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Topic: DNA binding protein

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	Protein-DNA interactions
		The procedure is the same, except that the protein is incubated with the DNA for a period of time to allow binding.
		For instance, Cro binds tightly to oR3 and weakly to oR1 and oR2; CI binds tightly (and cooperatively) to oR1 and oR2, weakly to oR3.
		Result: DNA molecules to which proteins bind move more slowly in the gel and are retarded relative to the sample with no protein.
	www.biochem.arizona.edu /classes/bioc568/protein_dna_interactions.htm (0 words)

	Maintaining protein stability through buffers, freezing, and lyophilization
		Typically, proteins are stored freeze-dried (lyophilized), frozen in appropriate buffers, or refrigerated at 4°C. For short-term storage of proteins (hours to days), a standard laboratory refrigerator at 4°C is satisfactory providing the buffer used to solvate the protein provides all the necessary components necessary to stabilize the protein of interest.
		Proteins can be stored long term (days to weeks) by quick-freezing the sample followed by storage at -20°C. Addition of stabilizers such as glycerol helps prevent damage to the protein during freezing and thawing.
		After the protein solution is frozen, it is attached to a lyophilizer where the frozen solution sublimes leaving the protein behind, usually as a fluffy white powder.
	www.btc-bti.com /spbioapplications/proteinstability.htm (1112 words)

	Welcome to NCCC
		DNA binding of the transcription factor PO-B is regulated during differentiation of HL-60 cells.
		DNA-dependent protein kinase: DNA binding and activation in the absence of Ku.
		Mutation of the Fourth Cytoplasmic Loop of Rhodopsin Affects Binding of Transducin and Peptides Derived from the Carboxyl-terminal Sequences of Transducin a and g Subunits..
	www.nccc.com /refs.html (0 words)

	Structure of the gene 2.5 protein, a single-stranded DNA binding protein encoded by bacteriophage T7 -- Hollis et al., ...
		Structure of the gene 2.5 protein, a single-stranded DNA binding protein encoded by bacteriophage T7 -- Hollis et al., 10.1073/pnas.171317698 -- Proceedings of the National Academy of Sciences
		Structure of the gene 2.5 protein, a single-stranded DNA binding protein encoded by bacteriophage T7
		The gene 2.5 protein (gp2.5) of bacteriophage T7 is a single-stranded DNA (ssDNA) binding protein that has essential roles
	www.pnas.org /cgi/content/abstract/171317698v1 (667 words)

	Mitochondrial Single-stranded DNA-binding Protein Is Required for Mitochondrial DNA Replication and Development in ...
		DNA hybridized with an mtDNA probe and with a single-copy genomic
		Protein fractions as described in MATERIALS AND METHODS were denatured and electrophoresed in a 17% SDS-polyacrylamide gel, transferred to nitrocellulose, and detected by immunoblotting with rabbit antiserum against D.
		Li, K., and Williams, R.S. Tetramerization and single-stranded DNA binding properties of native and mutated forms of murine mitochondrial single-stranded DNA-binding proteins.
	www.molbiolcell.org /cgi/content/full/12/4/821 (0 words)

	DNA Binding Protein,Replication,Recombination,DNA Polymerase Activity,Gene Mutants (Site not responding. Last check: )
		DNA Binding Protein - The T4 DNA binding protein is specified by gene 32.
		The protein is therefore able to maintain ssDNA in that state.
		The DNA binding protein maintains DNA in the single stranded state ahead of the replication fork.
	www.microbiologyprocedure.com /bacteriophages/DNA-binding-protein.htm (206 words)

	DNA-binding protein Summary
		DNA binding proteins are central to the regulation and execution of essential cellular processes such as replication, transcription, translation and repair.
		The specific base sequences at which protein molecules bind to the DNA are frequently palindromic which means they read the same forwards and backwards (the word "refer" is a palindromic sequence of letters).
		Proteins with a helix-turn-helix motif are found in most organisms and examples include the repressor from the bacterial virus (bacteriophage) Lambda, and the lac and trp repressors from the bacterium Escherichia coli.
	www.bookrags.com /DNA-binding_protein (860 words)

