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Protein-DNA Interaction Analysis Service

Protein-DNA interactions play a key role in biological processes, and the precise resolution of them is essential for in-depth studies of gene regulatory mechanisms under physiological and pathological conditions. As a company that has specialized in proteomics research for many years, Creative Proteomics can provide professional protein-DNA interaction analysis service to facilitate your protein research.

What is Protein-DNA Interaction

Interactions between DNA and proteins are associated with many cellular life activities, like DNA replication and recombination, mRNA transcription and modification, virus infection and proliferation, etc. There are many methods used to research protein-DNA interactions, such as EMSA, DNase I footprinting assay, methylation interference, yeast one-hybrid, and ChIP-Seq, etc. Chromatin Immunoprecipitation Sequencing (ChIP-Seq) is a classic method for studying protein-DNA interactions in vivo. It is an antibody-based technique, and is commonly used for the study of protein-DNA interactions such as histones and transcription factors. ChIP-Seq technology combines ChIP with second-generation sequencing technology to efficiently detect DNA segments interacting with histones, transcription factors and others on a genome-wide scale.

The Principle of Protein-DNA Interaction Analysis Methods

EMSA. In the presence of an electric field, DNA migration rate is inversely proportional to the logarithm of its molecular weight. The binding of proteins increases the molecular weight of DNA and blocks its migration.

DNase I footprinting assay.The binding of a specific protein to a DNA segment protects it from DNaseI cleavage. Thus, it does not produce the cleavage molecule, which is separated by gel electrophoresis and appears as a blank area, called a "footprint".

Methylation interference. DMS can methylate the exposed guanine (G) residues in DNA, and hexahydropyridine, in turn, chemically cleaves the methylated G residues specifically, and an experimental method was designed based on this principle.

Yeast one-hybrid DNA-binding proteins bind to DNA cis-acting elements to regulate reporter gene expression, and protein-DNA interactions can be analyzed by phenotypic detection of reporter genes.

ChIP-Seq. ChIP-Seq is based on the principle that it specifically enriches the DNA fragments bound with target proteins by ChIP, and then purifies them and constructs libraries, and next sequences the enriched DNA fragments by high-throughput sequencing. Then, the large number of sequence tags obtained are precisely localized to the genome to obtain DNA segment information in genome-wide interactions with proteins such as histones, transcription factors, etc.

Fig. 1. Schematic of ChIP-Seq

Fig. 1. Schematic of ChIP-Seq (Orlov Y, et al., 2012)

It is best to choose the analysis method that is appropriate for the research needs according to the advantages and disadvantages of each method. The following is an overview of each method's advantages and disadvantages.

Table 1. Advantages and disadvantages of each method

Methods Advantages Disadvantages
EMSA Show the binding site and sequence
Highly sensitive
Can distinguish different proteins
Qualitative and quantitative		 Multiple and complex steps
Low affinity binding is difficult to recognize
Difficult to realistically reflect in vivo binding
DNase I footprinting assay Large amounts of data
Show the binding site and sequence		 Requires a high protein concentration
Can disrupt specific interactions
High substrate requirement
Multiple components cannot be automatically distinguished
Methylation interference assay Analyze the relationship between proteins and G residues at the binding site
Identify the precise location of protein-DNA interactions		 Only methylates G and A residues
Yeast one-hybrid High sensitivity
Simple operation
Rapid		 Prone to false positives and false negatives
Some proteins may be toxic
Endogenous proteins interfere
ChIP-Seq Directly visualize the dynamic binding in vivo
Highly sensitive
Can be combined with other technologies		 Experiment conditions must be more stringent
Multi-protein binding to the same sequence is difficult to analyze
Chromatin can be binded indirectly by proteins

Our Services

Creative Proteomics provides considerate and high-quality protein-DNA interactions analysis services. And we offer all the analytical methods described above and can provide you with the optimal solution for your research requirements. In addition, we provide protein-protein interaction analysis service, protein-metabolite interaction analysis service and protein-RNA interaction analysis service.

Fig. 2. Protein-DNA interaction analysis workflow by ChIP-Seq

Fig. 2. Protein-DNA interaction analysis workflow by ChIP-Seq

Applications of Protein-DNA Interaction

Analysis of protein-DNA interactions contributes to a clear understanding of the overall properties of DNA-protein complexes. It allows the analysis of DNA conformation and the exact sequence of bases that bind to proteins, the identification of binding proteins based on specific DNA sequences, the identification of proteins on the surface of DNA, and, in addition, the study of the tertiary structure of proteins and their conformational changes in complexes, etc.

Advantages of Protein-DNA Interaction Analysis

Creative Proteomics provides comprehensive and high-quality proteomics analysis services. If you are interested in protein-DNA interaction analysis, please contact us for more details.

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