Screening Services of Plant Proteins Interacting with Nucleic Acid

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Screening Services of Plant Proteins Interacting with Nucleic Acid

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CD BioSciences provides services to screen and discover specific binding proteins for known genes. Our combination of DNA/RNA pull-down technology and mass spectrometry (MS), ChIRP-MS, and yeast one-hybrid screening library services, allows for high-throughput screening of known gene-plant transcription factor interaction networks, helping clients to understand the processes that regulate gene expression at the transcriptional level.

Crystal structure of protein-nucleic acid interactions. Figure 1. Crystal structure of protein-nucleic acid interactions. (Khrapunov, S., et al., 2006)

Protein-nucleic acid interactions are widely present in plant life activities, including gene replication, transcription, translation, and modification. The research of plant protein-nucleic acid interactions is a fundamental tool in the study of life sciences and is essential for understanding the functions of plant proteins in regulating cellular processes.

Service Content

DNA/RNA pull-down service

We provide DNA/RNA pulling services to clients for screening plant proteins interacting with known nucleic acids. By combining with MS, interacting proteins can be qualified simultaneously, which is significant for unraveling the functional mechanism of plant proteins.

Advantages Limitations
  • Enrichment of low-abundance targets.
  • End-labeled DNA can be generated by a variety of methods.
  • Separation of intact complexes.
  • Compatible with immunoblotting and mass spectrometry.
  • Long DNA probes show non-specific binding.
  • Requires specific antibodies against natural proteins.
  • Requires nuclease-free conditions.
  • The assay must be performed in vitro.

Plant yeast one-hybrid library construction and screening service

We offer yeast one-hybrid (Y1H) construction and screening services for characterizing plant proteins that interact with given nucleic acid sequences. Our Y1H technology is highly sensitive and widely used for cloning plant transcription factors that are difficult to purify by biochemical methods.

Advantages Limitations
  • No need to isolate and purify the protein.
  • Overcomes the disadvantage that proteins are usually in an unnatural conformation for in vitro studies.
  • Identifies multiple transcription factors.
  • Identify interactions with low abundance transcription factors.
  • Cloning of DNA-binding proteins by Y1H eliminates the need for specific optimization ofin vitro conditions.
  • Possible interaction of target elements with yeast endogenous transcriptional activators, producing false positives.
  • AD fusion proteins are toxic to cells, are not stably expressed, or misfold, interfering with binding ability and generating false negatives.

Chromatin isolation by RNA purification (CHIRP)-MS service

Our ChIRP-MS service combines ChIRP with mass spectrometry to identify plant proteins that interact with target RNAs, helping clients gain insight into the protein composition of plant chromatin regions.

Advantages Limitations
  • Identifies binding sites anywhere in the genome.
  • Interactions between complexes formed by RNA, proteins, and DNA can be researched, as well as two-by-two interactions between them.
  • Not limited by RNA length.
  • Non-specific oligonucleotide interactions.
  • Chromatin may be disrupted during the preparation phase.

Application Fields

  • Decipher the transcriptional and post-transcriptional regulatory networks that control gene expression.
  • Insight into the regulation of chromatin states and epigenetic marks contributes to understanding the inheritance of traits, cellular memory, and the impact of epigenetic dysregulation on plant development and disease.
  • Decipher the complex interactions between transcription factors, co-regulators, and cis-regulatory elements, providing insights into developmental processes, stress responses, and cell signaling pathways.
  • Understand the regulation of RNA maturation, selective splicing, RNA localization, and stability and identify potential RNA-based therapeutic targets.

CD BioSciences is dedicated to plant protein research, with cutting-edge instruments and rich experience in plant molecular biology. We provide a one-stop solution for clients who are researching gene regulation, chromatin structure, transcriptional networks, RNA processing, and more. If you have any questions, please feel free to contact us.

Reference

  1. Khrapunov, S., et al. (2006). Binding then bending: a mechanism for wrapping DNA. Proceedings of the National Academy of Sciences of the United States of America. 103(51), 19217–19218.

For research use only, not for clinical use.