Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation


Activation-induced cytidine deaminase (AID) is a protein required for B cells to undergo class switch recombination and somatic hypermutation (SHM)—two processes essential for producing high-affinity antibodies1. Purified AID catalyses the deamination of C to U on single-stranded (ss)DNA2,3,4. Here, we show in vitro that AID-catalysed C deaminations occur preferentially on 5′ WRC sequences in accord with SHM spectra observed in vivo. Although about 98% of DNA clones suffer no mutations, most of the remaining mutated clones have 10–70 C to T transitions per clone. Therefore, AID carries out multiple C deaminations on individual DNA strands, rather than jumping from one strand to another. The avid binding of AID to ssDNA could result from its large net positive charge (+11) at pH 7.0, owing to a basic amino-terminal domain enriched in arginine and lysine. Furthermore, AID exhibits a 15-fold preference for C deamination on the non-transcribed DNA strand exposed by RNA polymerase than the transcribed strand protected as a RNA–DNA hybrid. These deamination results on ssDNA bear relevance to three characteristic features of SHM: preferential mutation at C sites within WRC hotspot sequences, the broad clonal mutagenic heterogeneity of antibody variable regions targeted for mutation5,6, and the requirement for active transcription to obtain mutagenesis7,8.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it


Prices may be subject to local taxes which are calculated during checkout

Figure 1: Processive AID-catalysed C deamination on ssDNA recapitulates SHM hotspots and clonal mutational heterogeneity.
Figure 2: AID-catalysed C → U deamination spectrum.
Figure 3: AID preferentially deaminates C in the non-transcribed strand during in vitro transcription of dsDNA.


  1. Kinoshita, K. & Honjo, T. Unique and unprecedented recombination mechanisms in class switching. Curr. Opin. Immunol. 12, 195–198 (2000)

    Article  CAS  Google Scholar 

  2. Bransteitter, R., Pham, P., Scharff, M. D. & Goodman, M. F. Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase. Proc. Natl Acad. Sci. USA 100, 4102–4107 (2003)

    Article  ADS  CAS  Google Scholar 

  3. Chaudhuri, J. et al. Transcription-targeted DNA deamination by the AID antibody diversification enzyme. Nature 421, 726–730 (2003)

    Article  ADS  Google Scholar 

  4. Dickerson, S. K., Market, E., Besmer, E. & Papavasiliou, F. N. AID mediates hypermutation by deaminating single stranded DNA. J. Exp. Med. 197, 1291–1296 (2003)

    Article  CAS  Google Scholar 

  5. Liu, Y. J. et al. Normal human IgD+IgM- germinal center B cells can express up to 80 mutations in the variable region of their IgD transcripts. Immunity 4, 603–613 (1996)

    Article  CAS  Google Scholar 

  6. Rada, C. et al. Immunoglobulin isotype switching is inhibited and somatic hypermutation perturbed in UNG-deficient mice. Curr. Biol. 12, 1748–1755 (2002)

    Article  CAS  Google Scholar 

  7. Maizels, N. Somatic hypermutation: how many mechanisms diversify V region sequences? Cell 83, 9–12 (1995)

    Article  CAS  Google Scholar 

  8. Peters, A. & Storb, U. Somatic hypermutation of immunoglobulin genes is linked to transcription initiation. Immunity 4, 57–65 (1996)

    Article  CAS  Google Scholar 

  9. Muramatsu, M. et al. Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell 102, 553–563 (2000)

    Article  CAS  Google Scholar 

  10. Revy, P. et al. Activation-induced cytidine deaminase (AID) deficiency causes the autosomal recessive form of the Hyper-IgM syndrome (HIGM2). Cell 102, 565–575 (2000)

    Article  CAS  Google Scholar 

  11. Gerber, A. P. & Keller, W. RNA editing by base deamination: more enzymes, more targets, new mysteries. Trends Biochem. Sci. 26, 376–384 (2001)

    Article  CAS  Google Scholar 

  12. Muramatsu, M. et al. Specific expression of activation-induced cytidine deaminase (AID), a novel member of the RNA-editing deaminase family in germinal center B cells. J. Biol. Chem. 274, 18470–18476 (1999)

