Enthalpy/entropy compensation: Influence of DNA flanking sequence on the binding of 7-amino actinomycin D to its primary binding site in short DNA duplexes

The effect of the context of the flanking sequence on ligand binding to DNA oligonucleotides that contain consensus binding sites was investigated for the binding of the intercalator 7-amino actinomycin D. Seven self-complementary DNA oligomers each containing a centrally located primary binding site, 5'-A-G-C-T-3', flanked on either side by the sequences (AT)(n) or (AA)(n) (with n = 2, 3, 4) and AA(AT)(2), were studied. For different flanking sequences, (AA)(n)-series or (AT)(n)-series, differential fluorescence enhancements of the ligand due to binding were observed. Thermodynamic studies indicated that the flanking sequences not only affected DNA stability and secondary structure but also modulated ligand binding to the primary binding site. The magnitude of the ligand binding affinity to the primary site was inversely related to the sequence dependent stability. The enthalpy of ligand binding was directly measured by isothermal titration calorimetry, and this made it possible to parse the binding free energy into its energetic and entropic terms.

Site-selective self-assembly of MPA-bridged CuHCF multilayers on APTMS-supported gold colloid electrodes

(3-Aminopropyl)trimethoxysilane (APTMS)-supported gold colloid electrode was constructed by virtue of a recently developed solution-based self-assembly strategy. The preparing procedure of 3-mercaptopropionic acid (MPA)-bridged copper hexacyanoferrate (CuHCF) multilayers on a planar macroelectrode (Bharathi et al. Langmuir 2001, 17, 7468) was copied to the as-prepared colloid electrode. The optical spectra, atomic force microscopy, and electrochemistry demonstrate successful copy of the multilayer system on a macroelectrode to the as-prepared colloid electrode. Remarkably, it was found that multilayer growth is highly selective to the nanoscale sites where gold nanoparticles are immobilized, and multilayer growth does not take place on the sites without nanoparticles. Interestingly, a preliminary electrochemical investigation indicates that electrochemical properties of multilayers systems on the colloid electrode are different from their counterparts on a planar macroelectrode, which might be due to high curvature effects of the gold nanoparticles. This indicates a different motif of multilayers on the colloid electrode from that on a planar macroelectrode.

Vibronic transitions and site substitution of Eu2+ and codoped ions in KMgF3 : Eu-X (X=Ce, Cr, Gd, Cu) system

The high-resolution emission spectra of KMgF3 : Eu and KMgF3 : Eu-X(X = Ce, Cr, Gd, Cu) single crystals were measured at 300 and 77 K. The vibronic side bands of Eu2+ were characterized and an assignment of the normal mode frequencies to particular vibrations has been made. The correlation between the vibronic frequencies of Eu2+ and the site substitution of other co-dopcd ions was first found. The relationship between vibronic intensity of Eu2+ and other doped ions concentration showed that Cr3+, Gd3+ ions competed K+ sites with Eu2+ ions. Ce3+ and Eu3+ occurred the electron transference. The introduction of Cu+ made for Eu2+ substuting for K+ sites.

Site substitution and energy transfer of Eu2+ and Ce3+ in KMgF3 : Eu and KMgF3 : Eu-Ce single crystals

The high-resolution emission spectra of KMgF3 : Eu and KMgF3 : Eu-Ce single crystals were measured at 77 K. The site substitution of Eu2+ and Eu2+-Ce3+ co-doped system in KMgF3 was discussed. Eu2+ substituted for K+ sites on three different site-symmetry: cubic, trigonal and tetragonal. The attribution of all lines occurring in the emission spectra were ascertained. The indirect energy transfer from P-6(5/2) states of Eu2+ to 4f5d states of Ce3+ in KMgF3 : Eu-Ce was observed and the energy transfer mechanism was studied. The d-d interaction among levels was proposed.

The site symmetry of Eu3+ in ZnS : Eu nanoparticle

Nanosized ZnS doped with different concentrations of Eu3+ were prepared and analyzed by x-ray diffraction technique. The experimental results show that ZnS belongs to the cubic structure. From the photoluminescence (PL) emission spectra, it can be seen that the ratio of the emission intensity of Eu3+ 616 nm to that at 590 nm increases as the increasing of Eu3+. This phenomenon reveals that the site symmetry of Eu3+ reduces as the increasing of Eu3+.

