Computational chemical analysis of DNA sequencing by reducing graphene oxide with the released H ion during polymer synthesis

Devinder Singh, Negi, Smruti Das
2014 Journal of Chemical and Pharmaceutical Research   unpublished
The DNA polymer synthesis is the addition of deoxynucleotide triphosphate units by phosphodiester bonds. The nucleotide bases are adenine A, guanine G, cytosine C and thymine T. The sequence of nucleotides bases in the genome is random. The phosphodiester bond is formed between 5 position carbon of one deoxynucleotide triphosphate with the 3 position carbon of another deoxynucleotide triphosphate. The addition reaction releases two unstable phosphate groups. The groups stabilised by joining
more » ... ther to release water molecule. The water molecule is protonated by acid to release H ion. The H ion is captured by pH sensitive carbon compound graphene oxide. The released H ion reduced the graphene oxide resulting in the pH change. The DNA polymer is a double stranded molecule and synthesis was performed on a template strand by complimentary addition of nucleotides, with A complimenting T, and C with G by di and tri hydrogen bonds respectively. The nucleotides in a prefixed sequence of A, G, C and T were flown for addition on the complimentary template strand. The addition of nucleotide was sensed by change in pH of sensor with the released H ion. The non addition did not confer any pH change signal in the sensor. The addition sequence of nucleotide in the polymers synthesis is recorded to infer the exact sequence of targeted region of genome. We have investigated an efficient cost effective fast method of DNA sequencing using a chemical computational model. This method provide the sequence of genome without using any dye labelled nucleotide and also no laser optics is required for recording the nucleotide addition signal. The repeat nucleotide sequence signals were in proportion to pH shift. The method can efficiently read the sequence size of upto 200 nucleotides. The computational analysis was performed by in silico synthesis of polymer on a complimentary template strand with capture of H ion on reducing graphene oxide and signal was recorded by measuring the shift in pH.