Antibodies specific for nucleic acid modifications

ABSTRACT

Nucleotide modifications constitute marks in RNA and DNA that contribute to gene regulation, development and other cellular processes. The understanding of their intricate molecular roles has been hampered by the high number of different modifications, the lack of effective methods and tools for their detection and quantification as well as by their complex structure-function relationship. The recent development of RNA and DNA immunoprecipitation followed by high-throughput sequencing (RIP- and DIP-seq) initiated detailed transcriptome- and genome-wide studies. Both techniques depend on highly specific and sensitive antibodies to specifically enrich the targeted modified nucleotides without background or potential biases. Here, we review the challenges and developments when generating and validating antibodies targeting modified nucleotides. We discuss antibody-antigen interactions, different strategies of antigen generation and compare different binder formats suitable for state-of-the-art high resolution mapping and imaging technologies.

KEYWORDS:

• Antibody
• epigenomics
• epitranscriptomics
• modified nucleotide
• nucleic acid modification

Disclosure of potential conflicts of interest

No potential conflicts of interest were disclosed. Some antibodies described in this review are from commercial sources. We are not recommending a particular antibody for a specific experiment but are only citing publications where they have been used. We have no competing financial interest.

Acknowledgments

We thank Andreas Moosmann and Gunter Meister for critical reading of the manuscript, Gunter Meister, Robert Hett and Thomas Carell for personal communications and sharing unpublished, and Matthias Q. Kurz for the chemical drawings in Table 1 and Fig. 2.

Funding

This work was supported by DFG grants SPP1784 and SFB1064 and by Institutional grants.