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	RNA polymerase - Wikipedia, the free encyclopedia
		The enzyme RNA polymerase or RNAP is a nucleotidyltransferase that polymerises ribonucleotides in accordance with the information present in DNA.
		In contrast to DNA polymerase, RNAP includes a helicase activity, therefore no separate enzyme is needed to unwind DNA.
		The sigma factor greatly reduces the affinity of RNAP for nonspecific DNA while increasing specificity for certain promoter regions, depending on the sigma factor.
	en.wikipedia.org /wiki/RNA_polymerase (400 words)

	Jin, Ding Jun, general information
		We propose that modulation of the stability of the initiation complexes of stringent promoters is a key element in regulation of stringent genes and suggest that the stability of initiation complexes is coupled to the transcription of stringent promoters because transcription and local supercoiling of the DNA template are interrelated.
		Interaction between core RNAP and different sigma factors forming a holoenzyme is the first step in transcription initiation.
		Almost all of this 110-kDa protein in the cell copurifies with RNAP holoenzyme as a 1:1 complex.
	rex.nci.nih.gov /RESEARCH/basic/lmb/Prsnl.d/jin.htm (647 words)

	Center for Cancer Research - Staff Pages
		Our results show that RNAP is located either within or surrounding the nucleoid; and that the distribution of RNAP is dynamic and influenced dramatically by environmental cues, such as growth conditions and nutrient starvation.
		Interestingly, these core RNAP suppressors also appeared to be defective in the phage Q-mediated antitermination, suggesting a functional overlap between the core-sigma interaction and the core-Q interaction.
		From this and mutational analyses of RNAP, we proposed that the intrinsic instability of initiation complexes at stringent promoters is a critical regulatory step for both the expression of stringent genes and the regulation of the stringent response.
	ccr.nci.nih.gov /staff/staff.asp?profileid=5787 (843 words)

	RNAP: A Resource Negotiation and Pricing Protocol (Site not responding. Last check: 2007-10-21)
		We present RNAP as a stand-alone protocol, but it is also possible to implement some components of RNAP as a layer on top of RSVP or other hop-by-hop reliable signaling protocols.
		RNAP is intended for use by both adaptive and non-adaptive applications.
		RNAP messages propagate hop-by-hop along the same path as customer data flows, from the first-hop LRN to the egress LRN, and in the reverse direction.
	www.cs.buffalo.edu /~xwang8/public/projects/RNAP_bak.html (1568 words)

	Facilitated Target Location on DNA by Individual Escherichia coli RNA Polymerase Molecules Observed with the Scanning ... (Site not responding. Last check: 2007-10-21)
		In two recent studies, fluorescence microscopy was used to observe the interactions of fluorescently labeled RNAP with DNA.
		b, intersegment transfer is the translocation of the RNAP from one point of the DNA to another distant point through the formation of a ternary structure.
		c, intradomain association and dissociation or "hopping" is the movements of the RNAP relative to the DNA through a series of collisions on a small scale.
	www.jbc.org /cgi/content/full/274/24/16665 (2658 words)

	[No title]
		The molecule is RNAP (for ribonucleic acid polymerase) and a bead-like molecule of that enzyme moves along the DNA template when an RNA copy is synthesized.
		Elsewhere on the DNA template, the molecule of RNAP is moving like the slider part of a zipper, separating DNA so that information can be transcribed to RNA, then allowing the DNA to come together again and moving on.
		Also, the transcribing RNAP molecule oscillates rapidly along five to 10 base pairs at a time -- almost as if the enzyme were performing a quality-assurance check of its work -- before moving on to catalyze the transcription of more bases.
	www.news.cornell.edu /Chronicle/99/1.28.99/genomics/wang.html (701 words)

	TFIIF-associating Carboxyl-terminal Domain Phosphatase Dephosphorylates Phosphoserines 2 and 5 of RNA Polymerase II -- ... (Site not responding. Last check: 2007-10-21)
		RNAP II is comprised of 52 repeats of the consensus sequence
		P-labeled RNAP IIA (lane 1) was converted to RNAP IIO by CTDK1/CTDK2 (lane 2), TFIIH (lane 3), P-TEFb (lane 4), MAPK2/ERK2 (lane 5), and Cdc2 kinase (lane 6).
		RNAP II and RNAP II in an elongation complex (32, 33), the
	www.jbc.org /cgi/content/full/277/48/45949 (5390 words)

	Role of Second-Largest RNA Polymerase I Subunit Zn-Binding Domain in Enzyme Assembly -- Naryshkina et al. 2 (5): 1046 ...
		The high-resolution structure of a 10-subunit core of RNAP II from yeast revealed eight bound Zn ions (2, 7).
		RNAP I, which is homologous to Rpb150 (8).
		The sequence is aligned with corresponding sequences from yeast RNAP II (Rpb150) and RNAP III (Rpc128), Pyrococcus abyssi RNAP (Pa), and E.
	ec.asm.org /cgi/content/full/2/5/1046 (4545 words)

