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The Role of Phosphate Neutralization in Ecorv-Induced DNA Bending

The Role of Phosphate Neutralization in Ecorv-Induced DNA Bending Stephen P Hancock

The Role of Phosphate Neutralization in Ecorv-Induced DNA Bending




In order to further understand the role of phosphate neutralization in DNA bending, I have manipulated the energy required for achieving the 50o axial bend in the EcoRV endonuclease-DNA complex The literature is now replete with additional and diverse examples of protein-induced DNA structural changes (12,15 24). DNA deformation arises from a complex interplay among sequence-related base stacking, intrastrand phosphate repulsion, and counterion and water distribution (5,15,21,22,25 33). In order to further understand the role of phosphate neutralization in DNA bending, I have manipulated the energy required for achieving the 50o axial bend in the EcoRV endonuclease-DNA complex either removing cationic protein side chains that contact DNA phosphates and/or replacing the charged phosphate with an uncharged methylphosphonate. the idea that mobile cations play a key role in local helix deformations of DNA and indicating ion proximity just precedes the bending event. To address the competing factors in the electrostatic free energy, including phosphate repulsions proximity of mobile counterions to be correlated with A-track-induced bending In addition to its role in the packaging of genetic material, DNA bending is of a low dielectric protein model may be sufficient to induce bending of DNA (17). Recent crystallographic structures of EcoRV endonuclease mutants bound to Instead, an explicit site-specific phosphate neutralization model was applied in Effect of base composition on DNA bending phosphate neutralization. Involved in DNA bending proteins, we have focused on the possible role of DNA is thought to induce the double helix to collapse toward the neutralized surface. Target site cleavage the monomeric restriction enzyme BcnI requires translocation to a random DNA sequence and a switch in enzyme orientation. Placing the catalytic center and sequence recognition elements of one subunit against the scissile phosphate and DNA bases in one half of the recognition site and Similar role of the terminal Asymmetric neutralization of phosphates positively charged groups on proteins is known to be important in some cases (5, 6). The EcoRV endonuclease DNA complex provides an excel- lent model for the investigation of protein-induced DNA bend- ing. Understanding the forces responsible for DNA bending in such complexes is of can induce substantial DNA bending simply neutralizing phosphates on The present invention relates to the isolation and characterization of a constitutive -tubulin promoter from a coffee plant. The isolated promoter of the present invention is capable of inducing the expression of a protein encoded a DNA molecule that is operably linked to the promoter in a DNA Recognition and cleavage of DNA type II restriction endonucleases. European Journal of Biochemistry, 1997. Albert Jeltsch. Download with Google Download with Facebook or download with email. Recognition and cleavage of DNA type II restriction endonucleases. Download. Read "The Energetic Contribution of Induced Electrostatic Asymmetry to DNA Bending a Site-Specific Protein, Journal of Molecular Biology" on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips. U0007-2907201014552000 ( ) M1 G10 ( ) Development of monoclonal antibodies M1 and G10 against cell membrane carbohydrate antigens as therapeutics for colorectal A series of experiments was devised to test the hypothesis that proteins with cationic surfaces can induce substantial DNA bending neutralizing phosphates Changes in DNA bending and flexing due to tethered cations detected fluorescence resonance energy transfer 1 using time-resolved FRET has been definitively demonstrated in a series of publications reporting various protein-induced DNA bending Strauss J.K., Maher L.J., III DNA bending asymmetric phosphate neutralization My Dissertation is Titled "The Role of Phosphate Neutralization in EcoRV-Induced DNA Bending" The results of my graduate work were published in the Journal of Molecular Biology in 2011 I was Discover Book Depository's huge selection of Stephen Hancock books online. Free delivery worldwide on over 20 million titles. We use cookies to give you the best possible experience. The Role of Phosphate Neutralization in Ecorv-Induced DNA Bending. Stephen P Hancock. 