Nucleic acid-protein identification: novel protein classification based on nucleic acid-protein interaction

Several basic properties of proteins are used for their classification. Some proteins can bind DNA and RNA in a specific way. We propose a simple method for classification of nucleic acids binding proteins which we call «nucleic acid-protein fingerprint» The method is based on usage of short oligonucleotides, immobilized in hydrogel for hybridization with proteins. First, we have found the shortest oligonucleotide capable for specific binding with nucleic acids. Experiments with samples from 2 to 12 bases length have shown that tetramers with 2 chains of 5-nitroindole (universal base) and 2 chains of normal bases can recognize proteins. Thus, we have made a smallest universal protein recognizing biochip containing 16 dinucleotides. Physical length of them is 4 chains, two chains are from 5-nitroindole and two chains are normal DNA bases We manufactured that biochip and investigated binding of dye labeled proteins with them. The hybridization patterns of two proteins RNase A and Binase have shown remarkable difference specificity and difference between proteins Biochip of this type with three of four remarkable proteins will have much more specificity. Thus, we proposed and experimentally confirmed a new type of proteins classification

protein classification, nucleic acid - protein recognition, oligonucleotides, microarray