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Nucleic Acids Research, 2002, Vol. 30, No. 16 e79
© 2002 Oxford University Press

Manufacturing DNA microarrays from unpurified PCR products

Frank Diehl, Boris Beckmann*, Nadine Kellner, Nicole C. Hauser1, Susanne Diehl and Jörg D. Hoheisel

Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 506, 69120 Heidelberg, Germany and 1 Fraunhofer-Institut für Grenzflächen- und Bioverfahrenstechnik, Nobelstraße 12, 70569 Stuttgart, Germany

*To whom correspondence should be addressed. Tel: +49 6221 424686; Fax: +49 6221 424687; Email: b.beckmann{at}dkfz.de
Present address:
Frank Diehl, The Johns Hopkins Oncology Center, 1650 Orleans Street, Baltimore, MD 21231, USA

For the production of DNA microarrays from PCR products, purification of the the DNA fragments prior to spotting is a major expense in cost and time. Also, a considerable amount of material is lost during this process and contamination might occur. Here, a protocol is presented that permits the manufacture of microarrays from unpurified PCR products on aminated surfaces such as glass slides coated with the widely used poly(L-lysine) or aminosilane. The presence of primer molecules in the PCR sample does not increase the non-specific signal upon hybridisation. Overall, signal intensity on arrays made of unpurified PCR products is 94% of the intensity obtained with the respective purified molecules. This slight loss in signal, however, is offset by a reduced variation in the amount of DNA present at the individual spot positions across an array, apart from the considerable savings in time and cost. In addition, a larger number of arrays can be made from one batch of amplification products.


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