	DNA Binding Proteins (Site not responding. Last check: )
		to interact with other subunits of the protein since most function as dimers.
		- a helix for binding with 6 bp in major groove (recognition helix) and a helix for interacting with the backbone
		-switching the DNA binding helix with other similar proteins indicates the specificity of binding by this helix.
	www.rhodes.edu /biology/glindquester/molbiol/mbprotected/DNAproteins.html (244 words)

	DNA-binding Proteins
		This protein is somewhat unusual in that it binds to the minor groove of DNA.
		The GCN4 transcription activator in yeast is a dimer in which the leucine zipper region helps to position the two basic regions that bind to the DNA recognition sequence.
		Many of these are homologous proteins from different species, nevertheless this number is indicative of the vast number of transcription factors now known that regulate the expression of eukaryotic genes.
	www.mun.ca /biochem/courses/3107/Lectures/Topics/DNA_binding_proteins.html (0 words)

	Characterization of the Escherichia coli SSB-113 mutant single-stranded DNA-binding protein. Cloning of the gene, DNA ...
		Cloning of the gene, DNA and protein sequence analysis, high pressure liquid chromatography peptide mapping, and DNA- binding studies -- Chase et al.
		DNA sequence is in the serine 39 codon, previously reported to be TCA and
		Escherichia coli single-stranded DNA-binding protein is a supercoiled template-dependent transcriptional activator of N4 virion RNA polymerase.
	www.jbc.org /cgi/content/abstract/259/2/805 (0 words)

	Modeling Dependencies in Protein-DNA Binding Sites
		This representation makes the strong assumption that binding site positions are independent of each other.
		In this work, we explore Bayesian network representations of binding sites that provide different tradeoffs between complexity (number of parameters) and the richness of dependencies between positions.
		We then evaluate the ramifications of these richer representations in characterizing binding site motifs and predicting their genomic locations.
	www.cs.huji.ac.il /labs/compbio/TFBN (215 words)

	Basal transcriptional regulation of human damage-specific DNA-binding protein genes DDB1 and DDB2 by Sp1, E2F, N-myc ...
		Keeney,S., Chang,G.J. and Linn,S. (1993) Characterization of a human DNA dmage binding protein implicated in xeroderma pigmentosum.
		Sitterlin,D., Lee,T.H., Prigent,S., Tiollais,P., Butel,J.S. and Transy,C. (1997) Interaction of the UV-damaged DNA-binding protein with hepatitis B virus X protein is conserved among mammalian hepadnaviruses and restricted to transactivation-proficient X-insertion mutants.
		Lin,G.Y., Paterson,R.G., Richardson,C.D. and Lamb,R.A. (1998) The V protein of the paramyxovirus SV5 interacts with damage-specific DNA binding protein.
	nar.oxfordjournals.org /cgi/content/full/31/2/562 (0 words)

	recA protein-promoted DNA strand exchange. Stable complexes of recA protein and single-stranded DNA formed in the ...
		Stable complexes of recA protein and single-stranded DNA formed in the presence of ATP and single-stranded DNA binding protein -- Cox and Lehman 257 (14): 8523 -- Journal of Biological Chemistry
		Stable complexes of recA protein and single-stranded DNA formed in the presence of ATP and single-stranded DNA binding protein
		DNA Pairing and Strand Exchange by the Escherichia coli RecA and Yeast Rad51 Proteins without ATP Hydrolysis.
	www.jbc.org /cgi/content/abstract/257/14/8523 (0 words)

	[No title]
		This is a family of eukaryotic single-stranded DNA binding-proteins with specificity to a pyrimidine-rich element found in the promoter region of the alpha2(I) collagen gene.
		IPR007591 Single-stranded DNA-binding protein, SSDP 82 - 296
		IPR007591 Single-stranded DNA-binding protein, SSDP 80 - 302
	www.ebi.ac.uk /interpro/DisplayIproEntry?ac=IPR007591&format=simple (0 words)

	Results
		The DNA binding domain of HIV integrase (below) is the protein which HIV uses to grab onto our DNA such that it can then connect its genetic code into ours.
		This movie shows a single trajectory of the unfolding of this protein under extreme denaturing conditions.
		This protein was designed by the Mayo Lab to fold into a "zinc finger" fold (a protein fold which typically binds to DNA).
	folding.stanford.edu /results.html (0 words)

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