Difference between revisions of "Part:BBa K4361004"
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<partinfo>BBa_K4361004 short</partinfo> | <partinfo>BBa_K4361004 short</partinfo> | ||
| − | + | BlcR is a transcription factor originating from the bacterium <i>Agrobacterium tumefaciens</i> ([[Part:BBa_K4361100]]). In a homodimer state it contains a single DNA-binding domain that specifically binds one of two DNA sequences. Both sequences are so-called inverted repeat pairs (IRs), short DNA sequences whose ends are reverse complements of each other. For the Blc operator, these sequences are 'ACTCTAATgATTCAAGT' (IR1) and 'ATTAGttgaactCTAAT' (IR2), as further explained in [[Part:BBa_K4361001]]. <br> | |
| − | + | The original IR1 sequence is not a perfect reverse complement of itself. This part and [[Part:BBa_K4361005]] have been designed to test whether or not exchanging IR1 for one of two perfect reverse complement sequences would increase its binding strength to BlcR. To create this part, the nucleotides on the 3' half of IR1 have been replaced by the reverse complement of those of the 5' half, resulting in 'ACTCTAATgATTAGAGT' (IR1 RV 1). The BlcR-binding domain of this part thus consists of IR1 RV 1-tca-IR2, where tca is the original 3 nt linker sequence between IRs. | |
| − | + | ||
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| − | <span class='h3bb'>Sequence and Features</span> | + | <span class='h3bb'><h3>Sequence and Features</h3></span> |
<partinfo>BBa_K4361004 SequenceAndFeatures</partinfo> | <partinfo>BBa_K4361004 SequenceAndFeatures</partinfo> | ||
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| + | <h3>Usage and Biology</h3> | ||
| + | The <i>blc</i> operator contains 2 pairs of inverted repeats, linked together by a 3 nt spacer, and each pair is assumed to bind one BlcR dimer (see [[Part:BBa_K4361100]]). With a spacer of specifically 3 nt, the centers of each pair are exactly 20 nt apart, which supports the hypothesis that the two dimers orient themselves at the same rotation angle to the DNA to form a tetramer. If the spacer were of a different length, the dimers would have different orientations to each other, possibly inhibiting tetramerization (see [[Part:BBa_K4361014]]). With two BlcR dimers bound and forming a tetramer, RNA polymerases originating from an upstream promoter are hindered from transcribing past the <i>blc</i> operator, inhibiting expression of downstream <i>blcABC</i> genes. Each BlcR monomer contains a binding site that is specific to <i>gamma</i>-butyrolactone (GBL) <i>gamma</i>-hydroxybutyric acid (GHB) and succinic semialdehyde (SSA). When a BlcR tetramer binds GHB with one of its binding sites, tetramerization is inhibited and BlcR becomes dissociated from the DNA, enabling downstream transcription and subsequent digestion of the newly present substrate (see <b>Figure 1</b>). | ||
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| + | <html> | ||
| + | <figure> | ||
| + | <a href="https://static.igem.wiki/teams/4361/wiki/parts/blcr-ssa.png"><img src="https://static.igem.wiki/teams/4361/wiki/parts/blcr-ssa.png" style="width:400px;margin-left:225px"></a> | ||
| + | <figcaption> <b>Figure 1.</b> General overview of the unbinding mechanism of BlcR from DNA in the presence of SSA. Left: two BlcR dimers bound to DNA as a tetramer. Middle: SSA is introduced into the system. Right: BlcR dimers bind SSA and unbind from the DNA.</figcaption> | ||
| + | </figure> | ||
| + | </html> | ||
| + | |||
| + | In our project, these oligos are used to tether BlcR to the surface of a gold electrode, of which we measure the capacitance. When BlcR molecules dissociate from the DNA in response to the binding of GHB, water molecules are displaced towards the surface of the electrode, which causes an increase in capacitance. This is the signal we interpret to indicate the presence of GHB. | ||
| + | |||
| + | '''Oligo variants'''<br> | ||
| + | The wildtype <i>blc</i> operator has been theorized to not bind BlcR optimally, since BlcR regulates its own expression and that of proteins involved in the breakdown of GHB-like molecules. This means BlcR has to quickly unbind if these molecules taken up by <i>A. tumefaciens</i>, such that the bacterium can digest the molecules for nutrients. In our system, however, we would like BlcR to be more stably bound to DNA, such that it will only unbind in the presence of high GHB concentrations. This can be accomplished through two approaches: adjusting BlcR itself (see [[Part:BBa_K4361200]] through [[Part:BBa_K4361227]] and [[Part:BBa_K4361300]] through [[Part:BBa_K4361319]]), or changing the DNA molecule it binds to. This set of Parts, ranging from [[Part:BBa_K4361000]] up to [[Part:BBa_K4361022]], shows our work on the second approach. | ||
| + | |||
| + | <html> | ||
| + | <h3>Results</h3> | ||
| + | As described in the Results section of </html>[[Part:BBa_K4361000]] and [[Part:BBa_K4361001]]<html>, an electrophoresis experiment was performed with the majority of our designed oligos, wherein the aforementioned parts act respectively as the negative and positive control. By incubating them with BlcR and running them on a gel, the binding strength of BlcR to each sequence can be estimated by looking at the bands of free DNA and DNA bound by the protein. As can be seen in <b>Figure 2</b>, significantly less DNA is bound by BlcR than with the wildtype sequence. This suggests a much lower binding affinity between BlcR and DNA, so this oligo was not selected for further analysis. | ||