	Recent study asserts that RNA polymerase makes mistakes when copying genes but knows how to find and fix them
		The error-prone nature of RNAP is not surprising given the size of its task.
		Using the optical clamp, researchers found that RNAP does not move at a steady pace along the DNA double helix but rather undergoes a fitful series of unexplained starts and stops.
		Certain antibiotics are known to increase the error rate during translation from RNA to protein, added applied physics graduate student Elio A. Abbondanzieri, co-lead author of the Nature paper and co-author of the Cell study.
	news-service.stanford.edu /news/2003/december3/rna-123.html (1028 words)

	RNA polymerase mutants defective in the initiation of transcription-coupled DNA repair -- Smith and Savery 33 (2): 755 ...
		RNAP from DNA in vivo and in vitro.
		to RNAP and to the DNA upstream of RNAP, and as the helicase/TRG
		A consensus sequence for the three residues required by Mfd was derived by alignment of RNAP ß subunit sequences from 47 eubacterial strains using the Conserved Domain Database (44).
	nar.oxfordjournals.org /cgi/content/full/33/2/755 (6626 words)

	RNA Polymerase II Holoenzyme Modifications Accompany Transcription Reprogramming in Herpes Simplex Virus Type ...
		Blots were probed with antibodies that recognize the RNAP II large subunit, the p56E subunit of TFIIE, the TBP subunit of TFIID, and the cdk7 subunit of TFIIH.
		Eluates were concentrated and analyzed by immunoblotting with antibodies that recognize the large subunit of RNAP II, the p56E subunit of TFIIE, the TBP subunit of TFIID, and the cdk7 subunit of TFIIH.
		RNAP II holoenzymes from infected cells are transcriptionally inactive.
	jvi.asm.org /cgi/content/full/75/20/9872 (8828 words)

	Direct Observation of One-Dimensional Diffusion and Transcription by Escherichia coli RNA Polymerase -- Guthold et al. ...
		A 1001-bp promoterless fragment, corresponding to the region from +12 to +1012 of the
		The DNA contour is traced with a thin line and the center of the RNAP is marked with a dot.
		During transcription, which proceeds toward the shorter arm, the RNAP remained stably bound to the surface while the DNA was pulled through the protein.
	www.biophysj.org /cgi/content/full/77/4/2284 (6224 words)

	Observing Transcription in Real Time (Site not responding. Last check: 2007-10-21)
		In most experiments, the RNAP remains bound to the surface while the DNA is pulled through the protein during the transcription.
		Imaging conditions were found in which the RNAP was firmly attached to the surface wherease the DNA molecules, although bound to the surface, were able to diffuse in two dimensions.
		In this case, the RNAP moved on the surface during the transcription.
	alice.berkeley.edu /~cjblab/transcription.html (405 words)

	Untitled Document
		RNAP is attached to a micron-sized polystyrene bead.
		The study of the mechanisms underlying RNAP transcription by conventional biochemical experiments, which report only ensemble averages, are complicated by the rapid loss of synchronization in populations of transcribing RNAP complexes.
		Recently, we've developed a two-bead assay for studying RNAP in which the RNAP is bound to one bead as above, but the end of the DNA is bound to another optically trapped bead (forming a "dumbbell").
	www.stanford.edu /group/blocklab/RNAP.html (817 words)

	Investigating RNA polymerase II carboxyl-terminal domain (CTD) phosphorylation -- Palancade and Bensaude 270 (19): 3859 ... (Site not responding. Last check: 2007-10-21)
		as a landmark of RNAP II molecules engaged in transcription.
		The ‘free’ RNAP II core enzyme is not phosphorylated on the CTD.
		RNAP II is less phosphorylated under heat-shock conditions.
	content.febsjournal.org /cgi/content/full/270/19/3859 (7076 words)

	The involvement of the aspartate triad of the active center in all catalytic activities of multisubunit RNA polymerase ...
		The structure of Taq RNAP core along with that of magnified domain of the active center is shown in ribbon representation.
		RNAPs were subjected to Fe -mediated affinity cleavage in the presence of various concentrations of Fe for the times indicated.
		Figure 5 Residual activity of mutant RNAP at different concentration of Mg Single nucleotide addition reaction (Figure 4B, lane 2) was performed in the presence of 1 µM CTP and indicated concentrations of Mg For each enzyme, the extent of 13A RNA elongation in the presence of 10 mM Mg was taken to be 100%.
	nar.oxfordjournals.org /cgi/content/full/33/13/4202 (5381 words)

	Active recruitment of [sigma]54-RNA polymerase to the Pu promoter of Pseudomonas putida: role of IHF and [alpha]CTD (Site not responding. Last check: 2007-10-21)
		Apart from the specific core sequence of target promoters, RNAP binding is determined in many cases by cis- and trans-acting elements which recruit the transcriptional machinery to the DNA (Ptashne and Gann, 1997).
		RNAP was used at 200 nM core enzyme with a 3-fold molar excess of purified
		A was detected in crude extracts by Western blot with the corresponding pre-adsorbed polyclonal rabbit antibodies as described by Fernández et al.
	www.nature.com /emboj/journal/v17/n17/full/7591207a.html (6802 words)

