A-stack probes do not show significant effects on Affymetrix GeneChip Data

G. N. MOJAI, F. N. MEMON, Z.U.A. KHUHRO, M. Y. KHUHAWAR

Abstract


Besides normal binding of a guanine with a cytosine, a guanine can interact to another guanine through Hoogsteen hydrogen bonding. Such an interaction produces a tetrad with four guanines in which each guanine binds with two other guanines. A stack of tetrads of guanines can then form unusual four-stranded structures known as G-Quadruplex structure. It is reported that these types of structures are not good for the well-known microarray technology used for gene expression measurements. In particular, it is declared that Affymetrix GeneChips® produces incorrect gene expression measurements due to G-quadruplex structures. A gene is represented on GeneChip® by a group of small nucleotide sequences called probes and probes with continuous guanines showed abnormal behavior that has been associated with the formation of G-quadruplex structures. These probes are not correlated with other members of their groups but they are correlated with each others. It showed that such probes are not good measures of gene expression. Since it is witnessed that an adenine can also bind to another adenine, it is therefore essential to find out its effects on Affymetrix GeneChip®. This paper presents the results of the examination of data of various GeneChip designs for the possible effects of adenine-adenine interaction. It is found that Affymetrix GeneChip® data does not show abnormal behavior due to the presence of probes with continuous adenines. Unlike guanine-guanine interaction, the GeneChip® is found unaffected of adenine-adenine binding.


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