We use Monte-Carlo simulations to study the effect of variable rigidity on plectoneme formation and localization in supercoiled double-stranded DNA. We show that the presence of soft sequences increases the number of plectoneme branches and that the edges of the branches tend to be localized at these sequences. We propose an experimental approach to test our results in vitro, and discuss the po...

Transcription factors (TFs) are regulatory proteins that bind DNA in promoter regions of the genome and either promote or repress gene expression. Here, we predict analytically that enhanced homooligonucleotide sequence correlations, such as poly(dA:dT) and poly(dC:dG) tracts, statistically enhance nonspecific TF-DNA binding affinity. This prediction is generic and qualitatively independent of ...

The emission of a specific blend of volatiles in response to Mythimna separata (herbivore-induced plant volatiles, HIPVs) plays a great ecological role by priming neighbouring plants. Maize plants placed downwind of infested, conspecific plants showed reduced larval development not only immediately after exposure to HIPVs but also when receiver plants were tested after a time lag of up to 5 day...

Aromatase in the mouse brain is expressed only in the nerve cells of specific brain regions with a transient peak during the neonatal period when sexual behaviors become organized. The aromatase-knockout (ArKO) mouse, generated to shed light on the physiological functions of estrogen in the brain, exhibited various abnormal behaviors, concomitant with undetectable estrogen and increased androge...

Well-characterized promoters are essential tools for metabolic engineering and synthetic biology. In Streptomyces coelicolor, the native kasOp is a temporally expressed promoter strictly controlled by two regulators, ScbR and ScbR2. In this work, first, kasOp was engineered to remove a common binding site of ScbR and ScbR2 upstream of its core region, thus generating a stronger promoter, kasOp3...

BACKGROUND/AIMS In recent years, with improvements in genotyping, a possible relationship between obesity-related gene polymorphisms and colorectal cancer (CRC) has been studied. The promoter region C-420G of the resistin gene is believed to have an important role in the development of malignancy. We prospectively evaluated the possible effect of the resistin C-420G polymorphism on the risk and...

The DNA sequence of 168 promoter regions (-50 to +10) for Escherichia coli RNA polymerase were compiled. The complete listing was divided into two groups depending upon whether or not the promoter had been defined by genetic (promoter mutations) or biochemical (5' end determination) criteria. A consensus promoter sequence based on homologies among 112 well-defined promoters was determined that ...

Calcimycin is a unique ionophoric antibiotic that is widely used in biochemical and pharmaceutical applications, but the genetic basis underlying the regulatory mechanisms of calcimycin biosynthesis are unclear. Here, we identified the calR3 gene, which encodes a novel TetR family transcriptional regulator and exerts a negative effect on calcimycin biosynthesis. Disruption of calR3 in Streptomy...

We have demonstrated that the ovine genomic clone SS1 can be used to generate transgenic mice that produce significant quantities of BLG protein in milk. The smallest BLG construct so far examined that retains the ability to direct BLG to mouse milk encompasses approximately 7.3 kb of genomic DNA, of which about 0.8 kb is derived from the promoter region. Gene expression is tissue-specific and ...

By gel retardation experiments with crude cell extracts of Paracoccus denitrificans it was demonstrated that a protein specifically binds to the promoter of the P. denitrificans recA gene. PCR mutagenesis of the recA promoter showed that the GAACN7GAAC motif is required for the formation of the DNA-protein complex. This protein also binds to the GTTCN7GTTC motif, which is present in the promote...