Ligation Errors in DNA Computing Y. Aoi, T. Yoshinobu, K. Tanizawa, K. Kinoshita and H. Iwasaki Biosystems 52(1999), pp Summarized by In-Hee Lee

Introduction In Adleman’s method – Generating solutions is important. – The ligation of nodes should be reliable. Investigate the reliability of the splint- aided ligation process.

Test of Errors Dependence on the number of mismatches – 300pmol of each oligo. – 2.8 units of T4 DNA ligase – Incubation for 20 h at 16 º C

Test of Errors # of mismatches 8% page, EtBr An error may occur in case of single mismatch

Test of Errors Dependence on the combination of bases Fluorescein isothiocyanate (FITC)

Test of Errors The yield of ligation 50 pmol of each oligo 0.8 units of T4 DNA ligase incubation at 16 º C for 10 m or 35 m

Test of Competing Two sets of experiments 1.1 base mismatch w/o competing  G-T or A-C 2.1 base mismatch w competing  S strand and 4 R strands 3.Perfect match

Test of Competing 100 pmol of each oligo 1.4 units of T4 DNA ligase Incubated for 30 m at 16 º C FITCEtBr staining

Test of Competing Product of 1 is at slightly lower position Product of 1 is not so much stained by EtBr. – Single stranded Main product of 2 is at the same position as the product of 3 – Main product of 2 is from perfect match – In competing condition, perfect match wins the race.