Genomic organization, nucleotide sequence analysis of the core histone genes cluster in Chlamys farreri and molecular evolution assessment of the H2A and H2B

This work represents the nucleotide sequence of the core histone gene cluster from scallop Chlamys farreri. The tandemly repeated unit of 5671 bp containing a copy of the four core histone genes H4, H2B, H2A and H3 was amplified and identified by the techniques of homology cloning and genomic DNA walking. All the histone genes in the cluster had the structures in their 3' flanking region which related to the evolution of histone gene expression patterns throughout the cell cycle, including two different termination signals, the hairpin structure and at least one AATAAA polyadenylation signal. In their 5' region, the transcription initiation sites with a conserved sequence of 5'-PyATTCPu-3' known as the CAP site were present in all genes except to H2B, generally 37-45 bp upstream of the start code. Canonical TATA and CAAT boxes were identified only in certain histone genes. In the case of the promoters of H2B and H2A genes, there was a 5'-GATCC-3' element, which had been found to be essential to start transcription at the appropriate site. After this element, in the promoter of H2B, there was another sequence, 5'-GGATCGAAACGTTC-3', which was similar to the consensus sequence of 5'-GGAATAAACGTATTC-3' corresponding to the H2B-specific promoter element. The presence of enhancer sequences (5'-TGATATATG-3') was identified from the H4 and H3 genes, matching perfectly with the consensus sequence defined for histone genes. There were several slightly more complex repetitive DNA in the intergene regions. The presence of the series of conserved sequences and reiterated sequences was consistent with the view that mollusc histone gene cluster arose by duplicating of an ancestral precursor histone gene, the birth-and-death evolution model with strong purifying selection enabled the histone cluster less variation and more conserved function. Meanwhile, the H2A and the H2B were demonstrated to be potential good marks for phylogenetic analysis. All the results will be contributed to the characterization of repeating histone gene families in molluscs.

Effect of block sequence and block length on the stimuli-responsive behavior of polyampholyte brushes: hydrogen bonding and electrostatic interaction as the driving force for surface rearrangement

Diblock polyampholyte brushes with different block sequences (Si/SiO2/poly(acrylic acid)-b-poly (2-vinylpyridine) (PAA-b-P2VP) brushes and Si/SiO2/P2VP-b-PAA brushes) and different block lengths were synthesized by sequent surface-initiated atom transfer radical polymerization (ATRP). The PAA block was obtained through hydrolysis from the corresponding poly(tert-butyl acrylate). The polyampholyte brushes demonstrated unique pH-responsive behavior. In the intermediate pH region, the brushes exhibited a less hydrophilic wetting behavior and a rougher surface morphology due to the formation of polyelectrolyte complex through electrostatic interaction between oppositely charged blocks. In the low pH and high pH regions, the rearrangement of polyampholyte brushes showed great dependence on the block sequence and block length. The polyampholyte brushes with P2VP-b-PAA sequence underwent rearrangement during alternative treatment by acidic aqueous solution (low pH value) and basic aqueous solution (high pH value).

7-Amino actinomycin D bound to single-stranded hairpin DNA enhanced by loop sequence-dependent luminescent Eu3+ and Tb3+ binding

Lanthanide Eu3+ and Tb3+ ions have been widely used in luminescent resonance energy transfer (LRET) for bioassays to study metal binding microenvironments. We report here that Eu3+ or Tb3+ can increase the binding affinity of antitumor antibiotic drug agent, 7-amino actinomycin D (7AACTD), binding to 5'-GT/TG-5' or 5'-GA/AG-5' mismatched stem region of the single-stranded hairpin DNA. Further studies indicate that the effect of Eu3+ or Tb3+ on 7AACTD binding is related to DNA loop sequence. Our results will provide new insights into how metal ions can enhance antitumor agents binding to their targets.

Comparison for DNA primary sequence

In this article, two schemes are suggested based on three exons of beta-globin gene belonging to 10 species for comparison of DNA primary sequences. At first, the positions of four nucleic acid bases were extracted, and then based on the information, as the numerical characterization of DNA sequences, the sequence invariants were derived. Sequences comparisons of 10 species selected in this work by using these invariants were performed. The results, especially with scheme 2, are quite satisfactory.

A novel invariant and sequence comparison for DNA

We consider numerical characterization of DNA primary sequence based on the positions of bases (a, t, c, g) and the pairs of bases X, Y in DNA (X, Y=a, t, c, g). This leads to a representation of DNA by a numerical sequence. Then, we extract a novel invariant (molecular connectivity index) from the derived numerical sequences. The suitable invariant can offer a characterization of DNA primary sequence. Finally, we provide an illustration of its utility by making a comparison between ten DNA sequences belonging to beta-globin gene in different species. The evolutionary relationships of ten species we have revealed in this contribution accord with phylogenetic tree properly.

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.

