Five-color-based high-information-content fingerprinting of bacterial artificial chromosome clones using type IIS restriction endonucleases

Y Ding; M D Johnson; W Q Chen; D Wong; Y J Chen; S C Benson; J Y Lam; Y M Kim; H Shizuya

doi:10.1006/geno.2001.6547

Five-color-based high-information-content fingerprinting of bacterial artificial chromosome clones using type IIS restriction endonucleases

Genomics. 2001 Jun 1;74(2):142-54. doi: 10.1006/geno.2001.6547.

Authors

Y Ding¹, M D Johnson, W Q Chen, D Wong, Y J Chen, S C Benson, J Y Lam, Y M Kim, H Shizuya

Affiliation

¹ Beckman Institute, Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.

PMID: 11386750
DOI: 10.1006/geno.2001.6547

Abstract

We have developed a high-information-content fingerprinting (HICF) system for bacterial artificial chromosome (BAC) clones using a Type IIS restriction endonuclease, HgaI, paired with a Type II restriction endonuclease, RsaI. In the method described, unknown five-base overhangs generated with HgaI are partially or fully sequenced by modified fluorescent dideoxy terminators. Using an in-lane size standard labeled with a fifth dye, fragments are characterized by both the size and the sequence of its terminal one to five bases. The enhanced information content associated with this approach significantly increases the accuracy and efficiency of detecting shared fragments among BAC clones. We have compared data obtained from this method to predicted HICF patterns of 10 fully sequenced BACs. We have further applied HICF to 555 BAC clones to assemble contigs spanning 16p11.2 to 16p13.1 of human chromosome 16.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Chromosomes, Artificial, Bacterial*
Chromosomes, Human, Pair 16
Contig Mapping
DNA Restriction Enzymes / metabolism*
Humans
Models, Genetic
Sequence Analysis, DNA / methods*

Substances

DNA Restriction Enzymes