Nature Of Divalent Ion Research Articles

Regulation of transcriptional pausing through the secondary channel of RNA polymerase

Transcriptional pausing has emerged as an essential mechanism of genetic regulation in both bacteria and eukaryotes, where it serves to coordinate transcription with other cellular processes and to activate or halt gene expression rapidly in response to external stimuli. Deinococcus radiodurans, a highly radioresistant and stress-resistant bacterium, encodes three members of the Gre family of transcription factors: GreA and two Gre factor homologs, Gfh1 and Gfh2. Whereas GreA is a universal bacterial factor that stimulates RNA cleavage by RNA polymerase (RNAP), the functions of lineage-specific Gfh proteins remain unknown. Here, we demonstrate that these proteins, which bind within the RNAP secondary channel, strongly enhance site-specific transcriptional pausing and intrinsic termination. Uniquely, the pause-stimulatory activity of Gfh proteins depends on the nature of divalent ions (Mg(2+) or Mn(2+)) present in the reaction and is also modulated by the nascent RNA structure and the trigger loop in the RNAP active site. Our data reveal remarkable plasticity of the RNAP active site in response to various regulatory stimuli and highlight functional diversity of transcription factors that bind inside the secondary channel of RNAP.

Transport Studies of Divalent Ions through Nafion-117 Ion Exchange Membrane in the Presence of Polyacrylate

The effect of binding of divalent ions (Mg2+ and Ba2+) with a polyacrylate anion on the Donnan membrane equilibrium distribution and the transport kinetics have been studied using Nafion-117 membrane. The extent of association of the divalent counterions with polyacrylate has been ascertained from the deviation from Donnan membrane equilibrium condition. The equilibrium concentrations of ions in polyacrylate compartment have been found to be in excess of expected equilibrium concentrations obtained from Donnan membrane equilibrium condition. This has been attributed to higher electrostatic interactions of divalent ions with the polyacrylate backbone compared to the monovalent ions. The strength of binding has been found to depend on the nature of divalent ion. Precipitation has been observed for Ba2+, thereby changing the total salt concentration of the polyacrylate compartment. Also, the strength of counterion binding has been found to depend on salt concentrations of the two compartments. The rate of transport of the ions with polyacrylate in the receiver solution has been calculated based on modified Nernst–Planck (NP) approach. The calculated transport kinetics have been found to agree with the experimental transport kinetics.

Use of Fluorescein-Labeled Oligonucleotide for Analysis of Formation and Dissociation Kinetics of T:A:T Triple-Stranded DNA: Effect of Divalent Cations

The formation and dissociation kinetics of homonucleotide oligo(dT):oligo(dA):oligo(dT) triplex have been analyzed by fluorescence measurements of fluorescein-labeled oligo(dT) providing considerably higher sensitivity to monitoring reaction kinetics than traditional hypochromicity and circular dichroism. The triplex is concluded to be formed by a bimolecular process corresponding to the addition of the oligo(dT) strand to a preserved oligo(dT):oligo(dA) duplex. The association rate was found to be faster the higher the divalent cation concentration and depends upon the nature of divalent ions in the following order of efficiency: Mn2+ > Mg2+ > Ni2+, Ca2+ > Ba2+. The more efficient metal ions for the triplex formation were found also more efficient for the stabilization. The dissociation kinetics of the third Hoogsteen-bound strand was monitored at below melting temperature by chasing the labeled dT strand from the triplex by excess of non-labeled oligonucleotide. The dissociation rate was found to be almost independent of concentration and nature of cation. The thermodynamic stabilization of triplex by cations is thus a consequence of the increased formation rate.