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Volumn 94, Issue 12, 2005, Pages 1-4

Unravelling the mechanism of RNA-polymerase forward motion by using mechanical force

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; BROWNIAN MOVEMENT; CATALYSIS; COMPLEXATION; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DIFFUSION; DNA; ESCHERICHIA COLI; FREE ENERGY; HYDROLYSIS; KINETIC THEORY; RNA;

EID: 85056017495     PISSN: 00319007     EISSN: 10797114     Source Type: Journal    
DOI: 10.1103/PhysRevLett.94.128102     Document Type: Article
Times cited : (60)

References (31)
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    • (a) R. A. Alberty J. Biol. Chem. 244, 3290 (1969); the standard Gibbs free energy ΔG is typically of the order of -20 kT for breaking NTP to form NMP and PPi, and the ΔG for phosphodiesther bond formation during DNA ligation has been estimated to be of the order of + 10 kT. In the case of a newly inserted base, there will also be an entropie penalty due to the base immobilization in the elongating chain,
    • (1969) J. Biol. Chem. , vol.244 , pp. 3290
    • Alberty, R.A.1
  • 9
    • 18144382855 scopus 로고    scopus 로고
    • note
    • The sequence 5′-ATCTGTT-3′, known to induce pause or arrest for the T7 RNAP, is present in λ DNA but at the end of the genome, in regions never explored in our experiment.
  • 12
    • 0345047725 scopus 로고    scopus 로고
    • K. C. Neuman et al., Cell 115, 437 (2003).
    • (2003) Cell , vol.115 , pp. 437
    • Neuman, K.C.1
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    • note
    • M with the correlation factor R = 0.99.
  • 21
    • 18144362357 scopus 로고    scopus 로고
    • note
    • In the two state model, it was also considered that the potential in state two could be modulated, but its minima are then at the same location as the minima in state one.
  • 22
    • 18144394956 scopus 로고    scopus 로고
    • note
    • PPi is released during NTP hydrolysis. No PPi is added to the solution. However PPi is generated as transcription proceeds. Taking the known analytic solution for diffusion from a source (the polymerase taken to be 5 nm of radius) generating particles (PPi) at a constant rate, the typical local concentration of PPi in the immediate vicinity of the polymerase is estimated to be below 0.03 μM when transcription proceeds at 100 b/sec.
  • 24
    • 0032582494 scopus 로고    scopus 로고
    • M. D. Wang et al., Science 282, 902 (1998).
    • (1998) Science , vol.282 , pp. 902
    • Wang, M.D.1
  • 28
    • 18144427024 scopus 로고    scopus 로고
    • note
    • 2 for 1 min 40 sec) in a sucrose gradient. The fraction containing beads with tethered DNA is collected and deposited on the sample (with supplementary 25 mM potassium glutamate): this procedure eliminates the excess of free polymerases, and also reduces the concentration of nucleotides present during initiation, to below 0.5 μM for each nucleotide.
  • 29
    • 18144364555 scopus 로고    scopus 로고
    • note
    • The T7 RNA polymerase is biotin tagged by adding the amino acid sequence MAGGLNDIFEAQKMEWRLE at the N terminus of the protein (the underlined Lysine corresponds to the biotinylated amino acid). The λ DNA substrate can be transcribed by the biotinylated T7 RNAP over more than 10 kb in our setup.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.