Difference between revisions of "Part:BBa K4347003"
 
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The backward inner primer (BIP) is one of the six primers needed to carry out Loop Mediated Isothermal Amplification (LAMP). This BIP was designed to detect conserved 16s rRNA regions in STEC E.coli strains, campylobacter, shigella and salmonella.
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[[File:BBa K4347002 BIP AND B3.PNG|300px|center|thumb|BIP of LAMP reaction from Wong et, al (2017)[[Part:BBa_K4347003#References|<sup>[1]</sup>]].]]
  
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The backward inner primer (BIP) is one of the six primers needed to carry out Loop Mediated Isothermal Amplification (LAMP).
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===Usage and Biology===
  
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The loop-mediated isothermal amplification (LAMP) is a rapid method that allows for the specific DNA amplification through the utilization of multiple primers and three major steps[[Part:BBa_K4347003#References|<sup>[2]</sup>]]. This method relies on 3 major components- Bst, a DNA polymerase, and two sets of  primers, and the target DNA/RNA. The first step, referred to as the “starting material producing step”, composes the stem-looped DNA that is needed for the second stage. The forward and backward inward and outer primers bind to the complementary sequences within the target DNA sequence[[Part:BBa_K4347003#References|<sup>[2]</sup>]]. The stem-looped DNA undergoes additional annealing within the target sequences and with the Bst polymerase, which produces stem-loop DNA which concludes the first step[[Part:BBa_K4347003#References|<sup>[2]</sup>]]. The stem-loop DNA enters into step two- “cycling amplification step”, which uses the internal primers FIP and BIP in hybridization and synthesis reactions to produce an original and a repaired stem-loop DNA strands[[Part:BBa_K4347003#References|<sup>[2]</sup>]]. For further amplification, loop primers can be inserted into the reactions[[Part:BBa_K4347003#References|<sup>[3]</sup>]]. The third step is “elongation and recycling”, where the DNA products are recycled and elongated through a BIP-primed strand displacement reaction[[Part:BBa_K4347003#References|<sup>[2]</sup>]].
  
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===Usage and Biology===
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[[File:BBa K4347000 LAMP.PNG|400px|center|thumb|Basic schematic of LAMP reaction from Wong et, al (2017)[[Part:BBa_K4347003#References|<sup>[1]</sup>]].]]
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Very brief explanation on what LAMP is (can re-use this explanation for all 6 parts). Explain specifically how BIP anneals to the DNA sequence.
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The loop-mediated isothermal amplification (LAMP) is a rapid method that allows for the specific DNA amplification through the utilization of multiple primers and three major steps (Notomi et al., 2000). This method relies on 3 major components- Bst, a DNA polymerase, and two sets of  primers, and the target DNA/RNA. The first step, referred to as the “starting material producing step”, composes the stem-looped DNA that is needed for the second stage. The forward and backward inward and outer primers bind to the complementary sequences within the target DNA sequence (Notomi et al., 2000). The stem-looped DNA undergoes additional annealing within the target sequences and with the Bst polymerase, which produces stem-loop DNA which concludes the first step (Notomi et al., 2000). The stem-loop DNA enters into step two- “cycling amplification step”, which uses the internal primers FIP and BIP in hybridization and synthesis reactions to produce an original and a repaired stem-loop DNA strands (Notomi et al., 2000). For further amplification, loop primers can be inserted into the reactions (Niessen & Vogel, 2010). The third step is “elongation and recycling”, where the DNA products are recycled and elongated through a BIP-primed strand displacement reaction (Notomi et al., 2000).  
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===References===
 
===References===
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Niessen, L., & Vogel, R. F. (2010). Detection of Fusarium graminearum DNA using a loop-mediated isothermal amplification (LAMP) assay. International Journal of Food Microbiology, 140(2–3), 183–191. https://doi.org/10.1016/j.ijfoodmicro.2010.03.036
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1. Wong, Y.-P., Othman, S., Lau, Y.-L., Radu, S., &amp; Chee, H.-Y. (2017). Loop-mediated isothermal amplification (LAMP): A versatile technique for detection of micro-organisms. Journal of Applied Microbiology, 124(3), 626–643. https://doi.org/10.1111/jam.13647
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2. Notomi, T., Okayama, H., Masubuchi, H., Yonekawa, T., Watanabe, K., Amino, N., & Hase, T. (2000). Loop-mediated isothermal amplification of DNA. Nucleic Acids Research, 28(12), e63–e63. https://doi.org/10.1093/nar/28.12.e63
  
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Notomi, T., Okayama, H., Masubuchi, H., Yonekawa, T., Watanabe, K., Amino, N., & Hase, T. (2000). Loop-mediated isothermal amplification of DNA. Nucleic Acids Research, 28(12), e63–e63. https://doi.org/10.1093/nar/28.12.e63
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3. Niessen, L., & Vogel, R. F. (2010). Detection of Fusarium graminearum DNA using a loop-mediated isothermal amplification (LAMP) assay. International Journal of Food Microbiology, 140(2–3), 183–191. https://doi.org/10.1016/j.ijfoodmicro.2010.03.036

Latest revision as of 19:08, 22 July 2022

Backward Inner primer (BIP)

The backward inner primer (BIP) is one of the six primers needed to carry out Loop Mediated Isothermal Amplification (LAMP). This BIP was designed to detect conserved 16s rRNA regions in STEC E.coli strains, campylobacter, shigella and salmonella.

BIP of LAMP reaction from Wong et, al (2017)[1].

Usage and Biology

The loop-mediated isothermal amplification (LAMP) is a rapid method that allows for the specific DNA amplification through the utilization of multiple primers and three major steps[2]. This method relies on 3 major components- Bst, a DNA polymerase, and two sets of primers, and the target DNA/RNA. The first step, referred to as the “starting material producing step”, composes the stem-looped DNA that is needed for the second stage. The forward and backward inward and outer primers bind to the complementary sequences within the target DNA sequence[2]. The stem-looped DNA undergoes additional annealing within the target sequences and with the Bst polymerase, which produces stem-loop DNA which concludes the first step[2]. The stem-loop DNA enters into step two- “cycling amplification step”, which uses the internal primers FIP and BIP in hybridization and synthesis reactions to produce an original and a repaired stem-loop DNA strands[2]. For further amplification, loop primers can be inserted into the reactions[3]. The third step is “elongation and recycling”, where the DNA products are recycled and elongated through a BIP-primed strand displacement reaction[2].

Basic schematic of LAMP reaction from Wong et, al (2017)[1].


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]


References


1. Wong, Y.-P., Othman, S., Lau, Y.-L., Radu, S., & Chee, H.-Y. (2017). Loop-mediated isothermal amplification (LAMP): A versatile technique for detection of micro-organisms. Journal of Applied Microbiology, 124(3), 626–643. https://doi.org/10.1111/jam.13647

2. Notomi, T., Okayama, H., Masubuchi, H., Yonekawa, T., Watanabe, K., Amino, N., & Hase, T. (2000). Loop-mediated isothermal amplification of DNA. Nucleic Acids Research, 28(12), e63–e63. https://doi.org/10.1093/nar/28.12.e63

3. Niessen, L., & Vogel, R. F. (2010). Detection of Fusarium graminearum DNA using a loop-mediated isothermal amplification (LAMP) assay. International Journal of Food Microbiology, 140(2–3), 183–191. https://doi.org/10.1016/j.ijfoodmicro.2010.03.036