Dual mode of IFI16 binding to supercoiled and linear DNA: A closer insight
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Replication protein A
Protein–DNA interaction
HMG-box
DNA binding site
DNA clamp
Membrane biology
Sequence (biology)
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Affect
HMG-box
DNA clamp
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Cruciform
HMG-box
DNA binding site
Replication protein A
Protein–DNA interaction
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Adenovirus DNA binding protein is a multifunctional protein essential for viral DNA replication. To investigate the role of the DNA binding protein in this process Its interaction with partial DNA duplexes was examined. Duplex regions of DNA, created when a short DNA strand is annealed to Its complementary sequence present In the single stranded form of M13 phage DNA, were efficiently unwound by DNA binding protein In a reaction that required neither ATP nor MgCl2. The unwinding activity of DNA binding protein was reduced by conditions which increased the stability of DNA duplexes. DNA unwinding by DNA binding protein was highly co-operative and required the single stranded DNA to be completely coated with the protein. Completely double stranded DNA could also be unwound by DNA binding protein but this reaction was sensitive to the G + C content of the DNA and could only be observed with relatively short DNA duplexes up to 45 base pairs in length. When these short double stranded DNA molecules contained binding sites for the transcription factors NFI and NFIII addition of the cognate factor blocked DNA binding protein mediated unwinding of that particular DNA duplex. Cleavage of DNA binding protein with chymotrypsin and isolation of the 39, 000 molecular weight C-terminal fragment Indicated that the unwinding activity was located in this domain of the protein. In support of this contention a monoclonal antibody, which had previously been mapped to this region, specifically inhibited the DNA unwinding activity. These activities of DNA binding protein are likely to be involved in DNA replication, where the destablllsatlon of DNA duplexes could be Important both during initiation and elongation.
Helix (gastropod)
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Proper maintenance and duplication of the genome require accurate recombination between homologous DNA molecules. In eukaryotic cells, the Rad51 protein mediates pairing between homologous DNA molecules. This reaction is assisted by the Rad54 protein. To gain insight into how Rad54 functions, we studied the interaction of the human Rad54 (hRad54) protein with double-stranded DNA. We have recently shown that binding of hRad54 to DNA induces a change in DNA topology. To determine whether this change was caused by a protein-constrained change in twist, a protein-constrained change in writhe, or the introduction of unconstrained plectonemic supercoils, we investigated the hRad54–DNA complex by scanning force microscopy. The architecture of the observed complexes suggests that movement of the hRad54 protein complex along the DNA helix generates unconstrained plectonemic supercoils. We discuss how hRad54-induced superhelical stress in the target DNA may function to facilitate homologous DNA pairing by the hRad51 protein directly. In addition, the induction of supercoiling by hRad54 could stimulate recombination indirectly by displacing histones and/or other proteins packaging the DNA into chromatin. This function of DNA translocating motors might be of general importance in chromatin metabolism.
Replication protein A
DNA clamp
HMG-box
In vitro recombination
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A hybrid protein (H144), consisting of Lac repressor and T7 endonuclease I, binds at the lac operator and cleaves relaxed double-stranded DNA at distal but distinct sites. These sites are shown here to coincide with a bacterial promoter, a phage T7 promoter, a site for gyrase and intrinsically bent DNA. The targets do not seem to share a particular DNA sequence, and in bent DNA, cleavage occurs at the physical center rather than at the common A-tracts. These results indicate that protein contact sites and intrinsic bends assume a non-canonical conformation in the absence of supercoiling or cognate protein binding. This feature may serve as a recognition signal or facilitate protein binding to initiate transcription and recombination. A hybrid protein (H144), consisting of Lac repressor and T7 endonuclease I, binds at the lac operator and cleaves relaxed double-stranded DNA at distal but distinct sites. These sites are shown here to coincide with a bacterial promoter, a phage T7 promoter, a site for gyrase and intrinsically bent DNA. The targets do not seem to share a particular DNA sequence, and in bent DNA, cleavage occurs at the physical center rather than at the common A-tracts. These results indicate that protein contact sites and intrinsic bends assume a non-canonical conformation in the absence of supercoiling or cognate protein binding. This feature may serve as a recognition signal or facilitate protein binding to initiate transcription and recombination.
