Ligation Errors in DNA Computing Y. Aoi, T. Yoshinobu, K. Tanizawa, K. Kinoshita and H. Iwasaki Biosystems 52(1999), pp.181-187 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 16ºC
Test of Errors 8% page, EtBr An error may occur in case of single mismatch # of mismatches
Test of Errors • Dependence on the combination of bases Fluorescein isothiocyanate (FITC)
Test of Errors • The yield of ligation 50 pmol of each oligo0.8 units of T4 DNA ligaseincubation at 16ºC for 10 m or 35 m
Test of Competing • Two sets of experiments • 1 base mismatch w/o competing • G-T or A-C • 1 base mismatch w competing • S strand and 4 R strands • Perfect match
Test of Competing • 100 pmol of each oligo • 1.4 units of T4 DNA ligase • Incubated for 30 m at 16ºC FITC EtBr 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.