Background

As one of the well-known service providers in biotechnology field, Creative Biolabs has years of experience in supplying a broad range of optimized platforms particularly in protein-nucleic acid interaction assays for global researchers. It attracts attention that protein-nucleic acid interaction data is developed for physiology and pathology study to illustrate the mechanisms of cell action and pathway. With the assistance of Creative Biolabs, there will be some advancement in the exploration of the equilibrium and dynamical considerations of how proteins interact with nucleic acids, what proteins are presenting in protein-nucleic acid complexes and which nucleic acid sequences are required to assemble these combinations. Creative Biolabs has a capability to provide powerful methods which generally classified into three categories, in vitro, in vivo, and in silico aspects, to detect protein-nucleic acid complexes.

Fig.1 Molecular surface of histones is shown in blue and the DNA in orange.

Featured Protein-Nucleic Acid Interaction Detection Approaches

Table 1. Protein-nucleic acid interaction assay services in Creative Biolabs.

Nucleic acids and proteins are two kinds of the most important biomolecules in any cell type and living organism. Nucleic acids store the genetic information, while proteins are responsible for executing and regulating the life processes. Interactions between proteins and nucleic acids are the molecular foundations of most key biological circumstances, such as gene expression, nucleic acid transport and structural formation of chromatin, also handle intracellular connections, metabolic and developmental control. There has been an increasing consciousness of the necessity for the characterization of protein-nucleic acid interactions since the first time the association of proteins-DNA strands was observed microscopically. Thence scientists were led to construct unique experimental tools for the assays to demonstrate the binding influence of protein and DNA or RNA on the structure and function of the corresponding nucleic acid. Proteins interact with nucleic acids broadly through direct forces or indirect, involving dipolar interactions (hydrogen bond), electrostatic interactions (salt bridges), entropic effects (hydrophobic interactions) and dispersion forces (base stacking). These physical forces contribute in varying degrees to proteins’ binding in sequence-specific (tight) or non-sequence-specific (loose) manners. And sometimes interactions are transient requiring stabilization by chemical crosslinking prior to separation of protein-nucleic acid partners. The features of above interacting activities, therefore, can determine which assays or approaches are the most suitable for studying complex assembly.

Fig.2 X-ray structure of the DNA-protein complex.

Protein-nucleic acid interaction is fundamental for maintaining genome and reproducing life in central biological functions/process ranging from DNA replication and repair to RNA packaging and maturation, recombination and transcription of DNA to translation and transport of RNA. These natural and specific interactions are susceptible to monitor by a number of well-established analytical techniques from Creative Biolabs including genetic, biochemical, biophysical and immunological methods depending on the purpose of clients for further progress.

Creative Biolabs works as an experienced agent in the field of protein-nucleic acid interactions and devotes to measuring the quantitative parameters of binding as described. Clearly, our rational design strategy and time-saving analysis revolutionize currently understanding of protein-nucleic acid complexes in cell development and reveal detailed molecular mechanisms of signal pathway. Creative Biolabs is always pleased to support scientific research with a high-quality presentation of assay results and satisfy each demand from customers.

Published Data

• Study of the Interactions and Epigenetic Functions of Human ALKBH6

Fig. 3 ALKBH6 binds with different types of DNAs. (Lulu Ma, 2022)

The homologue of human AlkB 6, called ALKBH6, plays a key role in DNA damage repair and tumor therapy. Here, the researchers analyzed the crystal structure of human total ALKBH6 and its complexes with ligands. Members of the AlkB family bind nucleic acids through nucleotide recognition capping NRL (also known as Flips), and NRL can recognize DNA, RNA, and reverse methylation lesions. The results show that ALKBH6 has Flip1 and Flip2 domains, which are different from other AlkB family members in sequence and conformation. In addition, its unique Flip3 domain has the functions of distinguishing double-stranded nucleic acids, blocking active centers, binding to other proteins, and inhibiting tumor growth. Structural analysis and substrate screening reveal how ALKBH6 distinguishes different types of nucleic acids and may also act as nucleic acid demethylases. At the same time, the interaction between ZMYND11 and ALKBH6 in tumor inhibition and the interaction between histone modification and nucleic acid modification in epigenetic regulation have been verified. These results are of great significance to the molecular mechanism of ALKBH6-related nucleic acid damage repair and tumor therapy.