Lac repressor
HMG-box
DNA binding site
Protein–DNA interaction
Transcription
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Lac repressor
HMG-box
Protein–DNA interaction
DNA binding site
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histone-like protein HU has been shown to interact with different topological forms of DNA. Using radiolabeled HU, we examine the effects of DNA supercoiling on HU-DNA interactions. We show that HU binds preferentially to negatively supercoiled DNA and that the affinity of HU for DNA increases with increases in the negative superhelical density of DNA. Binding of HU to DNA is most sensitively influenced by DNA supercoiling within a narrow but physiologically relevant range of superhelicity (
Protein–DNA interaction
HMG-box
Linking number
DNA clamp
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The C-terminal region of Brh2 (Brh2(CT)), the BRCA2 homolog in Ustilago maydis, is highly conserved and aligns with the DSS1/DNA-binding domain (DBD) of mammalian BRCA2, while the N-terminal region (Brh2(NT)) is poorly conserved and has no obvious functional domain except for the single Rad51-interacting BRC element. Paradoxically, Brh2(NT), but not Brh2(CT), complements the DNA repair and recombination deficiency of the brh2 mutant. We show here that Brh2(NT) exhibits an unexpected DNA binding activity with properties similar to that of the full-length protein. Deletion mapping localized the region responsible for the DNA binding activity to a stretch of residues between the BRC element and the canonical DBD. A heterologous DNA-binding domain from the large subunit of replication protein A substituted for the endogenous binding region within Brh2(NT) in supporting DNA repair. Rad51-promoted strand invasion was stimulated by Brh2(NT), but required the presence of the BRC element. The findings suggest a model in which Brh2(NT) serves as the principal site for association with DNA, while the Brh2(CT) provides a means for regulation.
Replication protein A
HMG-box
B3 domain
DNA binding site
Protein–DNA interaction
DNA clamp
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DNA Protein interactions play very vital roles in any living cell. It controls various cellular processes which are very essential for living beings, viz. replication, transcription, recombination, DNA repair etc. There are several types of proteins found in a cell. But only those proteins interact with DNA, which have the DNA binding domains. Each DNA binding domain has at least one motif, which is a conserved amino acid sequence of this protein, which can potentially recognize a double stranded or a single stranded DNA. These DNA binding domains possess an affinity to bind to either double stranded or single stranded DNA. There are mainly two broad types of DNA protein interactions: 1) Sequence specific DNA binding and 2) Sequence non-specific DNA binding. In case of sequence specific DNA protein interactions, a DNA binding protein binds to a DNA on a site having a specific nucleotide sequence. But in case of sequence non specific DNA protein interactions, the DNA binding protein can bind to a DNA in a random position on the DNA. As for example, the sequence specific DNA protein interaction is found to occur in case of transcription. The transcription factors are a special kind of DNA binding proteins. They can only recognize a specific DNA sequence. The sequence non-specific DNA protein interaction occurs in replication. During replication the DNA double strand is melted by helicase enzyme, and a replication fork is made. A special kind of protein called single strand binding protein or SSB binds to the melted single strand of DNA and stabilizes the system by preventing them to be re-natured. There are several motifs present, which are involved in DNA binding, for example, helix-turn-helix, leucine zipper, zinc finger, helix-loop-helix etc. In this review, comprehensive analyses of DNA-protein interactions are made. The detailed discussions on the topic would be very much essential for all fields of biochemistry and biophysics. Keywords: DNA-protein binding, Specificity of binding, Non-specific interaction, DNA binding motifs, Domains, DNA.
HMG-box
Replication protein A
DNA binding site
Protein–DNA interaction
DNA clamp
Origin recognition complex
In vitro recombination
DNA polymerase II
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