High-Quality Isolation of Cytoplasmic and Nuclear RNA Using the AffiEXTRACT Method: A Detailed Protocol

The compartmentalization of RNA molecules within the cytoplasm and nucleus of eukaryotic cells is fundamental for understanding gene expression and regulation. AffiEXTRACT is an advanced method designed for the precise extraction of cytoplasmic and nuclear RNA, ensuring high yield and purity. This article delves into the technical aspects of AffiEXTRACT, highlighting its methodology, advantages, troubleshooting, and application in molecular biology research.

RNA plays a critical role in various cellular processes, including transcription, splicing, translation, and regulation. The spatial distribution of RNA within the cell necessitates methods that can efficiently separate and purify cytoplasmic and nuclear RNA. Traditional methods often suffer from cross-contamination and low yield. AffiEXTRACT offers a reliable solution by employing specific affinity-based separation techniques to isolate high-quality RNA from both cellular compartments.

Materials and Methods

Reagents and Equipment

  • AffiEXTRACT Kit (comprising lysis buffers, wash buffers, and elution buffers)
  • Centrifuge
  • Microcentrifuge tubes
  • Pipettes and tips
  • RNAse-free water
  • RNA quantification and integrity assessment tools (e.g., NanoDrop, Bioanalyzer)
  • Protease inhibitor cocktail (optional for samples prone to degradation)
  • DNase I (optional for DNA contamination removal)
  • Ethanol (for washing steps)

Cell Preparation

  • Harvesting Cells: Grow eukaryotic cells to the desired confluency (70-90%) and harvest by centrifugation (300 x g for 5 minutes at 4°C).
  • Washing: Wash the cell pellet with cold PBS to remove any residual media and cellular debris.

Lysis and Fractionation

  • Cytoplasmic Lysis: Resuspend the cell pellet in the cytoplasmic lysis buffer provided in the AffiEXTRACT kit. Incubate on ice for 5 minutes with gentle pipetting to ensure complete lysis.
  • Separation: Centrifuge the lysate at 500 x g for 5 minutes at 4°C. Carefully transfer the supernatant (cytoplasmic fraction) to a new tube without disturbing the pellet.
  • Nuclear Lysis: Resuspend the remaining pellet (nuclear fraction) in the nuclear lysis buffer. Incubate on ice for 5 minutes with intermittent vortexing to ensure thorough nuclear membrane disruption.

RNA Purification

  • Binding: Add the appropriate binding buffer to the cytoplasmic and nuclear lysates. Mix thoroughly by gentle inversion. Load the lysates onto RNA affinity columns provided in the AffiEXTRACT kit.
  • Washing: Wash the columns with the provided wash buffers to remove impurities, including proteins and other cellular contaminants. Perform multiple wash steps to ensure maximum purity.
  • Elution: Elute the RNA using the elution buffer. Pre-warm the elution buffer to 65°C to enhance RNA recovery. Collect the purified RNA in RNase-free tubes.

Quality Assessment

  • Quantification: Measure RNA concentration using a NanoDrop spectrophotometer by assessing absorbance at 260 nm.
  • Integrity: Assess RNA integrity using an Agilent Bioanalyzer or agarose gel electrophoresis. High integrity RNA should show distinct 18S and 28S ribosomal RNA bands.


The AffiEXTRACT method provides distinct and high-quality RNA from both cytoplasmic and nuclear fractions. Typical yields range from 2-5 µg of RNA per million cells, depending on cell type and growth conditions. RNA integrity numbers (RIN) generally exceed 8.0, indicating high-quality extractions suitable for downstream applications such as qPCR, RNA-Seq, and Northern blotting.

Yield and Purity

  • Cytoplasmic RNA: Yields typically range between 3-4 µg per million cells, with minimal contamination from nuclear RNA as verified by the absence of U6 snRNA (a nuclear RNA marker).
  • Nuclear RNA: Yields range between 2-3 µg per million cells, with purity confirmed by the enrichment of U6 snRNA and depletion of GAPDH mRNA (a cytoplasmic RNA marker).


AffiEXTRACT's affinity-based separation ensures minimal cross-contamination between cytoplasmic and nuclear RNA. The method's efficiency and ease of use make it a valuable tool for researchers studying RNA localization and function. The high purity of the extracted RNA is crucial for accurate gene expression analyses and other molecular biology applications.


  • High Purity: Minimizes cross-contamination between cytoplasmic and nuclear RNA.
  • Efficiency: Rapid and straightforward procedure, typically completed within 2 hours.
  • Scalability: Suitable for small and large-scale extractions, accommodating various sample sizes.


  • Low Yield: Ensure complete lysis by optimizing incubation times and buffer volumes. Verify cell count and condition prior to extraction.
  • Degraded RNA: Include RNase inhibitors during the lysis step and handle samples with care to prevent degradation.
  • Contamination: Perform thorough washing steps and avoid overloading the affinity columns.


  • Gene Expression Studies: Understanding differential gene expression in cellular compartments.
  • RNA-Protein Interactions: Studying the localization and function of RNA-binding proteins.
  • Splicing Research: Investigating splicing events and their regulation within the nucleus.
  • Transcriptomics: High-throughput RNA sequencing to explore transcriptome dynamics.

The AffiEXTRACT method represents a significant advancement in RNA extraction technology, providing researchers with a reliable and efficient means to obtain high-quality cytoplasmic and nuclear RNA. Its application spans various fields of molecular biology, contributing to a deeper understanding of RNA dynamics and function within the cell.

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Development and Optimization of Cytoplasmic and Nuclear DNA Extraction Protocol Using AffiEXTRACT