Expert Protein-Nucleic Acid Interaction (PNI) Assay Service

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For over two decades, Creative Biolabs has stood at the forefront of biotechnology, providing the global scientific community with unparalleled expertise and cutting-edge solutions. At Creative Biolabs, we have cultivated a state-of-the-art platform dedicated to the comprehensive analysis of Protein-Nucleic Acid Interactions (PNI). Our services are meticulously designed to provide deep, actionable insights into the affinity, kinetics, specificity, and functional consequences of these interactions. We empower researchers to move beyond qualitative observations to quantitative, high-resolution data, accelerating discovery pipelines and enabling groundbreaking science.

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Our Integrated PNI Assay Technology Platform

We offer a multi-faceted approach, combining classic methodologies with next-generation technologies to address any research question. Our platform is structured to provide maximum flexibility, from targeted, hypothesis-driven studies to large-scale, discovery-oriented screens.

Fig. 1 Different protein-nucleic acid interaction detection approaches. (OA Literature). Fig. 1 Overview of the different protein-nucleic acid interaction detection approaches.¹

Label-Free, Real-Time Interaction Analysis

Gain precise, real-time insights into the dynamic nature of PNI. These methods are ideal for accurately determining kinetic parametersand equilibrium constants without the need for fluorescent or radioactive labeling, which can interfere with molecular interactions.

Technology	Principle & Applications	Key Advantages
Surface Plasmon Resonance (SPR)	Measures changes in refractive index near a sensor surface as molecules bind and dissociate. Ideal for kinetic and affinity determination of purified components.	Real-time monitoring High sensitivity (pM to mM range) Label-free Requires one immobilized interactor
Bio-Layer Interferometry (BLI)	Uses interference of white light to measure the thickness of the molecular layer on a biosensor tip. Excellent for high-throughput screening and kinetics.	High-throughput (96/384-well format) Crude sample compatibility Label-free Real-time data acquisition
Isothermal Titration Calorimetry (ITC)	Directly measures the heat released or absorbed during a binding event, providing a complete thermodynamic profile.	Gold standard for affinity Measures binding stoichiometry Label-free, in-solution No immobilization required

In Vivo and Cellular Interaction Analysis

Investigate PNI within the native cellular environment to capture physiologically relevant interactions, including the influence of cellular machinery and post-translational modifications.

Service	Description & Applications	Creative Biolabs' Edge
Chromatin Immunoprecipitation (ChIP) & ChIP-seq	Identify the genomic locations where a specific protein (e.g., transcription factor, histone) binds in vivo. ChIP-qPCR validates binding at specific loci, while ChIP-seq provides a genome-wide map.	End-to-end service from cell culture to bioinformatics Low cell input protocols High-resolution mapping Expertise in both narrow and broad peak analysis
Crosslinking-Immunoprecipitation (CLIP) & CLIP-seq	A powerful technique to identify the specific RNA targets of an RNA-binding protein (RBP) in vivo. UV crosslinking creates a covalent bond at the site of interaction for precise mapping.	HITS-CLIP, PAR-CLIP, and iCLIP methodologies Single-nucleotide resolution mapping Comprehensive bioinformatics for motif discovery and target identification
Yeast One-Hybrid (Y1H) / Three-Hybrid (Y3H) Systems	Reporter-based genetic assays to screen for protein-DNA (Y1H) or protein-RNA-protein (Y3H) interactions in a eukaryotic context. Ideal for large-scale library screening.	High-quality custom library construction and screening Rigorous validation of positive hits Scalable for high-throughput discovery

Classic and High-Throughput In Vitro Assays

Our portfolio includes a robust selection of established and scalable methods for validating interactions, screening inhibitors, and characterizing binding specificity.

Assay	Description & Applications	Throughput
Electrophoretic Mobility Shift Assay (EMSA)	A gel-based method to detect protein binding to a labeled nucleic acid probe by observing a shift in electrophoretic mobility. Ideal for confirming interactions and studying binding specificity.	Low to Medium
DNA/RNA Pull-Down Assays	Uses a biotinylated nucleic acid probe to "pull down" its interacting proteins from a cell lysate or protein mixture, followed by identification via Western Blot or Mass Spectrometry.	Medium
Filter Binding Assays	A quantitative method where protein-nucleic acid complexes are retained on a nitrocellulose membrane while free nucleic acids pass through. Excellent for determining binding constants.	Medium to High
Protein-Nucleic Acid ELISA	An ELISA-based format for high-throughput screening of PNI. One interactor is immobilized on a plate to capture its binding partner, which is then detected with a specific antibody.	High

Applications of Our PNI Assay Services

Our services are tailored to support a diverse range of research and development objectives across multiple scientific disciplines.

Drug Discovery & Development:

Screening for small molecules or biologics that inhibit or modulate specific PNI.
Validating drug-target engagement in a cellular context.
Characterizing the mechanism of action for novel therapeutics targeting transcription factors, RNA-binding proteins, or viral proteins.

Gene Regulation & Epigenetics:

Mapping transcription factor binding sites across the genome.
Identifying proteins that bind to specific DNA or RNA regulatory elements (promoters, enhancers, silencers).
Investigating the role of histone modifications and chromatin remodelers in gene expression.

RNA Biology:

Discovering the RNA targets of uncharacterized RNA-binding proteins.
Validating miRNA-target interactions.
Mapping RNA modification "reader" proteins.