	TATA-Binding Protein-Interacting Protein 120, TIP120, Stimulates Three Classes of Eukaryotic Transcription via a Unique ...
		RNAP II was purified from calf thymus as described by Hodo and
		The primary event of transcription entails the assembly of GTFs and RNAP II on a promoter to form the PIC (17).
		RNAP II was incubated with template DNA in the presence or absence
	mcb.asm.org /cgi/content/full/19/12/7951 (7243 words)

	Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and ...
		RNAP I, II, and III subunits RPA1, RPB1, and RPC1.
		RpoD and RpoL, eukaryotic RNAP I and III subunits RPC5 and RPC9
		) have counterparts in archaeal and eukaryotic RNAP.
	www.pnas.org /cgi/content/full/98/3/892 (3828 words)

	The Rockefeller University - Heads of Laboratories
		In both prokaryotes and eukaryotes, the “core” form of the RNAP is catalytically competent to processively synthesize RNA chains from a DNA template but is unable to recognize promoters and initiate specific RNA synthesis from double-stranded templates.
		We hope to gain insight into dynamic processes of the RNAP by trapping transient states of the RNAP during open complex formation, transcription initiation, transcription elongation and transcription termination.
		We also hope to use a combination of high-resolution structures of individual components or sub-assemblies, structures of higher order macromolecular complexes, and molecular modelling to shed light on the molecular mechanisms of regulatory factors acting on the different stages of the transcription cycle, particularly during transcription initiation.
	www.rockefeller.edu /labheads/darst/darst.html (618 words)

	A sigma 32 mutant with a single amino acid change in the highly conserved region 2.2 exhibits reduced core RNA ...
		to core RNAP was one to one, approximately 60 fmol of transcripts
		We examined the core RNAP binding affinities of E81G and P74R (Fig.
		A few studies have been performed to identify the core RNAP binding region of sigma factors (10, 11, 29).
	www.pnas.org /cgi/content/full/94/10/4907 (4021 words)

	Nanotech instruments allow first direct observations of RNA 'proofreading'
		Their results - based on actual observations of individual molecules of RNAP - are posted on Nature's website: http://www.nature.com.
		In their experiments, the Block team conducted more than 300 observations of single RNAP molecules extracted from E. coli bacteria.
		Although structurally somewhat different from human RNAP, the E. coli enzyme plays a very similar role in the complex transfer from gene to RNA to protein.
	www.eurekalert.org /pub_releases/2003-11/su-nia112503.php (1028 words)

	Faculty Page
		The RNA polymerase (RNAP) core enzyme is evolutionarily conserved from bacteria to man, as has been strikingly confirmed by recent crystallographic studies.
		In addition, RNAP remains an important antibiotic target and therefore mechanistic studies of RNAP will guide both the improvement of existing antibiotics and the development of new antibiotics that target RNAP.
		We have developed a variety of genetic tools for examining functionally relevant protein-protein interactions between the subunits of RNAP, between transcription regulators and RNAP, and between the DNA-binding domains of RNAP and conserved promoter elements.
	www.hms.harvard.edu /dms/bbs/fac/hochschild.html (470 words)

	Characterization of an Unusual, Sequence-specific Termination Signal for T7 RNA Polymerase -- He et al. 273 (30): 18802 ...
		Two types of signals are known to cause pausing and/or termination by T7 RNAP (7, 8).
		The RNAP is here envisaged to be able to actively displace the RNA product (24), but this feature is not essential to the model.
		Passage of the RNAP through a region of the template in which the NT strand is not complementary to the T strand (e.g.
	www.jbc.org /cgi/content/full/273/30/18802 (7168 words)

	RNAP: A Resource Negotiation and Pricing Protocol
		RNAP enables negotiation between user applications and the access network, as well as between adjoining network domains, and also enables the distribution and collation of price and charging information.
		Wang, H. Schulzrinne, ``RNAP: A Framework for Congestion-based Pricing and Charging for Adaptive Multimedia Applications,'' 1st International workshop on Quality of future Internet Services (QofIS'2000), GMD Fokus, Berlin, Germany, Sep. 2000.
		Wang, H. Schulzrinne, ``RNAP: A Resource Negotiation and Pricing Protocol,'' International Workshop on Network and Operating System Support for Digital Audio and Video (NOSSDAV), (Basking Ridge, New Jersey), Jun. 1999.
	www.cs.columbia.edu /~xinwang/public/projects/RNAP.html (613 words)

	Molecular anatomy of a transcription activation patch: FIS-RNA polymerase interactions at the Escherichia coli rrnB P1 ... (Site not responding. Last check: 2007-10-21)
		RNAP was used at 0.4 nM in (B).
		RNAP concentrations were chosen to give the same amount
		RNAP were not important for activation of transcription by RNAP
	embojournal.npgjournals.com /cgi/content/full/16/1/154 (5372 words)

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