Statistical analysis of Bacteria GeneChips for possible effects caused by Hoogesteen hydrogen bonding between Guanines

Abstract

According to Watson-Crick base pairing, Guanine binds to Cytosine and Adenine binds to Thymine to form a double helix DNA molecule; however, it is observed that guanine can also bind with another guanine through hoogesteen hydrogen bonding at about 90 degrees. Thus a tetrad is formed if four guanines are attached with each other. These tetrads are the cause of the formation of unusual structures called G-quadruplex structures. These structures not only formed by a single guanine rich nucleic acid sequence but their formation is also possible by two or four parallel sequences collectively. These structures (or guanine rich sequences through which they are formed) affect a well known technology named Affymetrix GeneChip which is popular for gene expression measurement effectively and cheaply. Since the nucleic acid sequences are placed very closely on GeneChip, they are able to interact with each other and then form G-quadruplex structures. In this case, they are not ready to hybridize with their target sequences. It is found that raw or hybridization level data of human, mouse and rat (mammalian in general) are affected by guanine rich sequences. This paper exhibits that GeneChips of two Bacterias are also affected by guanine-guanine interaction and hence measurement of gene expressions using these chips could be misleading.