Difference between revisions of "Part:BBa K5047006"

Latest revision as of 11:53, 30 September 2024

Constitutive promoter in Lactococcus lactis

This DNA sequence encodes a short hairpin RNA shRNA designed to target a specific region within the chitin synthase gene of the Asian hornet Vespa velutina. The target region is located on an exon common to all isoforms of the chitin synthase gene GeneID 124951980 Genbank XM_047501172.1 within the genomic coordinates NC_062188.1 19915311-19930067 iVesVel2.1 genome GCF_912470025.1. The specific target sequence spans from positions 19925853 to 19925878. This shRNA has been designed to keep GC content intermediate approx. 30 - 50% with 48% in this variant to avoid strong secondary structure. Additionally, this shRNA is the variant with the lowest number of potential off-target interactions compared to TS2 BBa_XXXXX TS3 BBa_XXXXX and TS4 BBa_XXXXX. This sequence has off-targets in Vespa mandarinia and Vespa crabro with one mismatch only.

This shRNA contains the standard UUCAAGAGA 9 nt loop Brummelkamp Thijn R et al. A system for stable expression of short interfering RNAs in mammalian cells Science New York N.Y. vol. 2965567 2002 550-3 doi10.1126science1068999.

Through secondary structure analysis performed by ViennaRNA the free energy of the thermodynamic ensemble is -48.96 kcalmol. The frequency of the minimum free energy structure in the ensemble is 40.08%. The ensemble diversity is 1.71.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE WITH RFC[1000]

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 <partinfo>BBa_K5047004 short</partinfo>
-There is a rhythm to discovery. Not the hurried beat of instant gratification, but a quieter, more subtle pulse that exists in the background of our everyday lives. It hums beneath the surface, especially for those who find themselves drawn to scientific pursuit. There’s a feeling of walking in two worlds simultaneously—one of the known and the other of the mysterious, waiting to be uncovered.
+This DNA sequence encodes a short hairpin RNA shRNA designed to target a specific region within the chitin synthase gene of the Asian hornet Vespa velutina. The target region is located on an exon common to all isoforms of the chitin synthase gene GeneID 124951980 Genbank XM_047501172.1 within the genomic coordinates NC_062188.1 19915311-19930067 iVesVel2.1 genome GCF_912470025.1. The specific target sequence spans from positions 19925853 to 19925878. This shRNA has been designed to keep GC content intermediate approx. 30 - 50% with 48% in this variant to avoid strong secondary structure. Additionally, this shRNA is the variant with the lowest number of potential off-target interactions compared to TS2 BBa_XXXXX TS3 BBa_XXXXX and TS4 BBa_XXXXX. This sequence has off-targets in Vespa mandarinia and Vespa crabro with one mismatch only.
-In the modern world, we often find ourselves absorbed by the rapid pace of change. Technology evolves faster than we can fully comprehend, new data is being generated at an astounding rate, and fields like molecular biology and synthetic biology seem to push the boundaries of what is possible with every passing day. Yet, even amid this whirlwind of progress, the personal journey of discovery remains a deeply introspective process.
+This shRNA contains the standard UUCAAGAGA 9 nt loop Brummelkamp Thijn R et al. A system for stable expression of short interfering RNAs in mammalian cells Science New York N.Y. vol. 2965567 2002 550-3 doi10.1126science1068999.
-Take, for example, the seemingly simple act of working in a wet lab. At first glance, it’s a routine filled with repetitive tasks: pipetting precise amounts of liquid, monitoring bacterial cultures, waiting for a gel to run. But beneath these actions lies the core of scientific discovery—a patient, methodical dance between curiosity and the pursuit of answers. As each step in the lab proceeds, there’s always the awareness that at any moment, something unexpected might occur, revealing a new aspect of a biological system, or even challenging established knowledge.
+Through secondary structure analysis performed by ViennaRNA the free energy of the thermodynamic ensemble is -48.96 kcalmol. The frequency of the minimum free energy structure in the ensemble is 40.08%. The ensemble diversity is 1.71.
-Working in a lab is not just about mastering techniques. It’s about learning to listen to the rhythms of nature, even when the data appears to be nothing more than noise. It’s in the subtle variations, the outliers, the experiments that didn’t work, that the story of discovery often unfolds. That’s where intuition begins to play a role. Scientific intuition isn’t magic—it’s born from countless hours spent observing, questioning, and recalibrating. Each mistake, every “failure,” is not an end but rather a part of this iterative process of learning.
-As someone invested in the biological sciences, it’s easy to get caught up in the excitement of what’s happening at the molecular level. Proteins folding into intricate shapes, bacteria exchanging genetic material, RNA molecules silencing specific genes—these are feats that nature has perfected over millions of years, and yet we are only beginning to understand their complexities. But beyond this molecular fascination, there’s a more profound question: What do we do with this knowledge?