STRUCTURE AND SITE-SYMMETRY INVESTIGATION ON THE HEXAGONAL KCAY(PO4)(2)

A new double phosphate, KCaY(PO4)(2), isostructural with hexagonal LaPO4, is reported. It crystallizes in the hexagonal system with a = 0.6903 nm and c = 0.6331 nm. Its vibrational spectra, IR and Raman spectra showed that the site symmetry of the PO4 anion slightly deviated from D-2 toward C-2.

CHEMICAL-IONIZATION MASS-SPECTROMETRY OF SOME NITRO-CONTAINING BIFUNCTIONAL AROMATIC-COMPOUNDS - LOCATION OF PROTONATION SITE

It is found that the nitro substituent of some aromatic bifunctional compounds shows unusual reactivity towards protonation. In the chemical ionization mass spectra of nitrobenzoic acids and their esters and amides, and of nitrophenols and their ethers, protonations on the carboxyl, ester, amide, hydroxyl or alkoxyl groups are highly suppressed by that on the nitro group. As a result, fragmentations based on protonation on these groups unexpectedly become negligible. Ortho effects were observed for all the ortho isomers where the initial protonation on the nitro group is followed by an intramolecular proton transfer reaction, which leads to the expected 'normal' fragmentations. Protonation on the nitro substituent is much more favourable in energy than on any of the other substituents. The interaction of the two substituents through the conjugating benzene ring is found to be responsible for this 'unfair' competitive protonation. The electron-attracting nitro group strongly destabilizes the MH+ ions formed through protonation on the other substituent; although the COR (R = OH, OMe, OEt, NH2) groups are also electron-withdrawing, their effects are weaker than that of NO2; thus protonation on the latter group produces more-stable MH+ ions. On the other hand, an electron-releasing group OR (R = H, Me, Et) stabilizes the nitro-protonated species; the stronger the electron-donating effect of this group the more stable the nitro-protonated ions.

A STUDY OF SITE OCCUPATION OF EU-3+ IN ME2Y8(SIO4)6O2 (ME=MG, CA, SR)

Alkaline earth (Mg, Ca. Sr) yttrium silicate oxyapatites doped with Eu3+ show red luminescence with comparable intensity. In this system of phosphors, the Eu3+ ions enter 4f sites and 6h sites simultaneously according to the fluorescence spectra, in which

Isolation, properties and spatial site analysis of gamma subunits of B-phycoerythrin and R-phycoerythrin

Polysiphonia urceolata R-phycoerythrin and Porphyridium cruentum B-phycoerythrin were degraded with proteinaseK, and then the nearly native gamma subunits were isolated from the reaction mixture. The process of degradation of phycoerythrin with proteinaseK showed that the gamma subunit is located in the central cavity of (alpha beta)(6) hexamer of phycoerythrin. Comparative analysis of the spectra of the native phycoerythrin, the phycoerythrin at pH 12 and the isolated gamma subunit showed that the absorption peaks of phycoerythrobilins on alpha or beta subunit are at 535 nm (or 545 nm) and 565 nm, the fluorescence emission maximum at 580 nm; the absorption peak of phycoerythrobilins on the isolated gamma subunit is at 589 nm, the fluorescence emission peak at 620 nm which overlaps the absorption maximum of C-phycocyanin and perhaps contributes to the energy transfer with high efficiency between phycoerythrin and phycocyanin in phycobilisome; the absorption maximum of phycourobilin on the isolated gamma subunit is at 498 nm, which is the same as that in native phycoerythrin, and the fluorescence emission maximum at 575 nm.

attB site disruption in marine Actinomyces sp M048 via DNA transformation of a site-specific integration vector

An efficient conjugation method has been developed for the marine Actinomyces sp. isolate M048 to facilitate the genetic manipulation of the chandrananimycin biosynthesis gene cluster. A phi C31-derived integration vector pIJ8600 containing oriT and attP fragments was introduced into strain M048 by bi-parental conjugation from Escherichia coli ET12567 to strain M048. Transformation efficiency was (6.38 +/- 0.41) x 10(-5) exconjugants per recipient spore. Analysis of eight exconjugants showed that the plasmid pIJ8600 was stably integrated at a single chromosomal site (attB) of the Actinomyces genome. The DNA sequence of the attB was cloned and shown to be conserved. The results of antimicrobial activity analysis indicated that the insertion of plasmid pIJ8600 seemed to affect the biosynthesis of antibiotics that could strongly inhibit the growth of E. coli and Mucor miehei (Tu284). HPLC-MS analysis of the extracts indicated that disruption of the attB site resulted in the complete abolition of chandrananimycin A-C production, proving the identity of the gene cluster. Instead of chandrananimycins, two bafilomycins were produced through disruption of the attB site from the chromosomal DNA of marine Actinomyces sp. M048.

