DNA

Part:BBa_K4933004:Design

Designed by: Kalyandeep Ghosh, Bhavya Joshi, Basil P.S., Ajad   Group: iGEM23_IISER-Mohali   (2023-10-11)

Templates

Double Stranded Template to maintain stock (Will be used to generate DNAzyme and Compliment sequence of DNAzyme):
CTGAAGAGTTGATGGTAGGTATGCTCTTCAGCGATGACTGATCCGTTATA
ATTCCCGTGGCCAGTCCACCCATGTTAGTGAATTCTCTAAACCAGCGTCA
CTAACGTTCGGTAACGGAGAAACTCTGCGGCATACTTTATTATATATATG
AAACGTGCCCAAGTGATGCTAAACAAGTCTTAGCTGGTTCCTGTGTTAGT
TTAAGGGTAAACATACAAGTTGATTGAACATGGGTTGGGGGCTTCAAATC
ATCGAAGACTCTATAGTATCTCGAAGACCAAGTAGGGCAGCCTATAGTTT
P.S. Single stranded template compliment to DNAzyme was also ordered and used

Primers for PCR

Asymmetric to obtain DNAzyme sequence:
AATTCTCTAAACCAGCGTCACTAAC
Tm = 55.0°C


Asymmetric to obtain compliment DNAzyme sequence:
GTTAGTGACGCTGGTTTAGAGAAT
Tm = 54.7°C
asymmetric-pcr.png

To obtain DNAzyme sequence from ssDNA template:
CTGAAGAGTTGATGGTAGGTATGCTCT
Tm = 57.7°C
pcr.png

ReqLoop Sequence Identities

CoVID specific sequence (X parameter): TTGATGGTAGGTATAATT
Delta specific sequence (Y parameter): TTATAATTCCCGT
Omicron specific sequence (Z parameter): ATTCTCTAAACCAGCG

References

[1] Genome Sequences of the Delta Variant (B.1.617.2) and the Kappa Variant (B.1.617.1) Detected in Morocco: https://doi.org/10.1128%2FMRA.00727-21 accession numbers MZ208926 and MZ571142
[2] SARS-CoV-2 B.1.1.529 (Omicron) Variant — United States, December 1–8, 2021: https://doi.org/10.15585%2Fmmwr.mm7050e1
[3] SARS-CoV-2 genome sequences: GISAID database identifiers: EPI_ISL_2110643 and EPI_ISL_2966236 NCBI GeneBank Accession numbers: MZ208926 and MZ571142
[4] Analysis Tool Web Services from the EMBL-EBI. (2013) McWilliam H, Li W, Uludag M, Squizzato S, Park YM, Buso N, Cowley AP, Lopez R Nucleic acids research 2013 Jul;41(Web Server issue):W597-600 doi:10.1093/nar/gkt376