Design considerations for array CGH to oligonucleotide arrays.

BACKGROUND: Representational oligonucleotide microarray analysis has been developed for detection of single nucleotide polymorphisms and/or for genome copy number changes. In this process, the intensity of hybridization to oligonucleotides arrays is increased by hybridizing a polymerase chain reaction (PCR)-amplified representation of reduced genomic complexity. However, hybridization to some oligonucleotides is not sufficiently high to allow precise analysis of that portion of the genome. METHODS: In an effort to identify aspects of oligonucleotide hybridization affecting signal intensity, we explored the importance of the PCR product strand to which each oligonucleotide is homologous and the sequence of the array oligonucleotides. We accomplished this by hybridizing multiple PCR-amplified products to oligonucleotide arrays carrying two sense and two antisense 50-mer oligonucleotides for each PCR amplicon. RESULTS: In some cases, hybridization intensity depended more strongly on the PCR amplicon strand (i.e., sense vs. antisense) than on the detection oligonucleotide sequence. In other cases, the oligonucleotide sequence seemed to dominate. CONCLUSION: Oligonucleotide arrays for analysis of DNA copy number or for single nucleotide polymorphism content should be designed to carry probes to sense and antisense strands of each PCR amplicon to ensure sufficient hybridization and signal intensity.     

WNK1基因不同转录本在小鼠肾脏中的表达及意义

目的研究WNK1基因长短两个转录本在小鼠肾脏组织中的表达分布特征,为进一步研究它们的生物学功能提供实验数据.方法 RT-PCR扩增两个转录本的特异性片段,Northern印迹杂交证实片段特异性后,将片段克隆入pGEM-T载体中,体外转录同位素标记的正义和反义RNA探针,在小鼠肾脏组织石蜡切片上进行原位杂交检测.结果 WNK1基因长转录本微弱广泛地表达在小鼠肾脏组织上,短转录本特异地表达在小鼠肾脏皮质部的远曲小管上.结论在肾脏,WNK1基因的短转录本是功能性转录本,其编码的蛋白质在生物学功能上可能与其它激酶不同.