| + | |||
| + | <figure> | ||
| + | <a href="https://static.igem.wiki/teams/4361/wiki/parts/oligos-04.png"><img src="https://static.igem.wiki/teams/4361/wiki/parts/oligos-04.png" style="width:300px;margin-left:275px"></a> | ||
| + | <figcaption> <b>Figure 2.</b> Results of the electrophoresis experiment in which the fraction of DNA bound to BlcR was determined for different types of oligos. The first bar and bottom dashed line represent the results with </html>[[Part:BBa_K4361000]]<html> (scrambled oligo, negative control), the second bar and top dashed line correspond to those with </html>[[Part:BBa_K4361001]]<html> (wildtype oligo, positive control). The third bar depicts the measured fraction of bound DNA for this part. Values represent the ratio between the intensity of the band corresponding to protein-bound DNA, and the sum of the protein-bound and protein-free bands.</figcaption> | ||
| + | </figure> | ||
| + | |||
| + | For further details on the experiments with our DNA oligos and the results, see <a href="https://2022.igem.wiki/tudelft/results">the Results page on our wiki</a>. | ||
| + | |||
| + | </html> | ||
Latest revision as of 15:28, 12 October 2022
BlcR-binding oligo, 51 bp, IR1 perfect RV 1 + IR2
BlcR is a transcription factor originating from the bacterium Agrobacterium tumefaciens (Part:BBa_K4361100). In a homodimer state it contains a single DNA-binding domain that specifically binds one of two DNA sequences. Both sequences are so-called inverted repeat pairs (IRs), short DNA sequences whose ends are reverse complements of each other. For the Blc operator, these sequences are 'ACTCTAATgATTCAAGT' (IR1) and 'ATTAGttgaactCTAAT' (IR2), as further explained in Part:BBa_K4361001.
The original IR1 sequence is not a perfect reverse complement of itself. This part and Part:BBa_K4361005 have been designed to test whether or not exchanging IR1 for one of two perfect reverse complement sequences would increase its binding strength to BlcR. To create this part, the nucleotides on the 3' half of IR1 have been replaced by the reverse complement of those of the 5' half, resulting in 'ACTCTAATgATTAGAGT' (IR1 RV 1). The BlcR-binding domain of this part thus consists of IR1 RV 1-tca-IR2, where tca is the original 3 nt linker sequence between IRs.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
Usage and Biology
The blc operator contains 2 pairs of inverted repeats, linked together by a 3 nt spacer, and each pair is assumed to bind one BlcR dimer (see Part:BBa_K4361100). With a spacer of specifically 3 nt, the centers of each pair are exactly 20 nt apart, which supports the hypothesis that the two dimers orient themselves at the same rotation angle to the DNA to form a tetramer. If the spacer were of a different length, the dimers would have different orientations to each other, possibly inhibiting tetramerization (see Part:BBa_K4361014). With two BlcR dimers bound and forming a tetramer, RNA polymerases originating from an upstream promoter are hindered from transcribing past the blc operator, inhibiting expression of downstream blcABC genes. Each BlcR monomer contains a binding site that is specific to gamma-butyrolactone (GBL) gamma-hydroxybutyric acid (GHB) and succinic semialdehyde (SSA). When a BlcR tetramer binds GHB with one of its binding sites, tetramerization is inhibited and BlcR becomes dissociated from the DNA, enabling downstream transcription and subsequent digestion of the newly present substrate (see Figure 1).
In our project, these oligos are used to tether BlcR to the surface of a gold electrode, of which we measure the capacitance. When BlcR molecules dissociate from the DNA in response to the binding of GHB, water molecules are displaced towards the surface of the electrode, which causes an increase in capacitance. This is the signal we interpret to indicate the presence of GHB.
Oligo variants
The wildtype blc operator has been theorized to not bind BlcR optimally, since BlcR regulates its own expression and that of proteins involved in the breakdown of GHB-like molecules. This means BlcR has to quickly unbind if these molecules taken up by A. tumefaciens, such that the bacterium can digest the molecules for nutrients. In our system, however, we would like BlcR to be more stably bound to DNA, such that it will only unbind in the presence of high GHB concentrations. This can be accomplished through two approaches: adjusting BlcR itself (see Part:BBa_K4361200 through Part:BBa_K4361227 and Part:BBa_K4361300 through Part:BBa_K4361319), or changing the DNA molecule it binds to. This set of Parts, ranging from Part:BBa_K4361000 up to Part:BBa_K4361022, shows our work on the second approach.
Results
As described in the Results section of Part:BBa_K4361000 and Part:BBa_K4361001, an electrophoresis experiment was performed with the majority of our designed oligos, wherein the aforementioned parts act respectively as the negative and positive control. By incubating them with BlcR and running them on a gel, the binding strength of BlcR to each sequence can be estimated by looking at the bands of free DNA and DNA bound by the protein. As can be seen in Figure 2, significantly less DNA is bound by BlcR than with the wildtype sequence. This suggests a much lower binding affinity between BlcR and DNA, so this oligo was not selected for further analysis.