IGEM:Hong Kong HKUST/2009/Notebook/Effects of vector to insert DNA ratio on ligation efficiency/Entry Base
Effects of vector to insert DNA ratio on ligation efficiency
Authors
- Chen Rui, Raymon
- Cheng Ka Yan
- Tsang Chor Shan, Candy
- Cheng Kar On
Abstract
This experiment is about the ligation of BBa_K823005 and BBa_K516030 and finding the optimal ratio of the vector and insert. The biobrick at the end is made by a vector and an insert. In this case, part of BBa_K516030 is cut and inserted to BBa_K823005. The aim of this experiment is to investigate the effects of vector to insert DNA ratio on ligation efficiency, so sets with different ratio are compared. Finally, the finding shows that the optimum molar vector to insert DNA ratio of four groups is 1:3.
Introduction
Ligation which is part of the cloning methods can join two linear DNA fragments together by forming covalent bonds with the help of ligase. By using this method, the DNA in cells can be altered.
This experiment is to ligate BBa_K823005 and BBa_K516030. Before ligation, a series of cloning processes are needed. Four different ratios of the vector and insert (1:0.5, 1:1, 1:3, and 1:10) are used for ligation. Transformation is applied again. At the end, the number of red colonies which represents successful ligation is counted and its percentage is then calculated. Cells in red colonies possess desired DNA while cells in the white may lack insert or being plasmid-free.
In this experiment, BBa_K823005 and BBa_K516030, which follow the RFC10 standard, are used because BBa_K823005 has a promoter while BBa_K516030 has ribosome binding site, reporter gene and double terminator. When they are put together, the whole DNA is functional and protein can be produced. In this experiment, BBa_K823005 and BBa_K516030 are the vector and insert respectively.
Therefore, specific enzymes could be used to cut the site XbaI and PstI of BBa_K516030 and the site of SpeI and PstI of BBa_K823005. Ligase is then used to insert the fragment of BBa_K516030 into BBa_K823005. A strong covalent bond called “scar” is formed between the X and S site.
Finding the optimal ratio is helpful for future experiments, for instance, it would be more efficient if someone needs to put two biobricks together. If someone needs to use this biobrick for his/her other research topics, using the optimal ratio for ligation can reduce the experimental errors.
Methods and Materials
Two plasmids, pSB1C3-BBa_K823005 and pSB1C3-BBa_K516030, were transformed into Escherichia coli (E. coli) DH10B strain respectively. To get enough plasmids, they were inoculated in Lysogeny Broth with chloramphenicol at 37 °C overnight. Plasmids were extracted out in the next day according to the Mini Plus™ Plasmid DNA Extraction System protocol. The concentration of the extracted DNA was measured by NanoDrop spectrophotometer. Next, the digestion of plasmids was proceeded to obtain target vector and insert. Four experimental groups together with four control groups without ligase were set. For digestion recipe, pSB1C3-BBa_K823005 groups were digested by PstI-HF® and SpeI-HF® while pSB1C3-BBa_K516030 groups were digested by PstI-HF® and XbaI. The volumes of all groups were brought to 20 μl with ddH2O. The length of expected vector is 2087 base pairs and expected insert is 897 base pairs. Gel extraction was then followed by gel purification which was done according to the Favorgen FavorPrep™ GEL/PCR Purification Mini Kit protocol. The linear DNA fragments were collected. The concentration of the digested DNA was assessed in order to calculate the volume of reagents.
| 1:0.5 | 1:0.5 (c) | 1:1 | 1:1 (c) | 1:3 | 1:3 (c) | 1:10 | 1:10 (c) | |
| vector 150ng (μl) | 6.58 | 4.24 | 6.58 | 4.24 | 6.58 | 6.58 | 6.58 | 6.58 |
| insert (μl) | 0.64 | 0.64 | 3.24 | 4.24 | 9.73 | 9.73 | 12.7 | 12.7 |
| ligase buffer (μl) | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| T4 DNA ligase (μl) | 1 | 0 | 1 | 0 | 1 | 0 | 1 | 0 |
| ddH2O | 12.78 | 16.12 | 10.18 | 12.52 | 3.69 | 4.69 | 0.72 | 1.72 |
| Total | 22 | 22 | 22 | 22 | 22 | 22 | 22 | 22 |
Due to different DNA concentration after ligation, the total volume of each group various. The reaction mixtures were put at room temperature for 1.5 hours. These recombinant plasmids were transformed into E. coli DH10B strain and incubated in chloramphenicol agar plates overnight. The number of red colonies and the total number of colonies could be counted next day.