Effect of DNA flanking sequence on charge transport in short DNA duplexes

Several factors can influence charge transport (CT)-mediated DNA, such as sequence, distance, base stacking, base pair mismatch, conformation, tether length, etc. However, the DNA context effect or how flanking sequences influence redox active drugs in the DNA CT reaction and later in DNA enzymatic repair and synthesis is still not well understood. The set of seven DNA molecules in this study have been characterized well for the study of flanking sequence effects. These DNA duplexes are formed from self-complementary strands and contain the common central four-base sequence 5'-A-G-C-T-3', flanked on both sides by either (AT)(n) or (AA)(n) (n = 2, 3, or 4) or AA(AT)(2). UV-vis, fluorescence, UV melting, circular dichroism, and cyclic voltammetry experiments were used to study the flanking sequence effect on CT-mediated DNA by using daunomycin or adriamycin cross-linked with these seven DNA molecules. Our results showed that charge transport was related to the flanking sequence, DNA melting free energy, and ionic strength. For (AA)(n) or (AT)(n) species of the same length, (AA)(n) series were more stable and more efficient CT was observed through the (AA)(n) series. The same trend was observed for (AA)(n) and (AT)(n) series at different ionic strengths, further supporting the idea that flanking sequence can result in different base stacking and modulate charge transport through these seven DNA molecules.

Polydispersity of ethylene sequence length in metallocene ethylene/alpha-olefin copolymers. I. Characterized by thermal-fractionation technique

In this article, the polydispersity of the ethylene sequence length (ESL) in ethylene/alpha-olefin copolymers was studied by atomic force microscopy (AFM) and the thermal-fractionation technique. The crystal morphology observation by AFM showed that morphology changed gradually with decreasing average ESL from complete lamellae over shorter and more curved lamellae to a granular-like morphology, and the mixed morphology was observed after stepwise crystallization from phase-separated melt. This result indicated that the ethylene sequence with different lengths crystallized into a crystalline phase with a different size and stability at the copolymer systems. The thermal-fractionation technique was used to characterize the polydispersity of ESL. Three of the following statistical terms were introduced to describe the distribution of ESL and the lamellar thickness: the arithmetic mean (L) over bar (n), the weight mean (L) over bar (w), and the broadness index I = (L) over bar (w)/(L) over bar (n). It was concluded that the polydispersity of ESL could be quantitatively characterized by the thermal-fractionation technique. The effects of temperature range, temperature-dependent specific heat capacity C-p of copolymer, and the molecular weight on the results of thermal fractionation were discussed,

Polydispersity of ethylene sequence length in metallocene ethylene/alpha-olefin copolymers. II. Influence on crystallization and melting behavior

In this work, crystallization and melting behavior of metallocene ethylene/alpha-olefin copolymers were investigated by differential scanning calorimetry (DSC) and atomic force microscopy (AFM). The results indicated that the crystallization and melting temperatures for all the samples were directly related to the long ethylene sequences instead of the average sequence length (ASL), whereas the crystallization enthalpy and crystallinity were directly related to ASL, that is, both parameters decreased with a decreasing ASL. Multiple melting peaks were analyzed by thermal analysis. Three phenomena contributed to the multiple melting behaviors after isothermal crystallization, that is, the melting of crystals formed during quenching, the melting-recrystallization process, and the coexistence of different crystal morphologies. Two types of crystal morphologies could coexist in samples having a high comonomer content after isothermal crystallization. They were the chain-folded lamellae formed by long ethylene sequences and the bundlelike crystals formed by short ethylene sequences. The coexistence phenomenon was further proved by the AFM morphological observation.

The polydispersity of ethylene sequence in metallocene ethylene/alpha-olefin copolymers III: crystallization and melting behavior of short ethylene sequence

Crystallization and melting behavior of short ethylene sequence of metallocene ethylene/alpha -olefin copolymer with high comonomer content have been studied by standard DSC and modulated-temperature differential scanning calorimetry (M-TDSC) technique. In addition to high temperature endotherm around 120 degreesC, a low temperature endotherm is observed at lower temperatures (40-80 degreesC), depending on time and temperature of isothermal crystallization. The peak position of the low temperature endotherm T-m(low) varies linearly with the logarithm of crystallization time and the slope, D, decreases with increasing crystallization temperature T-c. The T-m(low) also depends on the thermal history before the crystallization at T-c, and an extrapolation of T-m(low) (30.6 degreesC) to a few seconds has been obtained after two step isothermal crystallization before the crystallization at 30 degreesC. The T-m(low) is nearly equal to T-c, and it indicates that the initial crystallization at low temperature is nearly reversible. Direct evidence of conformational. entropy change of secondary crystallization has been obtained by using M-TDSC technique. Both the M-TDSC result and the activation energy analysis of temperature dependence suggest that crystal perfection process and conformational entropy decreasing in residual amorphous co-exist during secondary crystallization.

Crystalline behavior and critical crystalline sequence length of propylene/alpha-olefin copolymer

The melting points(T-m), crystalline temperature(T-c) and crystallinity(chi(c)) of propylene/alpha-olefin (pentene-l, octene-1 and decene-1) copolymers have been investigated, The results show that the T-m, T-c and chi(c) of the copolymers are lower than those of propylene homopolymer, indicating that lower alpha-olefin incorporation in copolymer has strongly hampered the crystallization of propylene, From critical crystalline sequence length of several propylene/alpha-olefin copolymers, it can be seen that a long chain alpha-olefin has much stronger effect on crystallization of PP than a short alpha-olefin does.