Differences in the kinetic properties of BamHI endonuclease and methylase with linear DNA substrates.

Nardone, Gerardo; George, J; Chirikjian, Jack G.

doi:10.1016/s0021-9258(18)67212-6

Cited by 59 publications

(22 citation statements)

References 24 publications

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“…Facilitated diffusion has since been demonstrated and quantified for a variety of DNA binding proteins (Dowd and Lloyd, 1990;Herendeen et al, 1992;Jack et al, 1982;Nardone et al, 1986;Ricchetti et al, 1988;Surby and Reich, 1996).…”

Section: Introductionmentioning

confidence: 99%

Mobility of Taxol in Microtubule Bundles

Ross

Fygenson

2003

Biophysical Journal

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Mobility of taxol inside microtubules was investigated using fluorescence recovery after photobleaching on flow-aligned bundles. Bundles were made of microtubules with either GMPCPP or GTP at the exchangeable site on the tubulin dimer. Recovery times were sensitive to bundle thickness and packing, indicating that taxol molecules are able to move laterally through the bundle. The density of open binding sites along a microtubule was varied by controlling the concentration of taxol in solution for GMPCPP samples. With >63% sites occupied, recovery times were independent of taxol concentration and, therefore, inversely proportional to the microscopic dissociation rate, k(off). It was found that 10k(off)(GMPCPP) approximately equal k(off)(GTP), consistent with, but not fully accounting for, the difference in equilibrium constants for taxol on GMPCPP and GTP microtubules. With <63% sites occupied, recovery times decreased as approximately [Tax](-1/5) for both types of microtubules. We conclude that the diffusion of taxol inside the microtubule bundle is hindered by rebinding events when open sites are within approximately 7 nm of each other.

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Section: Introductionmentioning

confidence: 99%

Mobility of Taxol in Microtubule Bundles

Ross

Fygenson

2003

Biophysical Journal

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“…Protein-DNA interactions play important roles in life processes, such as DNA replication, transcription, recombination, damage, and repair. [10][11][12][13][14] The restriction endonuclease is a well-studied class of DNA-binding proteins and has been one important tool in the development of modern molecular biology. 10,15,16 However, to our best knowledge, there has been no report on the DNA analysis based on the cleavage of endonuclease.…”

mentioning

confidence: 99%

“…[10][11][12][13][14] The restriction endonuclease is a well-studied class of DNA-binding proteins and has been one important tool in the development of modern molecular biology. 10,15,16 However, to our best knowledge, there has been no report on the DNA analysis based on the cleavage of endonuclease. We have developed a new approach for qualitative and quantitative HCV detection based on site-specific DNA cleavage of BamHI endonuclease.…”

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confidence: 99%

Electrochemical detection of hepatitis C virus based on site-specific DNA cleavage of BamHI endonuclease

et al. 2009

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“…In general, the facilitated location of an operator by a protein is likely to consist of a sequence of sliding, hopping or intersegmental transfer events [27]. A growing body of evidence exists that many regulatory proteins, such as repressors [28], [29] RNAP's [30]- [34], nucleases [35] and methylases [36] locate their operator sites in this way.…”

Section: Protein Slidingmentioning

confidence: 99%

Salerno's Model of DNA Re-Analysed: Could Breather Solitons have Biological Significance?

Bashford

2006

J Biol Phys

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Abstract.We investigate the sequence-dependent behaviour of localised excitations in a toy, nonlinear model of DNA base-pair opening originally proposed by Salerno. Specifically we ask whether "breather" solitons could play a role in the facilitated location of promoters by RNA polymerase (RNAP). In an effective potential formalism, we find excellent correlation between potential minima and Escherichia coli promoter recognition sites in the T7 bacteriophage genome. Evidence for a similar relationship between phage promoters and downstream coding regions is found and alternative reasons for links between AT richness and transcriptionally-significant sites are discussed. Consideration of the soliton energy of translocation provides a novel dynamical picture of sliding: steep potential gradients correspond to deterministic motion, while "flat" regions, corresponding to homogeneous AT or GC content, are governed by random, thermal motion. Finally we demonstrate an interesting equivalence between planar, breather solitons and the helical motion of a sliding protein "particle" about a bent DNA axis.

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Differences in the kinetic properties of BamHI endonuclease and methylase with linear DNA substrates.

Cited by 59 publications

References 24 publications

Mobility of Taxol in Microtubule Bundles

Mobility of Taxol in Microtubule Bundles

Electrochemical detection of hepatitis C virus based on site-specific DNA cleavage of BamHI endonuclease

Salerno's Model of DNA Re-Analysed: Could Breather Solitons have Biological Significance?

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