Otranto revealed a great variety of primary bedding structures and secondary burrowing features. The regional distribution of the sediments according to their structural, textural, and compositional properties reflects the major morphologic subdivisions of the strait into shelf, slope, and trough bottom (e.g., the bottom of the northern end of the Corfu-Kephallinia Trough, which extends from the northeastern Ionian Sea into the Strait of Otranto): (1) The Apulian shelf (0 to -170m) is only partly covered by very poorly sorted, muddy sands without layering. These relict(?) sands are rich in organic carbonate debris and contain glauconite and reworked (?Pleistocene) ooids. (2) The slope sediments (-170 to -1,000 m) are poorly sorted, sandy muds with a high degree of burrowing. One core (OT 5) is laminated and shows slump structures. An origin of these slumped sediment masses from older deposits higher on the slope was inferred from their abnormal compaction, color, texture, organic content, and mineral composition. (3) Cores from the northern end of the Corfu-Kephallinia Trough (-980 to -1,060 m) display a few graded sand layers, 2-5 cm (maximum 30 cm) thick with parallel and ripple-cross-laminations, deposited by oceanic bottom or small-scale turbidity currents. They are intercalated with homogeneous lutite. (4) Hemipelagic sediments prevail in the more southerly part of the Corfu-Kephallinia Trough and on the "Apulian-Ionian Ridge", the southern submarine extension of the Apulian Peninsula. Below a core depth of 160 cm, these cores have a laminated ("varved") zone, representing an Early Holocene (Boreal-Atlanticum) "stagnation layer" (14C age approximately 9,000 years). The terrigenous components of the surface sediments as well as those of the deeper sand layers can be derived from the Apulian shelf and the Italian mainland (Cretaceous Apulian Plateau and Gargano Mountains, southern Apennines, volcanic province of the Monte Vulture). Indicated by the heavy mineral glaucophane, a minor proportion of the sedimentary material is probably of Alpine origin. If this portion is considered to be first-cycle clastic material it reaches the Strait of Otranto after a longitudinal transport of 700 km via the Adriatic Sea. The lack of phyllosilicates in the coarse- to medium-grained shelf samples might be explained by the activity of the "Apulian Current" (surface velocities up to 4 knots) which in the past possibly has affected the bottom almost down to depths of the shelf edge. The percentage of planktonic organisms, and also the plankton: benthos ratio in the sediments is a useful indicator for bathymetry (depth zonation).

(Table 1.5) Contents of some volatile components in glassy MORB from the north part of the Bougault anomaly, Mid-Atlantic Ridge 15°N

Structure and composition of sub-surface bottom sediments from the southwest Barents Sea have been under study. The study has revealed heterogeneity of sediment structure resulted from temporal irregularity and variability of sedimentation processes. The study of the heavy minerals from 0.1-0.01 mm grain size fraction has shown prevalence of green hornblende, epidote, garnet, and ilmenite in all types of sediments; these minerals are the basis of terrigenous-mineralogical province. At the same time in different areas local terrigenous-mineralogical associations have been identified. Clay mineral composition of in the sediments was quite uniform: biotite, chlorite, hydromica, smectite. Despite this, a number of features indicating initial stages of clay mineral transformation has been identified. Differences in material composition and structure of the studied sediments are associated with rapid change in paleogeographic situation on the land - ice cover melting on the Kola Peninsula and subsequent Holocene climatic situation.

Geochemistry of North Atlantic Igneous Province basalts

New Sr-Nd-Pb-Hf data require the existence of at least four mantle components in the genesis of basalts from the the North Atlantic Igneous Province (NAIP): (1) one (or more likely a small range of) enriched component(s) within the Iceland plume, (2) a depleted component within the Iceland plume (distinct from the shallow N-MORB source), (3) a depleted sheath surrounding the plume and (4) shallow N-MORB source mantle. These components have been available since the major phase of igneous activity associated with plume head impact during Paleogene times. In Hf-Nd isotope space, samples from Iceland, DSDP Leg 49 (Sites 407, 408 and 409), ODP Legs 152 and 163 (southeast Greenland margin), the Reykjanes Ridge, Kolbeinsey Ridge and DSDP Leg 38 (Site 348) define fields that are oblique to the main ocean island basalt array and extend toward a component with higher 176Hf/177Hf than the N-MORB source available prior to arrival of the plume, as indicated by the compositions of Cretaceous basalts from Goban Spur (~95 Ma). Aside from Goban Spur, only basalts from Hatton Bank on the oceanward side of the Rockall Plateau (DSDP Leg 81) lie consistently within the field of N-MORB, which indicates that the compositional influence of the plume did not reach this far south and east ~55 Ma ago. Thus, Hf-Nd isotope systematics are consistent with previous studies which indicate that shallow MORB-source mantle does not represent the depleted component within the Iceland plume (Thirlwall, J. Geol. Soc. London 152 (1995) 991-996; Hards et al., J. Geol. Soc. London 152 (1995) 1003-1009; Fitton et al., 1997 doi:10.1016/S0012-821X(97)00170-2). They also indicate that the depleted component is a long-lived and intrinsic feature of the Iceland plume, generated during an ancient melting event in which a mineral (such as garnet) with a high Lu/Hf was a residual phase. Collectively, these data suggest a model for the Iceland plume in which a heterogeneous core, derived from the lower mantle, consists of 'enriched' streaks or blobs dispersed in a more depleted matrix. A distinguishing feature of both the enriched and depleted components is high Nb/Y for a given Zr/Y (i.e. positive DeltaNb), but the enriched component has higher Sr and Pb isotope ratios, combined with lower epsilon-Nd and epsilon-Hf. This heterogeneous core is surrounded by a sheath of depleted material, similar to the depleted component of the Iceland plume in its epsilon-Nd and epsilon-Hf, but with lower 87Sr/86Sr, 208Pb/204Pb and negative DeltaNb; this material was probably entrained from near the 670 km discontinuity when the plume stalled at the boundary between the upper and lower mantle. The plume sheath displaced more normal MORB asthenosphere (distinguished by its lower epsilon-Hf for a given epsilon-Nd or Zr/Nb ratio), which existed in the North Atlantic prior to plume impact. Preliminary data on MORBs from near the Azores plume suggest that much of the North Atlantic may be 'polluted' not only by enriched plume material but also by depleted material similar to the Iceland plume sheath. If this hypothesis is correct, it may provide a general explanation for some of the compositional diversity and variations in inferred depth of melting (Klein and Langmuir, 1987 doi:10.1029/JB092iB08p08089) along the MAR in the North Atlantic.

Chemical composition of layer silicates from the Sado Ridge, Sea of Japan

Detailed mineralogical investigations of high-Fe layer silicates from loose sediments (glauconite sands) of the Sado Ridge revealed that green aggregates found on submarine rises of the Japan Sea floor have different genesis. It was demonstrated that round dark green grains approximate micas in composition. Primary volcanic rocks presumably have undergone extensive secondary alterations and then were disintegrated. Their disintegration products (protoceladonite) filling pores were redeposited and buried in sediments for a long time. Angular green grains mainly represented by smectite also formed at lower temperatures during disintegration of altered volcanosedimentary rocks. These younger grains had no prolonged exposure. Pseudomorphs of siliceous microplankton consist of both hydromica and smectites. They are presumably authigenic products formed with participation of microorganisms or electrostatic processes (spherical shape), or their combination. The formation mechanism of minerals filling cavities in pyroclastics is not entirely clear.