DNA-binding protein
A DNA-binding protein is a protein that binds to DNA.
Properties
DNA-binding proteins are found in all living organisms and DNA viruses. Have at least one protein domain which is capable of binding to DNA. The binding may take place at various functional groups. The backbone of DNA consists of alternating phosphate and deoxyribose units. Through the phosphate groups, the DNA is proportional provided to the chain length having negative charges, to the by other protein domains with positively charged amino acids (e.g. lysine, arginine ), or protein domains with negatively charged amino acids can bind to the complexed cations (eg Mg2 - or Zn2 complexes ). Since the deoxyribose phosphate backbone is repeated constantly, a binding exclusively to the backbone protein can not bind a specific DNA sequence ( no sequence specificity). A sequence-specific binding is at least in part by binding to a specific sequence of nucleotide bases, the backbone may also be partly be bound.
Sequence specificity
DNA-binding proteins with no sequence specificity are described, for example, polymerases, helicases and, in general proteins, which slide along the DNA ( e.g., DNA - clip). Sequence -specific DNA-binding proteins are, eg, transcription factors at defined points (promoter ) trigger gene expression. Due to the higher proportion of nucleic bases in the surface of sequence-specific DNA-binding molecules bind more in the major groove of the DNA double helix. While some sequence-specific DNA-binding proteins preferably bind single-stranded DNA (e.g., single-strand binding protein), others bind double-stranded DNA (most ) a few and also heteroduplexes of DNA and RNA (e.g., telomerase reverse transcriptase, RNase H).
Binding single-stranded DNA
Single-stranded DNA occurs at the telomeres in eukaryotes permanent before and temporarily, among other things in the replication, transcription, recombination and DNA repair, such as single-stranded binding protein and certain DNA repair enzymes.
Binding double-stranded DNA
Double-stranded DNA having a complementary base pairing forming a double helix of (B- DNA). These DNA double helix has a large and a small furrow. The minor groove has a smaller proportion of nucleic bases in the surface of the molecule, which is why it is less suitable for a sequence - specific binding. Different DNA-binding molecules such as lexitropsins, netropsin, distamycin, Hoechst 33342, pentamidine, DAPI, or SYBR Green I binding sequence regardless to the minor groove of double stranded DNA. Double-stranded binding proteins include histones and DNA -binding protein H- NS, high mobility group proteins, DNA polymerases, DNA-dependent RNA polymerases, helicases, topoisomerases, gyrases, ligases, polynucleotide kinases, nucleases, some DNA repair enzymes. Sequence -specific dsDNA -binding proteins include transcription factors and some endonucleases. Prokaryotic transcription factors are mostly smaller than the products of gene expression controlled by them, during eukaryotic transcription factors are usually larger than their controlled products that sometimes have multiple copies of a DNA -binding domain.
DNA-binding protein domain
Typical protein domains in dsDNA -binding proteins, the zinc finger domain, the DNA clamp and the -turn-helix motif helix DNA binding or the Leucinzipperdomäne ( bZIP ) dimerization. For single-stranded DNA among others, the OB- fold domain has been described.
Identification
Methods for the determination of protein -DNA interactions ( linked DNA sequence, DNA-binding proteins ) are, for example, EMSA, DNase footprinting assay chip DAMiD, chip-on- chip or chip -Seq.
Modeling
Different approaches to molecular modeling have been described. Algorithms have been developed as for the determination of the bound DNA sequence. As part of a protein design, for example, zinc finger proteins can be designed.
Molding
DNA ( orange) with histones (blue).
The lambda repressor helix-turn- helix motif to DNA.
The restriction enzyme EcoRV (green) with DNA.
DNA clamp.