DNA recognition by Zn [Cysteinyl-His-OMe]2: A minimal zinc finger docking unit

Zinc fingers, 30-residue peptides anchored on Zn(II) coordinated to pairs of cysteines and histidines, recognize DNA triplets and, as tandem modules, effect sequence read out. The focus of zinc finger-DNA interaction studies thus far has been to probe the nature of the binding of the 12-residue recognition element of the finger with DNA code bases. To understand the possible role of the Zn(II) ligand and to assess its own DNA interaction profile, [(CH)₂Zn] (C: cysteine; H: histidine; Figure 1) was constructed from bis-^t Boc-cystinyl-di-His-OMe via thiol-disulfide exchange, Zn(II) complexation, and deprotection. [(CH)₂Zn] binds with polyd- (G·C)·polyd(G·C) with association constants—1.8 × 10⁷ M⁻¹ (specific DNA-phosphate) and 3.3 × 10³ M⁻¹ (nonspecific DNA-phosphate); perturbs its B-DNA profile; and enhances the T_m from 62.5 to 70.15°C in a concentration-independent manner, with an ideal reversal profile on cooling, not observed in the DNA alone; releases polyd(G·C)·polyd(G·C)-bound ethidium bromide; enhances the fluorescence of polyd(G·C)·polyd(G·C)-bound ethidium bromide at low concentrations; and quenches it at higher ranges. [(CH)₂Zn] also binds to d(ACGCTGGGCGT), the sequence associated with Zif-268, 3-finger binding site. Such interactions were not seen in parallel studies with (a) polyd(A·T)·polyd(A·T) and [(CH)₂Zn] and (b) {[C′H₂] (C′: cystine; H: histidine; the direct metal-free precursor of [(CH)₂Zn]}, ionic zinc nitrate, and covalent zinc acetyl acetonate Zn(AcAc)₂, with poly[d(G·C)·polyd(G·C)]. The results are rationalized on the basis of two types of association between [(CH)₂Zn] and polyd(G·C)·polyd(G·C), a nonspecific recognition of the sugar phosphate backbone, by an imidazole of [(CH)₂Zn] and a specific one involving the amino group of [(CH)₂Zn] and the guanine base of DNA. Control experiments show that the latter greatly promotes DNA recognition. The possibility for such specific interactions with relatively small structures of the type [(CH)₂Zn] would be of use in the design of DNA recognition elements and also provide an explanation for the experimentally found variation in the placement of the zinc finger docking unit around the major groove of DNA. © 1997 John Wiley & Sons, Inc.     

Simulated microgravity promoted differentiation of bipotential murine oval liver stem cells by modulating BMP4/Notch1 signaling

Faster growth and differentiation of liver stem cells to hepatocyte is one of the key factors during liver regeneration. In recent years, simulated microgravity, a physical force has shown to differentially regulate the differentiation and proliferation of stem cells. In the present work, we studied the effect of simulated microgravity on differentiation and proliferation of liver stem cells. The cells were subjected to microgravity, which was simulated using indigenously fabricated 3D clinostat. Proliferation, apoptosis, immunofluorescence assays and Western blot analysis were carried out to study the effects of simulated microgravity on liver stem cells. Microgravity treatment for 2 h enhanced proliferation of stem cells by twofold without inducing apoptosis and compromising cell viability. Analysis of hepatocyte nuclear factor 4‐α (HNF4‐α) expression after 2 h of microgravity treatment revealed that microgravity alone can induce the differentiation of stem cells within 2–3 days. Probing bone morphogenic protein 4 (BMP4) and Notch1 in microgravity treated stem cells elaborated downregulation of Notch1 and upregulation of BMP4 after 2 days of incubation. Further, blocking BMP4 using dorsomorphin and chordin conditioned media from chordin plasmid transfected cells attenuated microgravity mediated differentiation of liver stem cells. In conclusion, microgravity interplays with BMP4/Notch1 signaling in stem cells thus inducing differentiation of stem cells to hepatocytes. Present findings can be implicated in clinical studies where microgravity activated stem cells can regenerate the liver efficiently after liver injury. J. Cell. Biochem. 112: 1898–1908, 2011. © 2011 Wiley‐Liss, Inc.     

An improved method for the purification of DNA-dependent RNA polymerase from Escherichia coli

DNA-dependent RNA polymerase from Escherichia coli was purified further by elution through heparin-Sepharose CL-6B column after the enzyme was obtained, partially purified, using Burgess and Jendrisak's method [(1975)Biochemistry 14, 4634] The total yield of the pure protein was 10 mg from 50 g of E.coli cells. The method was found to be very reproducible and convenient. The enzyme preparation had 60% active molecules and the elongation rate of RNA synthesis by this enzyme was measured to be 11 bases/s over delta D111 T7 DNA.     

Spectroscopic studies on the mode of binding of ATP, UTP and alpha-amanitin with yeast RNA polymerase II

The binding affinity between the substrates ATP and UTP with the purified yeast RNA polymerase II have been studied here in the presence and absence of Mn2+. In the absence of template DNA, both ATP and UTP showed tight binding with the enzyme without preference for any specific nucleotide, unlike Escherichia coli RNA polymerase. Fluorescence titration of the tryptophan emission of the enzyme by nucleoside triphosphate substrates gave an estimated Kd value around 65 microM in the absence of Mn2+ whereas in the presence of Mn2+, the Kd was 20 microM. The effect of substrates on the longitudinal relaxation of the HDO proton in enzyme-substrate complex also yielded a similar Kd value.     

Understanding protein-protein interactions by genetic suppression

Protein-protein interactions influence many cellular processes and it is increasingly being felt that even a weak and remote interplay between two subunits of a protein or between two proteins in a complex may govern the fate of a particular biochemical pathway. In a bacterial system where the complete genome sequence is available, it is an arduous task to assign function to a large number of proteins. It is possible that many of them are peripherally associated with a cellular event and it is very difficult to probe such interaction. However, mutations in the genes that encode such proteins (primary mutations) are useful in these studies. Isolation of a suppressor or a second-site mutation that restores the phenotype abolished by the primary mutation could be an elegant yet simple way to follow a set of interacting proteins. Such a reversion site need not necessarily be geometrically close to the primary mutation site.     

Structure of the water-soluble feeding stimulant for Scolytus multistriatus: A revision

The feeding stimulant for the smaller European elm bark beetle has been revised to (+)-catechin 7-β-d-xylopyranoside (III) from the structure (I) bearing the sugar at the 5-position.