Many changes, it is necessary so that it extends from the transition to transcription initiation occurs in RNA polymerase II (Pol II) transcription complex. In the intermediate stage of the transfer, the trigger contact factors are lost and stable relationship with nascent transcripts has been established. These include collective promoter clearance is included. After transcription elongation complex, the property has reached a point that could not be distinguished from those of the composite transcript promoter clearance much longer is complete. The distance method of Pol II, is composed of a series of steps, the distance downstream surprisingly long transfer extends to. It is part of a Special Issue, and this article is entitled: transcription elongation of RNA polymerase II.

By monitoring stretched mechanically rolling, the extended end-to-end single DNA molecule, the RNA polymerase (RNAP), to monitor the change of the extension corresponding to the arrangement around the turn of the promoter DNA directly we I was able. By carrying out the experiments in parallel with winding DNA positively and negatively, we extended to be due to (RNAP-dependent DNA compaction and (at ≈ 1-BP resolution) changes the extension caused by RNAP-dependent DNA evolution with a resolution of ≈ 5nm was able to deconvolution the change). For the quantification of the effects supercoiled and dynamics, the degree of development and integration, development, of the dense, sequence, the nucleotide ppGpp Noto, we were using this approach. Further, in order to detect the recycling of promoter and promoter clearance by a succession molecules RNAP, we were using this approach. We (by the number and position of the coiled-coil) exercise super coil structure (rather than through the torque) the mechanical effects believe that stable rate and formation of advanced composite body as being dependent deeply in super coil. This approach should allow the analysis of nucleic acid processing and other factors that cause changes in DNA compaction and / or twist of DNA.

Comprising the reaction sequence initiation of transcription,: (I), the promoter DNA around in order to bind to the promoter DNA to form the RNAP promoter gated, to form (II) RNAP RNA polymerase holoenzim is (RNAP) (III) RNAP avoid promoter (in a process called “promoter clearance”) and, (referred to as “promoter relaxation”) RNAP open promoter complex that generates one rotation, the RNA productive by elongation complex of RNAP-DNA I go into the synthesis.

We have developed the approach of the DNA molecule nano manipulation that we can develop the promoter by RNAP, to detect the promoter well-formed, characterized. Our approach is using the experimental apparatus was developed for the DNA polymer physics originally. In this experiment, the multiple links paramagnetic beads multiple links to the glass surface is connected at one end to the other end double-stranded DNA molecules containing a promoter region, DNA is limited mechanically has been, by applying a pair of magnets in the helical axis of the tension DNA twisting, between the glass surface and the neck (corresponding to the extension of the DNA end-to-end, L) surface of the glass and the head of the The distance between can be observed in real time using a video microscope. A pair of magnets is rotated, the supercoiled off rotation is provided a lock-step on the neck, was introduced into the torsion limit DNA molecule registry lockstep, which is supercoiling, therefore, L is changed . In this experiment, it is possible to construct a calibration curve experimental rotational speed of counterclockwise relates superhelical turns or negative or positive clockwise pair of L magnet thus is easy. Over a wide range of supercoiled positive and negative changes in L of 56 ± 5 nanometers supercoiled turn, under the conditions of our and l varies with the number of turns of the coiled-coil of the positive or negative linearly.