mutm single c2c2 zinc finger dna interaction

... real-time replication rate of a single DNA polymerase (DNAP) on a single- stranded DNA (ssDNA) stretched by a magnetic trap as shown in Fig 5A Similarly to RNAP, DNAP reads the Fig (A) Schematic ... requirements: (1) the stretched DNA molecules should preserve the base stacking structure of unstretched DNA, thus allowing normal DNA protein interactions; (2) the DNA should be immobilized in ... 186 immobilized DNA than on a coiled DNA, since along the former the protein follows a straight 1D path along the DNA Stretching DNA is also useful if one wishes to monitor its interactions with...

Ngày tải lên: 22/06/2014, 18:20

... Joung JK, Dobbs D: ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool Nucl Acids Res 2010, 38:W462-468 35 Mandell JG, Barbas CF: Zinc finger tools: custom DNA- binding domains for ... file 2, are protein motifs capable of targeted DNA- binding [34-36] Each individual zinc finger usually recognizes three nucleotide bases, but many zinc fingers can be combined to generate an array ... are presented for the first time Results Identification of HSV-2 genome specific zinc finger array (ZFAs) and zinc finger nucleases (ZFN) Using the FASTA format of the nucleotide sequences of the...

Ngày tải lên: 13/08/2014, 16:20

... DNA as Polymer DNA is a macromolecule consisting of numerous basic repetitive units (DNA backbones) These repetitive units furthermore form the DNA double helix structure The doublestranded DNA ... Concentration on the Affinity of NAP-1 to Histone Octamers 42 CHAPTER SINGLE MOLECULE STUDY ON MVAT/MVAU -DNA AND MVAT MUTANTS -DNA INTERACTIONS 44 ii 3.1 INTRODUCTION 45 3.2 ... iii Abstract Single molecule manipulation techniques have become versatile tools to study the force and motions of biological molecules such as DNA and proteins, and DNA- protein interaction in...

Ngày tải lên: 12/10/2015, 17:34

... discrimination rendered by the presence of a single mismatch in the DNA on the Fig ATP induced aggregation of MutS-MutL in presence of homo ⁄ heteroduplex DNA MutS-MutL -DNA complexes were formed by incubating ... duplex DNA) were heat denatured with SDS loading buffer, analysed by 10% SDS ⁄ PAGE, followed by silver staining to visualize both proteins and DNA [(C) Heteroduplex DNA (D) homoduplex DNA; lane ... analysis of Rh changes following DNA addition seems to suggest that MutS interaction with heteroduplex DNA rapidly generates a particle size similar to that of homoduplex DNA (14 nm) following which...

Ngày tải lên: 07/03/2014, 12:20

... establish that abrogation of interactions mediated by a single amino acid, namely Lys182, with the primary binding site is alone sufficient to abolish specific DNA protein interactions and downstream ... failed to A B Fig DNase I footprinting (A) DNase I footprint of WT DevR protein (0.5 lM and 1.0 lM concentration) and fdxA promoter DNA containing WT ⁄ C8G ⁄ T9A mutant P box DNA sequencing ladder ... is defective for interaction with DNA Fig TSP mapping The fdxA TSP (shown by arrow) was mapped using RNA isolated from aerobic (A) and hypoxic (H) cultures and fdxA tsp primer DNA sequence of...

Ngày tải lên: 22/03/2014, 16:20

... mutant mice by gene expression 4242 analysis This approach identified the Promyelocytic Leukemia Zinc Finger (PLZF) gene as a putative gene target of CUX1 PLZF was originally identified as a t(11;17) ... a repression domain ` BTB ⁄ POZ (bric-a-brac, tramtrack, brad complex ⁄ poxvirus zinc finger) and nine Kruppel zinc fingers [20] ¨ This repression domain allows PLZF to recruit corepressors such ... triplicate ChIP assays Genomic DNA amplification, reporter plasmid constructs and mutagenesis The 3-kb 5¢-UTR region of the human PLZF gene was amplified by PCR from purified genomic DNA isolated from the...

