Direct haplotyping of kilobase-size DNA using carbon nanotube probes

Authors

Adam T. Woolley, Harvard University, Cambridge, MA
Chantal Guillemette, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
Chin Li Cheung, University of Nebraska at LincolnFollow
David E. Housman, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
Charles M. Lieber, Harvard University, Cambridge, MA

Date of this Version

May 2002

Comments

Published in Nature Biotechnology 18 (2000), pp. 760–763; doi:10.1038/77760 Copyright © 2000 Nature America Inc. Used by permission.
http://biotech.nature.com

Abstract

We have implemented a method for multiplexed detection of polymorphic sites and direct determination of haplotypes in 10-kilobasesize DNA fragments using single-walled carbon nanotube (SWNT) atomic force microscopy (AFM) probes. Labeled oligonucleotides are hybridized specifically to complementary target sequences in template DNA, and the positions of the tagged sequences are detected by direct SWNT tip imaging. We demonstrated this concept by detecting streptavidin and IRD800 labels at two different sequences in M13mp18. Our approach also permits haplotype determination from simple visual inspection of AFM images of individual DNA molecules, which we have done on UGT1A7, a gene under study as a cancer risk factor. The haplotypes of individuals heterozygous at two critical loci, which together influence cancer risk, can be easily and directly distinguished from AFM images. The application of this technique to haplotyping in population-based genetic disease studies and other genomic screening problems is discussed.