    Article  CAS  Google Scholar 

  13. Petersen-Mahrt, S. K., Harris, R. S. & Neuberger, M. S. AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification. Nature 418, 99–103 (2002)

    Article  ADS  CAS  Google Scholar 

  14. Di Noia, J. & Neuberger, M. S. Altering the pathway of immunoglobulin hypermutation by inhibiting uracil-DNA glycosylase. Nature 419, 43–48 (2002)

    Article  ADS  CAS  Google Scholar 

  15. Bebenek, K. & Kunkel, T. A. Analyzing the fidelity of DNA polymerases. Methods Enzymol. 262, 217–232 (1995)

    Article  CAS  Google Scholar 

  16. Rogozin, I. B. & Kolchanov, N. A. Somatic hypermutagenesis in immunoglobulin genes. II. Influence of neighbouring base sequences on mutagenesis. Biochim. Biophys. Acta 1171, 11–18 (1992)

    Article  CAS  Google Scholar 

  17. Berek, C. & Milstein, C. The dynamic nature of the antibody repertoire. Immunol. Rev. 105, 5–26 (1988)

    Article  CAS  Google Scholar 

  18. Dorner, T., Foster, S. J., Brezinschek, H.-P. & Lipsky, P. E. Analysis of the targeting of the hypermutational machinery and the impact of subsequent selection on the distribution of nucleotide changes in human VHDJH rearrangements. Immunol. Rev. 162, 161–171 (1998)

    Article  CAS  Google Scholar 

  19. Rogozin, I. B., Pavlov, Y. I., Bebenek, K., Matsuda, T. & Kunkel, T. A. Somatic mutation hotspots correlate with DNA polymerase eta error spectrum. Nature Immunol. 2, 530–536 (2001)

    Article  CAS  Google Scholar 

  20. Shapiro, G. S., Aviszus, K., Murphy, J. & Wysocki, L. J. Evolution of Ig DNA sequence to target specific base positions within codons for somatic hypermutation. J. Immunol. 168, 2302–2306 (2002)

    Article  CAS  Google Scholar 

  21. Ramiro, A. R., Stavropoulos, P., Jankovic, M. & Nussenzweig, M. C. Transcription enhances AID-mediated cytidine deamination by exposing single-stranded DNA on the nontemplate strand. Nature Immunol. 4, 452–456 (2003)

    Article  CAS  Google Scholar 

  22. Gearhart, P. J. & Bogenhagen, D. F. Clusters of point mutations are found exclusively around rearranged antibody variable genes. Proc. Natl Acad. Sci. USA 80, 3439–3443 (1983)

    Article  ADS  CAS  Google Scholar 

  23. Betz, A. G., Rada, C., Pannell, R., Milstein, C. & Neuberger, M. S. Passenger transgenes reveal intrinsic specificity of the antibody hypermutation mechanism: Clustering, polarity, and specific hot spots. Proc. Natl Acad. Sci. USA 90, 2385–2388 (1993)

    Article  ADS  CAS  Google Scholar 

  24. Michael, N. et al. Effects of sequence and structure on the hypermutability of immunoglobulin genes. Immunity 16, 123–134 (2002)

    Article  CAS  Google Scholar 

  25. Goodman, M. F. Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Annu. Rev. Biochem. 71, 17–50 (2002)

    Article  CAS  Google Scholar 

  26. Kunkel, T. A., Pavlov, Y. I. & Bebenek, K. Functions of human DNA polymerases η, κ, and ι suggested by their properties, including fidelity with undamaged DNA templates. DNA Repair 2, 135–149 (2003)

    Article  CAS  Google Scholar 

  27. Martin, A. & Scharff, M. D. AID and mismatch repair in antibody diversification. Nature Rev. Immunol. 2, 605–614 (2002)

    Article  CAS  Google Scholar 

Download references


This work was supported by National Institutes of Health Grants. P.P. and R.B. were supported on an NIH-NIA training grant. The authors acknowledge the intellectual contributions and encouragement of M. D. Scharff regarding all aspects of this work.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Myron F. Goodman.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Pham, P., Bransteitter, R., Petruska, J. et al. Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation. Nature 424, 103–107 (2003).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing