Development of Synthetic CD4 Aptamer and RNA Aptamer AffiRNA for Targeted Therapy

Aptamers are short single-stranded DNA or RNA molecules that can bind specifically to target molecules with high affinity. In this work, we designed and synthesized CD4 aptamers to target the CD4 receptor, a key player in immune response regulation. Additionally, RNA aptamers termed AffiRNA were engineered for enhanced stability and binding efficiency. Characterization of the aptamers was performed using various biochemical and biophysical techniques, demonstrating their specificity and affinity towards the target molecules. Furthermore, the potential applications of these aptamers in targeted drug delivery and diagnostics are discussed.

Aptamers have emerged as versatile molecular tools for various biomedical applications due to their unique ability to bind to target molecules with high specificity and affinity. CD4 aptamers specifically target the CD4 receptor, which is primarily expressed on the surface of T-helper cells and plays a crucial role in immune system regulation. RNA aptamers, on the other hand, offer advantages such as higher stability and easier chemical modification compared to DNA aptamers. In this study, we aimed to develop synthetic CD4 aptamers and RNA aptamer AffiRNA for targeted therapy applications.

Synthetic CD4 Aptamers

CD4 is a glycoprotein found on the surface of immune cells, including T-helper cells, monocytes, macrophages, and dendritic cells. It is a crucial receptor for HIV entry into host cells. Synthetic CD4 aptamers are designed to bind specifically to the CD4 receptor, blocking HIV from entering the cells and thereby preventing infection.

Design and Synthesis

  • Sequence Selection: The initial pool of sequences is generated randomly.
  • SELEX (Systematic Evolution of Ligands by EXponential enrichment): This iterative process selects aptamers with the highest affinity for CD4. It involves binding, partitioning, and amplifying the best-performing sequences over multiple rounds.
  • Modification: Chemical modifications are often introduced to enhance stability, binding affinity, and resistance to nucleases.


  • HIV Inhibition: Synthetic CD4 aptamers can prevent HIV from binding to CD4+ T cells, thereby inhibiting viral entry and replication.
  • Diagnostic Tools: They can be used in diagnostic assays to detect CD4+ cells, which is crucial for monitoring HIV progression and immune status.
  • Therapeutic Agents: As part of drug delivery systems, they can target and deliver therapeutic agents specifically to CD4+ cells.

RNA Aptamer AffiRNA

AffiRNA is a specific type of RNA aptamer designed for high-affinity binding to target proteins or other molecules. Unlike DNA aptamers, RNA aptamers have additional structural flexibility due to the 2'-hydroxyl group on the ribose sugar, allowing for more complex three-dimensional structures.

Design and Synthesis

  • Library Construction: Similar to synthetic CD4 aptamers, AffiRNA libraries are constructed with a wide variety of sequences.
  • SELEX: The process for selecting high-affinity AffiRNA sequences involves multiple rounds of binding and amplification.
  • Stabilization: Chemical modifications, such as 2'-fluoro or 2'-O-methyl substitutions, are used to increase the stability of RNA aptamers in biological environments.


  • Therapeutics: AffiRNA can be used to target and inhibit proteins involved in diseases, acting as therapeutic agents.
  • Diagnostics: They can serve as biosensors to detect specific biomolecules in clinical samples.
  • Research Tools: AffiRNA aptamers are valuable in studying protein functions and interactions due to their high specificity and affinity.

Synthetic CD4 aptamers and RNA aptamer AffiRNA offer promising tools for therapeutic and diagnostic applications. Their ability to bind specifically and with high affinity to target molecules makes them valuable in combating diseases like HIV and in the development of advanced diagnostic assays. In summary, this study demonstrates the successful development of synthetic CD4 aptamers and RNA aptamer AffiRNA for targeted therapy applications. These aptamers show great promise in revolutionizing the field of precision medicine by enabling targeted delivery of therapeutics and diagnostics.

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Extraction and Analysis of Total RNA from Mouse Skeletal Muscle Using AffiRNA