Ngày tải lên: 29/03/2014, 21:20

... mhlblt DNase I digestion throughout the DNA fragment, this could be the result of nonspecific interaction with DNA or direct inhibition of the enzyme itself A major problem with using DNase I ... (9) A single ActD molecule would thus cover about bp of DNA However, DNase I has a small loop, important to the binding process, that fits mto the minor groove of DNA, and spans 3-4 bp of DNA (20) ... binding to DNA causesthe cleavage agent, DNase I, to redistribute to DNA sites not blocked by bound drug (11) The DNase I footprmtmg experiments were carried out in the presence of calf thymus DNA as...

Ngày tải lên: 11/04/2014, 09:40

... for DNA affinity purification of sequence-specific DNA- binding proteins The different DNA affinity resins that have been employed include plasmid DNA adsorbed to cellulose, biotinylated DNA fragments ... sequence-specific DNA- binding proteins by DNA affinity chromatography DNA affinity chromatography was originally developed with nonspecific DNAs, such as calf thymus DNA, attached to cellulose I and agarose ... If the DNA is too long, it can be fragmented by sonication Also, a mixture of different competitor DNAs can be used in a single experiment The appropriate amount and type of competitor DNA to...

Ngày tải lên: 11/04/2014, 10:11

... E-cadherin is downregulated during tumor progression and such factors as snail, slug/snail2, zinc finger E-box binding homeobox (ZEB) and ZEB2 have been shown to directly bind to the Ecadherin ... miR-205 induces an epithelial-mesenchymal transition (EMT)-like phenotype through regulating zinc finger Ebox binding homeobox (ZEB2) expression OE21 Het-1A miR-205 5s RNA C Figure MiRNA-10a ... precursor C Figure MiR-205 reduces epithelial-mesenchymal transition(EMT) through regulating zinc finger E-box binding homeobox2 (ZEB2) expression Knockdown of miR-205 by transfection with 50...

Ngày tải lên: 18/06/2014, 19:20

... Carballo E, Thorn JM, Kennington EA, Blackshear PJ: Interactions of CCCH zinc finger proteins with mRNA Binding of tristetraprolin-related zinc finger proteins to AU-rich elements and destabilization ... the zinc finger protein TIS11 Biochem Biophys Res Commun 2002, 293:1242-1247 263 Arthritis Research & Therapy 264 Vol No Carrick et al 37 Blackshear P, Phillips RS, Lai WS: Tandem CCCH zinc finger ... conformational shift in the resonances of the first zinc finger in the peptide, while simultaneously permitting the demonstration of second zinc finger resonances that had been apparently unstructured...

Ngày tải lên: 09/08/2014, 01:24

... C2H2-type zinc- finger repeats Within such an array, each sequential zinc finger is predicted to bind a sequential trinucleotide on a target DNA molecule, suggesting that PRDM9 could bind DNA with ... encoding the zinc- finger array of PRDM9 has a minisatellite-like structure Each finger is encoded by 28 amino acids, with residue positions 6, and 12 (-1, +3 and +6 relative to the zinc- finger alpha ... that the motif was likely to be bound by a zinc- finger protein with at least 12 fingers Subsequent computational searching identified five candidate zinc- finger proteins, of which only one stands...

Ngày tải lên: 09/08/2014, 20:21

... Thibodeau-Beganny S, Joung JK, Dobbs D, Miller L, Voytas DF: Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc- finger arrays Nucleic Acids Res 2009, 37:D279-283 ... 2:162-180 Brown RS: Zinc finger proteins: getting a grip on RNA Curr Opin Struct Biol 2005, 15:94-98 Gamsjaeger R, Liew CK, Loughlin FE, Crossley M, Mackay JP: Sticky fingers: zinc- fingers as protein-recognition ... RNA; SC: synthetic complete; ssDNA: single- stranded DNA; TAP: tandem-affinity purification; TOP: terminal oligopyrimidine; UTR: untranslated region; ZnF: zinc finger Acknowledgements We thank...

