Difference between revisions of "Part:BBa K3790006"

Revision as of 16:52, 21 October 2021

E.ssb

Introduction

E.ssb is a single-stranded binding protein from Escherichia coli str. K-12 substr. MG1655[1]. We wanted to test whether the single-stranded binding protein could enhance the enzymatic activity of Bst Pol using the change in the activity of the fusion protein composed of it and Bst Pol.

Usage and Biology

In past studies, double-stranded binding proteins, represented by sso7d, were often thought to enhance the activity of DNA polymerase A or DNA polymerase B. However, as a single-stranded binding protein that can also bind DNA, there is no study to prove whether it can increase the activity of DNA polymerase. Therefore, we chose E.ssb, a single-stranded binding protein from scherichia coli str. K-12 substr. MG1655 to verify whether the single-stranded binding protein could enhance the enzymatic activity of Bst Pol.

Experimental Results

Since the length of the E.ssb fragment is less than 600bp, we chose to synthesize the sequence ourselves by Oligo assembly using Phanta polymerase. We obtained the sequence information from NCBI[2] and designed synthetic primers for synthesis.

Figure 1. Oligo assembly by PCR. It is generally used to construct completely new or special-purpose DNA. This method may have the disadvantage of a high mutation rate when operated. Once, we had to sequence nine clones of the same construct to get a single correct one. The reason for this is most likely due to complex annealing and amplification. We suggest to have 10-15 rounds amplification without F1 or R1 primer, then add those two primers to have another 25 rounds. Must use high-fidelity enzymes for this method. Due to the pricing, we always use 60bp primers, 58 overlapping annealing temperature, to assemble 300-500bp DNA fragment.

The length of E.ssb DNA was 531 bp, which is approximately 550 bp after adding homology arms to both ends for PCR cloning. We isolated the DNA of interest by gel extraction for subsequent reactions.

Figure 2. Assembled DNA binding proteins, albA1, S.ssb, E.ssb. The first lane was loaded with DNA ladder, sizes were marked on the image. The brightest band of 750 bp was about 100 ng, and other bands about 50 ng. Lanes with correct sized amplified DNA were labeled. After PCR cloning, several bacterial clones were picked, grew into cultures and sent for Sanger sequencing. Then, we verified the sequencing results, and used the correct ones for further experiments.

Reference

Sequence and Features