PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 14525509

Sequence dependent DNA-mediated conduction.

Stephan Roche
View original source ↗Export metadata ↓

Abstract

We report on coherent charge transport studies in periodic Poly(dG)-Poly(dC) and aperiodic lambda-phage DNA sequences. The extent and efficiency of charge transfer is discussed as a function of sequence dependent energetics, of temperature dependent base-base couplings, and in relation with experiments.

Explore related subjects

Bacteriophage lambdaBase SequenceDNA, ViralElectric ConductivityElectrochemistryElectrodesModels, ChemicalMolecular Sequence DataPolydeoxyribonucleotidesJournal Article

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Stephan Roche. 2003-09-03. Sequence dependent DNA-mediated conduction.. https://doi.org/10.1103/physrevlett.91.108101

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2004

A column method for determination of DNA cytosine-C5-methyltransferase activity.

DNA methylation at the 5th position of cytosine has been found to be correlated with tumorigenesis. An inhibitor of DNA methylase could, therefore, be used as an anticancer drug. However, only a few inhibitory compounds have been discovered due to the limitations for assaying the DNA methylation. In this study, we describe a modification of DNA cytosine-C5-methyltransferase assay system utilizing [(3)H]-labeled S-adenosyl-methionine (SAM) and Sephadex G-25 column. Pre-treatment of either lambda DNA or the promoter region of human telomerase (hTERT) with HaeIII methylase greatly reduced the digestion of the DNAs with the corresponding restriction enzyme HaeIII endonuclease (over 100-fold), and the result was further confirmed by agarose gel electrophoresis. Application of this column method to another modification/restriction system, EcoRI methylase/endonuclease, gave rise to the similar results. Our data suggest that the newly developed column method could be effective for rapid screening of large number of cytosine methylase inhibitors and could also be applicable to other DNA methylases.

Bacteriophage lambda↗
PubMed2004

Calculating biological behaviors of epigenetic states in the phage lambda life cycle.

The biology and behavior of bacteriophage lambda regulation have been the focus of classical investigations of molecular control of gene expression. Both qualitative and quantitative aspects of this behavior have been systematically characterized experimentally. Complete understanding of the robustness and stability of the genetic circuitry for the lysis-lysogeny switch remains an unsolved puzzle. It is an excellent test case for our understanding of biological behavior of an integrated network based on its physical, chemical, DNA, protein, and functional properties. We have used a new approach to non-linear dynamics to formulate a new mathematical model, performed a theoretical study on the phage lambda life cycle, and solved the crucial part of this puzzle. We find a good quantitative agreement between the theoretical calculation and published experimental observations in the protein number levels, the lysis frequency in the lysogen culture, and the lysogenization frequency for mutants of O(R). We also predict the desired robustness for the lambda genetic switch. We believe that this is the first successful example in the quantitative calculation of robustness and stability of the phage lambda regulatory network, one of the simplest and most well-studied regulatory systems.

Bacteriophage lambda↗
PubMed2004

Sensitivity of OR in phage lambda.

We investigate the sensitivity of the right operator in bacteriophage lambda. In particular, the system is probed in the three different regulatory protein concentration-regimes: 1), lysogen (CI dominates); 2), during induction (CI and Cro at comparable concentrations); and 3), after induction (Cro dominates). Systematic perturbations of the protein-operator binding energies show in a lysogen that the activity (production rate) at promoter PRM is robust to variations, in contrast to PR, where the sensitivity is high. Both promoters, however, show large sensitivity in regimes 2 and 3. In all regimes we identify several suppressors, meaning that for a given large perturbation (+/-2 kcal/mol) of one binding energy, there exist compensating perturbation(s) that restore the wild-type activity.

Bacteriophage lambda↗