Element enrichment and U-series isotopic characteristics of the hydrothermal sulfides at Jade site in the Okinawa Trough

The geochemical and U-series isotopic characteristics of hydrothermal sulfide samples from the Jade site (127A degrees 04.5'E, 27A degrees 15'N, water depth 1300-1450 m) at Jade site in the Okinawa Trough were analyzed. In the hydrothermal sulfide samples bearing sulfate (samples HOK1 and HOK2), the LREEs are relatively enriched. All the hydrothermal sulfide samples except HOK1 belong to Zn-rich hydrothermal sulfide. In comparison with Zn-rich hydrothermal sulfides from other fields, the contents of Zn, Pb, Ag, Cd, Au and Hg are higher, the contents of Fe, Al, Cr, Co, Ni, Sr, Te, Cs, Ti and U lower, and the Pb-210 radioactivity ratios and Pb-210/Pb ratios very low. In the hydrothermal sulfide mainly composed of sphalerite, the correlations between rare elements Hf and U, and Hf and Mn as well as that between dispersive elements Ga and Zn, are strongly positive; also the contents of Au and Ag are related to Fe-sulfide, because the low temperature promotes enrichment of Au and Ag. Meanwhile, the positive correlations between Fe and Bi and between Zn and Cd are not affected by the change of mineral assemblage. Based on the Pb-210/Pb ratios of hydrothermal sulfide samples (3.99x10(-5)-5.42x10(-5)), their U isotopic composition (U-238 content 1.15-2.53 ppm, U-238 activity 1.07-1.87 dpm/g, U-234 activity 1.15-2.09 dpm/g and U-234/U-238 ratio 1.07-1.14) and their Th-232 and Th-230 contents are at base level, and the chronological age of hydrothermal sulfide at Jade site in the Okinawa Trough is between 200 and 2000 yr.

Grain-size records at ODP site 1146 from the northern South China sea: Implications on the east Asian monsoon evolution since 20 Ma

273 samples from Ocean Drilling Program (ODP) Site 1146 in the northern South China Sea (SCS) were analyzed for grain-size distributions using grain-size class vs. standard deviation method and end-member modeling algorithm (EMMA) in order to investigate the evolution of the East Asian mon-soon since about 20 Ma. 10-19 mu m/1.3-2.4 mu m, the ratio of two grain-size populations with the highest variability through time was used to indicate East Asian winter monsoon intensity relative to summer monsoon. The mass accumulation rate of the coarsest end member EM1 (eolian), resulting from EMMA, can be used as a proxy of winter monsoon strength and Asian inland aridity, and the ratio of EM1/(EM2+EM3) as a proxy of winter monsoon intensity relative to summer monsoon. The combined proxies show that a profound enhancement of East Asian winter monsoon strength and winter monsoon intensity relative to summer monsoon occurred at about 8 Ma, and it is possible that the summer monsoon simultaneously intensified with winter monsoon at 3 Ma. Our results are well consistent with the previous studies in loess, eolian deposion in the Pacifc, radiolarians and planktonic foraminifera in the SCS. The phased uplift of the Himalaya-Tibetan Plateau may have played a significant role in strengthening the Asian monsoon at 8 Ma and 3 Ma.

The Yellow Sea cold bottom water - an oversummering site for Calanus sinicus (Copepoda, Crustacea)

The vertical distribution and stage-specific abundance of Calanus sinicus were investigated on three key transects in the southern Yellow Sea and the northern East China Sea in August 1999. The results showed that in summer C. sinicus shrank its distribution area to the central cold (less than or equal to10degreesC) bottom water in the Yellow Sea, i.e. the Yellow Sea Cold Bottom Water, remaining in high abundance (345.7 ind m(-3)). In the northern East China Sea on a transect from the mouth of the Yangtze River to the Okinawa trench, only a few individuals appeared in the inner side and none had been found either in the upper layer or in the deep layer of the outer shelf area. The population of C. sinicus in YSCBW consisted of mainly adults (46.83%) and C5 (37.41%). C1-C4 only accounted for 15.76%. The low proportion of the earlier copepodite stages and the high female:male ratio (11.39) indicated that the reproduction of C. sinicus in YSCBW was at a very low level due to the low temperature and low food concentration. It is concluded that the dramatic decrease of C. sinicus population in the shelf area of China seas in summer is caused by the shrinkage of its distribution area and the YSCBW served as an oversummering site.