Structural Biology:

Validating interactions and determining binding affinity to guide co-crystallization or cryo-EM efforts.
Mapping binding interfaces and identifying key residues for interaction.

The Creative Biolabs Advantage: Your Partner in Discovery

Choosing Creative Biolabs means partnering with a team of seasoned experts committed to the success of your project. With over 20 years of dedicated experience, we deliver more than just data; we provide comprehensive solutions.

Unrivaled Expertise: Our Ph.D.-level scientists possess deep domain knowledge to help you design the optimal experimental strategy, troubleshoot complex challenges, and interpret nuanced results.
Cutting-Edge Technology: We continuously invest in the latest platforms, from high-sensitivity SPR systems to next-generation sequencers, ensuring your research benefits from the most advanced tools available.
Customized Project Design: We recognize that every research question is unique. We work closely with you to tailor our services to your specific needs, from protein and nucleic acid production to final bioinformatics analysis.
Quality and Transparency: We operate with the highest scientific standards, providing detailed reports, raw data, and transparent communication throughout the project lifecycle.

Explore Our Related Biomolecular Interaction Services

Creative Biolabs offers a fully integrated service portfolio to support every stage of your research. Explore our related services to seamlessly advance your project from concept to conclusion. Explore our full range of biomolecular interaction services here: Biomolecular Interaction based Binder Discovery

Other optional Protein-Nucleic Acid Interaction (PNI) Assay Services

Contact Us Today to discuss your project with one of our PNI experts or Request a Quote to get started. Let our two decades of expertise power your next discovery.

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Frequently Asked Questions (FAQs)

Q: With so many available techniques, how do I choose the right PNI assay for my research?

A: Choosing the optimal assay depends entirely on your scientific question. As a general guide:

For precise kinetics and affinity: If you have purified components and need to measure binding strength and on/off rates in real-time, label-free methods like Surface Plasmon Resonance (SPR), Bio-Layer Interferometry (BLI), or Isothermal Titration Calorimetry (ITC) are the gold standard.
To identify interactions in a native cellular context: If your goal is to see where a protein binds to DNA or RNA within a living cell, Chromatin Immunoprecipitation (ChIP-seq) for DNA targets or Crosslinking-Immunoprecipitation (CLIP-seq) for RNA targets are the most powerful approaches.
For large-scale discovery or screening: If you need to screen a library of proteins against a specific nucleic acid sequence (or vice versa), high-throughput methods like Yeast One-Hybrid (Y1H) systems or our Protein-Nucleic Acid ELISA platforms are most efficient.

Our experts are available for a free consultation to help you design the most effective and resource-efficient experimental plan.

Q: What materials do I need to provide to start a PNI project?

A: This varies by project, but typically you would need to provide one or more of the following:

The sequence information for your protein and/or nucleic acid of interest.
A high-purity sample of your recombinant protein.
The specific cell line (and any necessary treatment conditions) for in vivo assays like ChIP or CLIP.
A specific antibody for your protein of interest (for IP-based methods).

Don't have these reagents? No problem. Creative Biolabs provides a seamless, integrated service pipeline. We can perform gene synthesis, recombinant protein expression, and custom antibody development as part of a comprehensive project package.

Q: My protein is difficult to express or has low stability. Can you still analyze its interactions?

A: Absolutely. Our team has over two decades of experience working with challenging proteins. We can employ several strategies, including:

Optimizing protein expression and purification protocols to enhance stability and yield.
Utilizing highly sensitive techniques like SPR, which require smaller amounts of material.
Adjusting buffer and assay conditions (pH, salt concentration, temperature) to find an optimal window for interaction analysis.
Leveraging in vivo or cellular lysate-based assays where the protein remains in a more native and stable environment.

Q: How does ChIP-seq differ from CLIP-seq?

A: Both are powerful immunoprecipitation-based techniques for mapping protein-nucleic acid interactions genome-wide, but they target different nucleic acids.

ChIP-seq (Chromatin Immunoprecipitation Sequencing) is used to identify the binding sites of DNA-binding proteins, such as transcription factors and histones, on the DNA.
CLIP-seq (Crosslinking and Immunoprecipitation Sequencing) is used to identify the binding sites of RNA-binding proteins (RBPs) on RNA transcripts. It involves a UV crosslinking step to create a covalent bond between the protein and its target RNA.

Q: What are the final deliverables for a PNI project?

A: We believe in providing comprehensive and transparent results. For every project, you will receive:

All raw and processed data.
A detailed, publication-quality report outlining the experimental design, methodology, and results.
High-quality figures and tables summarizing key findings.
A concluding summary and interpretation of the data, prepared by our Ph.D.-level scientists.
For sequencing projects, we offer a full suite of bioinformatics analysis services.

Q: How do I get a quote and what is the typical turnaround time?

A: The first step is to Contact Us. One of our technical specialists will schedule a no-obligation consultation to discuss your specific research goals and project requirements. Following this discussion, we will provide you with a detailed, customized proposal including a project timeline and pricing. Turnaround times are project-dependent and can range from a few weeks for straightforward in vitro assays to several weeks for complex, multi-stage projects like ChIP-seq analysis.

Reference

Cozzolino, Flora, et al. "Protein–DNA/RNA interactions: an overview of investigation methods in the-omics era." Journal of Proteome Research 20.6 (2021): 3018-3030. Distributed under Open Access license CC BY 4.0, without modification. https://doi.org/10.1021/acs.jproteome.1c00074

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