Visualization of Single Molecules of RNA Polymerase Sliding Along DNA

Kabata, Hiroyuki; Kurosawa, Osamu; Arai, I.; Washizu, Masao; Margarson, S.; Glass, Robert E.; Shimamoto, Nobuo

doi:10.1126/science.8248804

Cited by 279 publications

(234 citation statements)

References 25 publications

Supporting

Mentioning

229

Contrasting

Order By: Relevance

“…By tracking a tagged RNAP itself, or by monitoring the incorporation of fluorescent nucleotides into an RNA chain, the processes of promoter search or elongation can be studied with minimal perturbation (19)(20)(21)(22)(23). Structural rearrangements of the TEC that occur during the transcription cycle can also be monitored using fluorescence (Förster) resonance energy transfer (FRET) (Figure 2) (6,24,25).…”

Section: Single-molecule Techniquesmentioning

confidence: 99%

Single-Molecule Studies of RNA Polymerase: Motoring Along

Herbert

Greenleaf

Block

2008

Annu. Rev. Biochem.

182

141

View full text Add to dashboard Cite

Single-molecule techniques have advanced our understanding of transcription by RNA polymerase. A new arsenal of approaches, including single-molecule fluorescence, atomic-force microscopy, magnetic tweezers, and optical traps have been employed to probe the many facets of the transcription cycle. These approaches supply fresh insights into the means by which RNA polymerase identifies a promoter; initiates transcription, translocates and pauses along the DNA template, proofreads errors, and ultimately terminates transcription. Results from single-molecule experiments complement knowledge gained from biochemical and genetic assays by facilitating the observation of states that are otherwise obscured by ensemble averaging, such as those resulting from heterogeneity in molecular structure, elongation rate, or pause propensity. Most studies to date have been performed with bacterial RNA polymerase, but work is also being carried out with eukaryotic polymerase (Pol II) and single-subunit polymerases from bacteriophages. We discuss recent progress achieved by single-molecule studies, highlighting some of the unresolved questions and ongoing debates.

show abstract

Section: Single-molecule Techniquesmentioning

confidence: 99%

Single-Molecule Studies of RNA Polymerase: Motoring Along

Herbert

Greenleaf

Block

2008

Annu. Rev. Biochem.

182

141

View full text Add to dashboard Cite

show abstract

“…Quite divers phenomena have been observed and exploited: Electrostretching of soft material such as mammalian cells 1 and of filamentous molecules such as DNA, 2,3 electroorientation of elongated objects such as fission yeast 4 and electrostretched DNA, 5 electrorotation of cells, 6 and electropumping of fluids 7,8 and ac electro-osmotic flow. 9 Still, the most widely exploited effect is dielectrophoresis ͑DEP͒, [10][11][12] i.e., the action of forces in inhomogeneous electric fields toward regions of highest field strength ͑positive DEP͒ or lowest field strength ͑negative DEP͒.…”

Section: Introductionmentioning

confidence: 99%

“…Often the term DEP is used in a somewhat wider sense when phenomena, such as electrostretching, electro-orientation, and DEP, take place simultaneously, as it is often the case when dealing with long DNA strands. 2, 5 Sometimes it is not obvious whether an observed accumulation of particles is caused by DEP or ac electro-osmosis. Although DEP of microscopical particles such as cells has been well characterized by both experiment and theory, 2,10,13-16 there are not many quantitative studies on submicroscopical objects, and even less on molecules.…”

Section: Introductionmentioning

confidence: 99%

Dielectrophoresis of DNA: Quantification by impedance measurements

2010

View full text Add to dashboard Cite

Dielectrophoretic properties of DNA have been determined by measuring capacitance changes between planar microelectrodes. DNA sizes ranged from 100 bp to 48 kbp, DNA concentrations from below 0.1 to 70 g / ml. Dielectrophoretic spectra exhibited maximum response around 3 kHz and 3 MHz. The strongest response was found for very long DNA ͑above 10 kbp͒ and for short 100 bp fragments, which corresponds to the persistence length of DNA. The method allows for an uncomplicated, automatic acquisition of the dielectrophoretic properties of submicroscopical objects without the need for labeling protocols or optical accessibility.

show abstract

“…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], RNAPs [30][31][32][33][34], nucleases [35] and methylases [36] locate their operator sites in this way.…”

Section: Protein Slidingmentioning

confidence: 99%

“…[30][31][32][33][34], invariably average behaviour over many individual sliding events, masking any sequence-dependent variation which might exist. On the other hand, a recent model of the hypothetical reading process [38] was built upon the assertion that .…”

Section: Protein Slidingmentioning

confidence: 99%

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

Bashford

2006

J Biol Phys

View full text Add to dashboard Cite

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.

show abstract

Visualization of Single Molecules of RNA Polymerase Sliding Along DNA

Cited by 279 publications

References 25 publications

Single-Molecule Studies of RNA Polymerase: Motoring Along

Single-Molecule Studies of RNA Polymerase: Motoring Along

Dielectrophoresis of DNA: Quantification by impedance measurements

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

Contact Info

Product

Resources

About