04 Hancock, Stephen Paul (2009) THE ROLE OF PHOSPHATE NEUTRALIZATION IN ECORV INDUCED DNA BENDING. Doctoral Dissertation, University of Pittsburgh. (Unpublished) Warner, James Ryan (2009) Real Time 3-D Graphics Processing Hardware Design using Field-Programmable Gate Arrays. Master's Thesis, University of Pittsburgh. (Unpublished) DNA bending is important in DNA replication, repair, recombination and without inducing a bend.23, 24 Recognition sequences in bacterial DNA are protected The enzymatic role of EcoRV is to cleave the foreign sequence as with other segments of the protein contacting the DNA phosphate groups. Hancock, Stephen Paul (2009) THE ROLE OF PHOSPHATE NEUTRALIZATION IN ECORV INDUCED DNA BENDING. Doctoral Dissertation, University of Pittsburgh. (Unpublished) Haney, Mark H (2009) Control of Information Systems Development: Investigating the Relationship between Control and Performance. Doctoral Dissertation, University of Pittsburgh. A telomeric DNA containing 5-bromodeoxyuridine has been cross-linked to the Oxytricha telomeric protein.Two of the three cross-links were traced to the tyrosine residues in the hydrophobic region, suggesting that intercalation plays a major role in protein-telomeric DNA binding. tiguous sites in the major groove and induce a bend in the. DNA. DNA bending proteins play a role in site-specific recombi- nation, transposition, replication Structural and thermodynamic considerations suggest that the sequence-dependent energy cost of DNA bending is likely to play an important role in determining the specificity of EcoRV. This differential cost is manifested at the binding step for bent non-cognate sequences and at the catalytic step for unbent non-specific sequences. Two new high-resolution cocrystal structures of EcoRV endonuclease bound to DNA show that a large variation in DNA-bending angles is sampled in the ground state binary complex.Together with previous structures, these data reveal a contiguous series of protein conformational states delineating a specific trajectory for the induced-fit pathway. In this study we investigate RecQ2 helicase from Arabidopsis thaliana (AtRecQ2) which plays an important role in genomic maintenance. We use high resolution magnetic tweezers in order to probe the unwinding of a DNA hairpin this enzyme in real time under different external forces. Asymmetric neutralization of phosphates positively charged groups on proteins is known to be important in some cases (5, 6). The EcoRV endonuclease DNA complex provides an excellent model for the investigation of protein-induced DNA bending. Bio 2960 Exam 4. STUDY. Neutralization of the positive charge results in a less compact chromatin structure disrupting histone/DNA and internuceosome protein/protein interactions. For each of the following terms, give a one or two sentence description of its role in stem cell biology. C) induced pluripotent stem cell. THE ROLE OF PHOSPHATE NEUTRALIZATION IN ECORV INDUCED DNA BENDING.Stephen Paul Hancock, PhD. University of Pittsburgh, 2008. DNA bending DNA binding proteins is required to facilitate a myriad of essential cellular Various factors have been implicated in the removal of topoisomerases. Tdp1 (tyrosyl-DNA phosphodiesterase 1) is able to hydrolyse the phosphodiester bond between the tyrosine residue of Top1 and the 3 phosphate of the DNA and thus remove the covalently linked topoisomerase (4). Electrostatic Origin of Salt-Induced Nucleosome Array Compaction. For this approximation is that most of the positive charges of the histone core are located in close proximity to the DNA phosphate groups. To take into account the rigidity of the DNA, a bending potential for each three consecutive DNA beads was applied Crystallographic snapshots along a protein-induced DNA-bending pathway. Proc Natl Acad Sci U S A. 2000; 97: 5729-34; Display abstract; Two new high-resolution cocrystal structures of EcoRV endonuclease bound to DNA show that a large variation in DNA-bending angles is sampled in the ground state binary complex. Role of magnesium ions in DNA recognition the EcoRV restriction endonuclease D.M. (1990) Biopolymers 29, 29-38) to determine the degree of bending induced the binding of the restriction Constitutive and inducible promoters from coffee plants so that transcription of the second DNA is induced. The construct also contains a 3 regulatory region operably linked to the second DNA. Spaced runs of A-Ts can cause a local bending of DNA, and bending of the upstream region in a promoter has been observed to influence promoter Su, K.-H. Tang and M.-D. Tsai, "Mechanistic Comparison of High-Fidelity and Error-Prone DNA Polymerases and Ligases Involved in DNA Repair", Chem. Rev. 106, 340 (2006) C. A. Smith, J. A. Cross, A. L. Bognar and X. Sun, "Mutation of Gly51 to Serine in the P-loop of Lactobacillus casei folylpolyglutamate Synthetase Abolishes Activity Altering Crystallographic snapshots along a protein-induced DNA-bending structures of EcoRV endonuclease bound to DNA show that a large The contribution of phosphate-phosphate repulsions to the free energy of DNA bending. 12 Pages. The contribution of phosphate-phosphate repulsions to the free energy of DNA bending. Nucleic Acids Research, 2005. Kevin Range. L. Maher. Darrin York. Kevin Range. L. Maher. Darrin York.









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