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Molecular and Cellular Biology, January 2007, p. 20-30, Vol. 27, No. 1
0270-7306/07/$08.00+0     doi:10.1128/MCB.00824-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

AID Associates with Single-Stranded DNA with High Affinity and a Long Complex Half-Life in a Sequence-Independent Manner{triangledown}

Mani Larijani,1 Alexander P. Petrov,2 Oxana Kolenchenko,1 Maribel Berru,1 Sergey N. Krylov,2 and Alberto Martin1*

Department of Immunology, University of Toronto, Medical Sciences Building, Toronto, Canada M5S 1A8,1 Department of Chemistry, York University, Toronto, Ontario, Canada M3J 1P32

Received 9 May 2006/ Returned for modification 29 June 2006/ Accepted 6 October 2006

Activation-induced cytidine deaminase (AID) initiates secondary antibody diversification processes by deaminating cytidines on single-stranded DNA. AID preferentially mutates cytidines preceded by W(A/T)R(A/G) dinucleotides, a sequence specificity that is evolutionarily conserved from bony fish to humans. To uncover the biochemical mechanism of AID, we compared the catalytic and binding kinetics of AID on WRC (a hot-spot motif, where W equals A or T and R equals A or G) and non-WRC motifs. We show that although purified AID preferentially deaminates WRC over non-WRC motifs to the same degree observed in vivo, it exhibits similar binding affinities to either motif, indicating that its sequence specificity is not due to preferential binding of WRC motifs. AID preferentially deaminates bubble substrates of five to seven nucleotides rather than larger bubbles and preferentially binds to bubble-type rather than to single-stranded DNA substrates, suggesting that the natural targets of AID are either transcription bubbles or stem-loop structures. Importantly, AID displays remarkably high affinity for single-stranded DNA as indicated by the low dissociation constants and long half-life of complex dissociation that are typical of transcription factors and single-stranded DNA binding protein. These findings suggest that AID may persist on immunoglobulin and other target sequences after deamination, possibly acting as a scaffolding protein to recruit other factors.

* Corresponding author. Mailing address: Department of Immunology, University of Toronto, Medical Sciences Bldg. 5265, Toronto, Canada M5S 1A8. Phone: (416) 978-4235. Fax: (416) 978-1938. E-mail: alberto.martin{at}utoronto.ca.

{triangledown} Published ahead of print on 23 October 2006.

Molecular and Cellular Biology, January 2007, p. 20-30, Vol. 27, No. 1
0270-7306/07/$08.00+0     doi:10.1128/MCB.00824-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.



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