FAQ

1. What is a protein-nucleic acid interaction assay and what are its common applications?

   A protein-nucleic acid interaction assay is a method used to study the binding interactions between proteins and nucleic acids (DNA or RNA). This type of assay is crucial for understanding various biological processes, such as DNA replication, transcription, repair, and RNA processing. Common applications include identifying binding sites on DNA or RNA, quantifying the strength and specificity of the interaction, and screening for molecules that can modulate these interactions in therapeutic applications.

2. What are some of the most widely used techniques for protein-nucleic acid interaction assays?

   Electrophoretic Mobility Shift Assay (EMSA) is used to monitor the binding of proteins to nucleic acids by observing the mobility shift of a nucleic acid-protein complex in a gel. Chromatin Immunoprecipitation (ChIP) is applied to identify the specific locations on DNA where proteins are bound in living cells. Surface Plasmon Resonance (SPR) and Bio-Layer Interferometry (BLI) are biophysical methods that provide real-time analysis of the interaction kinetics between proteins and nucleic acids. Each of these methods offers unique advantages depending on the specific requirements of the study.

3. How do protein-nucleic acid interaction assays contribute to drug discovery and development?

   Protein-nucleic acid interaction assays are fundamental in the field of drug discovery and development, particularly for targeting diseases linked to genetic or epigenetic factors. These assays can be used to identify and characterize the interactions between regulatory proteins and their nucleic acid targets, which is crucial for developing drugs that can modulate these interactions. For example, assays can help in discovering molecules that inhibit or enhance protein-DNA interactions involved in cancer cell proliferation or viral replication, paving the way for novel therapeutic agents.

4. What role do protein-nucleic acid interaction assays play in understanding genetic regulation?

   Protein-nucleic acid interaction assays are critical for elucidating the mechanisms of genetic regulation. These interactions are central to controlling gene expression, where proteins such as transcription factors bind to specific DNA sequences to either promote or inhibit the transcription of genes. By using these assays, researchers can identify which proteins are bound to specific genomic regions, understand the impact of these bindings on gene activity, and discover how mutations or disruptions in these interactions could lead to diseases. This insight is vital for developing strategies to manipulate gene expression in therapeutic contexts.

5. What advancements have improved the accuracy and efficiency of protein-nucleic acid interaction assays?

   High-throughput sequencing techniques coupled with traditional ChIP (ChIP-Seq) or newer methods like CLIP-Seq (Crosslinking and Immunoprecipitation followed by sequencing) for RNA-binding proteins have allowed for a more comprehensive and precise mapping of protein-nucleic acid interactions across the genome. Additionally, improvements in surface plasmon resonance and bio-layer interferometry technology have provided tools for real-time, label-free analysis of the kinetics of these interactions. These advancements facilitate a deeper understanding of the dynamic nature of protein-nucleic acid interactions and their role in cellular functions.

6. What are the limitations of protein-nucleic acid interaction assays in studying dynamic interactions?

   While protein-nucleic acid interaction assays are invaluable for understanding the static snapshot of interactions, they can sometimes fall short in capturing the dynamic and transient nature of these interactions within living cells. Many assays require the isolation or fixation of components, which can disrupt the physiological context or miss transient interactions that occur quickly or only under specific conditions. Techniques such as live-cell imaging combined with fluorescence resonance energy transfer (FRET) are being developed to address these limitations by allowing researchers to observe these interactions in real time within living cells.

7. How are protein-nucleic acid interactions quantitatively analyzed?

   Techniques such as quantitative EMSA, quantitative ChIP (qChIP), and quantitative PCR (qPCR) following immunoprecipitation are commonly used. These methods allow for the determination of binding affinities, kinetic rates, and concentration effects in a quantitative manner. Additionally, more advanced methods like isothermal titration calorimetry (ITC) provide detailed thermodynamic profiles of the binding interactions, offering insights into the energy changes and forces driving these interactions.

Resources

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