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Nucleic Acids Research, 2000, Vol. 28, No. 8 E31-00
© 2000 Oxford University Press

Mass spectrometry of single-stranded restriction fragments captured by an undigested complementary sequence

Norman H. L. Chiu1,2,*, Kai Tang1, Ping Yip1, Andreas Braun1, Hubert Koster1 and Charles R. Cantor1,2

1Sequenom Inc., 11555 Sorrento Valley Road, San Diego, CA 92121, USA and 2Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA

In this report, we describe a simple and accurate method to analyze restriction fragments using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The two complementary strands of restriction fragments are separated through hybridization to a capture probe, which is a single-stranded undigested fragment. Using the biotin–streptavidin linkage, the hybrid is immobilized on streptavidin-coated magnetic beads. After conditioning the captured restriction fragments, they are eluted from the probe and their molecular weights are determined. The proposed method greatly improves the quality, and reduces the complexity of the mass spectrum by analyzing only one of the complementary strands of restriction fragments.

* To whom correspondence should be addressed at: Sequenom Inc., 11555 Sorrento Valley Road, San Diego, CA 92121, USA. Tel: +1 858 350 0345; Fax: +1 858 350 9237; Email: nchiu@sequenom.com


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