Ngày tải lên: 09/08/2014, 22:23

... used one of the three zinc finger motifs of the SP1 -zinc- finger as a template for our chemically synthesized zinc finger probes, which were of the C2H2 type (Figure 1) The DNA- binding region was ... of the zinc finger molecules (see Figures and 4) However, these were sufficient for our experiments We have measured for the first time the specific binding of synthetic single- motif zinc finger ... , Yukio : Natural and artificial zinc finger proteins Riken Review 2001, 35: Wolfe , Scot A, Nekludova , Lena , Pabo , Carl O: DNA Recognition by Cys2His2 Zinc Finger Proteins Biophys Biomol Struc...

Ngày tải lên: 11/08/2014, 00:22

... reactive towards the zinc finger motif in the NC proteins might also react with the zinc finger motif of the M2-1 protein of RSV Therefore, we have tested some of the zinc finger reactive compounds ... spumaretrovirus group [7]) contain one or two copies of a zinc finger motif This zinc finger motif is essential for viral replication, as mutations in the zinc- coordinating residues lead to the loss of ... Given the functional similarity between the zinc finger containing proteins of retroviruses and RSV, and similarity in basic architecture of the zinc finger motifs in these proteins, we have noted...

Ngày tải lên: 12/08/2014, 04:21

... there are four CCCH-type zinc- finger motifs Disruption of the second or fourth finger abolished the antiviral activity of ZAP, while disruption of the first or third finger had little effect ... a CCCH-type zinc finger protein Science 2002, 297:1703-1706 Muller S, Moller P, Bick MJ, Wurr S, Becker S, Gunther S, Kummerer BM: Inhibition of filovirus replication by the zinc finger antiviral ... MacDonald MR: Expression of the zinc- finger antiviral protein inhibits alphavirus replication J Virol 2003, 77:11555-11562 Guo X, Ma J, Sun J, Gao G: The zinc- finger antiviral protein recruits...

Ngày tải lên: 12/08/2014, 23:23

... 3' direction to the average length of the DNA fragments in the sequenced DNA library The signal map is the integer count of the number of overlapping DNA fragments at each nucleotide position ... important source of noise signal - nonspecific DNA binding by TFs This noise signal is difficult to control, as TFs must nonspecifically bind to DNA in order to efficiently access their unique ... transcription factor dynamics at the single- molecule level in a living cell showed that TFs spend as much as 90% of their time non-specifically bound to and diffusing along DNAs [15] Like the ability to...

Ngày tải lên: 13/08/2014, 16:20

... HIV-pol gene/HIV-1-proviral -dsDNA binding zinc finger arrays and construct of HIV-pol gene/HIV-1-proviral-dsDNA cleaving zinc finger nucleases First, using the Zinc Finger Consortium’s software ... recognition of the ‘-GNN-3 ‘ family of DNA sequences by zinc finger domains J Mol Biol 2000, 303(4):489-502 34 Mandell JG, Barbas CF: Zinc finger tools: custom DNA- binding domains for transcription ... restriction enzymes created by covalently linking a DNA- binding zinc finger (Zif) domain (composed of three to six finger- arrays) to the non-specific DNA cleavage domain (or simply FN) of the Flavobacterium...

Ngày tải lên: 13/08/2014, 16:20

... reveals coded interactions Proc Natl Acad Sci U S A 1994, 91(23):11168-11172 Choo Y, Klug A: Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed ... protein -DNA interfaces: why is there no simple code for recognition? J Mol Biol 2000, 301(3):597-624 Choo Y, Klug A: Selection of DNA binding sites for zinc fingers using rationally randomized DNA ... for selecting high-affinity zinc finger proteins for diverse DNA target sites Science 1997, 275(5300):657-661 Wolfe SA, Greisman HA, Ramm EI, Pabo CO: Analysis of zinc fingers optimized via phage...

Ngày tải lên: 14/08/2014, 14:21

... procedure is sufficient to stretch the DNA strands when DNA is brought in small droplet The interaction between DNA and the hydrophobic surface is very strong, so that DNA can be considered as grafted ... exposition time ranging from 100 ms to s Results Interaction between DNA and C1q DNA is described as an activator of human complement system [30] The DNA- dependent activation of Complement may result ... for the binding to DNA When incubation of T4 DNA and C1q* was performed with various amounts of CLR, the analysis of the resulting combed DNA showed that the binding of C1q* to DNA strands started...

Ngày tải lên: 16/03/2014, 23:20