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Construction of coding region enriched genomic library by S1 nuclease treatment of partially denatured rice genomic DNA

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Abstract

Designing high density DNA arrays representing all the genes of an organism could be limited when the entire genome sequence of the organism is not available or if only a limited number of ESTs are available. In an effort to prepare coding sequences as DNA sources for a microarray, we found that coding region enriched genomic DNA libraries can be produced by S1 nuclease treatment of partially denatured genomic DNA. Sequence analysis of about 1,000 clones using BLASTN and BLASTX searches showed that 46% of the clones in the library have regions which share significant similarity with sequences deposited in the rice EST and nr data bases. These data suggested that clones produced in this library could be directly used as PCR templates, where the resulting PCR products could be spotted on slides for microarray analysis. This technique might be applicable in designing a high density DNA array for an organism whose entire genome sequence is not available.

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Abbreviations

BLAST:

basic local alignment search tool

EST:

expressed sequence tags

LTR:

long terminal repeat

SNP:

single nucleotide polymorphism

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Authors and Affiliations

  1. Green Gene Bio Tech Inc., Myongji University, 449-728, Youngin, Republic of Korea

    Yeon-Ki Kim & Baek-Hie Nahm

  2. Department of Molecular Genetics and Bioinformatics, Myongji University, 449-728, Youngin, Republic of Korea

    Jeong-Sook Kim, Pil-Joong Cheong, Min-Jeong Kim, Tae-Ho Lee, Joungsu Joo, Ju-Kon Kim, Baek-Hie Nahm & Sang Ik Song

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  1. Yeon-Ki Kim
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  2. Jeong-Sook Kim
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  4. Min-Jeong Kim
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  9. Sang Ik Song
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Correspondence to Sang Ik Song.

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Kim, YK., Kim, JS., Cheong, PJ. et al. Construction of coding region enriched genomic library by S1 nuclease treatment of partially denatured rice genomic DNA. J. Korean Soc. Appl. Biol. Chem. 52, 213–220 (2009). https://doi.org/10.3839/jksabc.2009.039

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  • DOI: https://doi.org/10.3839/jksabc.2009.039

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