Ligation Errors in DNA Computing

1
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

2
Introduction

• In Adlemans method
• Generating solutions is important.
• The ligation of nodes should be reliable.
• Investigate the reliability of the splint-aided
  ligation process.

3
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

4
Test of Errors
8 page, EtBr An error may occur in case of
single mismatch
of mismatches
5
Test of Errors

• Dependence on the combination of bases

Fluorescein isothiocyanate (FITC)
6
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
7
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

8
Test of Competing

• 100 pmol of each oligo
• 1.4 units of T4 DNA ligase
• Incubated for 30 m at 16ºC

FITC
EtBr staining
9
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.