For Reference Essay

Words: 954
Pages: 4

KimNgoc Huynh
Bimm101
Section: CO2
TA: Pagkapol Yhew Pongsawakul Bioinformatics Homework#1
Question#1:
The sequence is 8654 nucleotides long.
Question#2:
-10 sequence for the lux operon: 5’-TGTTATA-3’ There are 2 nucleotides different that are G and A.
Question#3:
The lux R, which has its own promoter and is transcribed in the opposite direction from the lux operon, could not be transcribed from the same strand because the RNA polymerase recognizes a promoter sequence only in the direction of 5’ to 3’, and the lux R gets transcribed in the opposite direction from the lux operon. Thus, the transcriptions of luxR and lux operon have to occur on two different strands including coding strand and template strand.
Question#4:
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c) The strand shown in NCBI is a coding strand, so the forward primer, which always anneals to a template strand, will not hybridize to it, yet the strand shown in NCBI will be annealed by the reverse primer, whereas the forward primer will hybridize with its complementary strand. d) PCR product: (6398- 4053)+1= 2346 nt e) No, the luxAB PCR product will not contain a promoter sequence because the promoter sequence is upstream of the luxAB genes indicating that it locates outside the amplification region ranging from 4053 to 6398. Thus, the promoter sequence does not get amplified along with the luxAB PCR product.
Question#7:
According to the paper “ First detection and genotyping of human-associated microsporidia in wild waterfowl of Slovakia,” microsporidial DNA from fecel samples of wild waterfowl in the eastern Slovakia was islolated applying the isolation kit DNA Sorb B and protocol in manufacturer’s instructions. In the process of SYBR Green PCR, the target DNA that was amplified was the ITS region located within the small subunit (SSU) and large subunit (LSU) rRNA genes of E.cuniculi, E. intestinalis, E.hellem at 60oC, and E.bieneusi at 54oC ( optimal annealing temperatures). Based on the published GenBank sequences of E.cuniculi, E. intestinalis, E.hellem, and E.bieneusi, the experimentors accordingly designed the forward and reverse primers that were complementary to the template and coding strands of the microsporidial DNA. The PCR reactions containing SYBR