Difference between revisions of "Part:BBa K4897002"

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<partinfo>BBa_K4897002 short</partinfo>
 
<partinfo>BBa_K4897002 short</partinfo>
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===What is it?===
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BS DNA-322 was designed by BS United China as a single-stranded DNA segment complementary to the 131 base pairs of the 16S rRNA gene of P. acne. The composition of the DNA has three categories: binding region (two ends), amplification region, and random region. The binding region is the key element in reacting with the P. acne 16s rRNA gene. The DNA ligase will perform the ligation of the single-strand DNA meanwhile the phi29 will generate double-stranded DNA through amplification primers
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BS DNA-322 was designed by BS United China as a single-stranded DNA segment complementary to the 131 base pairs of the 16S rRNA gene of P. acne. The composition of the DNA has three categories: binding region (two ends), amplification region, and random region. The binding region is the key element in reacting with the P. acne 16s rRNA gene [1]. The DNA ligase will perform the ligation of the single-strand DNA meanwhile the phi29 will generate double-stranded DNA through amplification primers
  
 
===Usage and Biology===
 
===Usage and Biology===
 
<html>
 
<html>
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<img src="https://static.igem.wiki/teams/4897/wiki/parts/l-rca-mechanism.png" border="2" width="900" height="auto" />
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<table width="100%" border="10" cellspacing="0" cellpadding="0">
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<br>
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  <tr>
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<p align="center">Fig. 1. The process of BS DNA binding to P. acne DNA.</p>  
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    <td align="center"><img src="https://static.igem.wiki/teams/4897/wiki/parts/l-rca-mechanism.png" width="900" height="auto" /> </td>
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<br>
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  </tr>
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  <tr>
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    <td align="center">Fig. 1. The process of BS DNA binding to P. acne DNA</td>
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  </tr>
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</table>
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</html>
 
BS DNA-322 is the red line like a padlock. The black sequence represents the P. acne’s DNA specific to the binding. The red boxes represent the binding regions of the two ends of BS DNA-322 (notice that the two ends are not connected). The purple boxes represent the random sequences generated. The Blue box represents the amplification region for RCA.
 
BS DNA-322 is the red line like a padlock. The black sequence represents the P. acne’s DNA specific to the binding. The red boxes represent the binding regions of the two ends of BS DNA-322 (notice that the two ends are not connected). The purple boxes represent the random sequences generated. The Blue box represents the amplification region for RCA.
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BS DNA-322 would bind the bacterial DNA of P. acne and show great sensitivity and specificity. It can stably bind to the specific bacterial DNA of P. acne and quantitatively indicate the amount of P. acne in the amplification result.
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===Characterization===
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==First==
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<html>
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<table width="100%" border="10" cellspacing="0" cellpadding="0">
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  <tr>
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    <td align="center"><img src="https://static.igem.wiki/teams/4897/wiki/parts/bs-dna-322.png" width="200" height="auto" /> </td>
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  </tr>
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  <tr>
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    <td align="center">Fig. 2. Amplification results of P. acne bacterial DNA by BS DNA-322 under the competition of randomly generated DNA fragment of size 322.</td>
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  </tr>
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</table>
 
</html>
 
</html>
  
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BS DNA-322 would bind the bacterial DNA of P. acne and show great sensitivity and specificity. It can stably bind to the specific bacterial DNA of P. acne and quantitatively indicate the amount of P. acne in the amplification result.  
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Lane M: DNA Ladder. Lane 1: Positive control group for successful amplification, only the BS DNA-322 is used to detect P. acne DNA. Lane 2: One randomly generated DNA and BS DNA-322 (with the same concentration).
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BS DNA-322 is successfully ligated and amplified in Lane 1 as all the initial DNA fragments of size 322 are extended beyond size 322. In contrast, Lane 2 shows that not all DNA fragments of 322 are extended beyond 322 because some randomly generated DNA cannot bind to P. acne DNA. It proves that BS DNA-322 can still bind to P. acne DNA under competition with randomly generated DNA of the same size.
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==Second==
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<html>
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<table width="100%" border="10" cellspacing="0" cellpadding="0">
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  <tr>
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    <td align="center"><img src="https://static.igem.wiki/teams/4897/wiki/parts/real-time-bs-dna-322.png" width="800" height="auto" /> </td>
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  </tr>
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  <tr>
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    <td align="center">Fig. 3. real-time L-RCA for detecting P. acne.</td>
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  </tr>
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</table>
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</html>
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BS DNA-322 can also work when using SYBR signals to perform real-time amplification. This can significantly reduce the time needed for detecting amplification.  
  
 
<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
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<partinfo>BBa_K4897002 parameters</partinfo>
 
<partinfo>BBa_K4897002 parameters</partinfo>
 
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===Reference===
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[1]Nakamura, M., Kametani, I., Higaki, S., & Yamagishi, T. (2003). Identification of Propionibacterium acnes by polymerase chain reaction for amplification of 16S ribosomal RNA and lipase genes. Anaerobe, 9(1), 5–10. https://doi.org/10.1016/s1075-9964(03)00061-1.

Latest revision as of 13:45, 11 October 2023


BS DNA-322 (BS DNA 3.0) using in L-RCA for detecting P. acne

What is it?

BS DNA-322 was designed by BS United China as a single-stranded DNA segment complementary to the 131 base pairs of the 16S rRNA gene of P. acne. The composition of the DNA has three categories: binding region (two ends), amplification region, and random region. The binding region is the key element in reacting with the P. acne 16s rRNA gene [1]. The DNA ligase will perform the ligation of the single-strand DNA meanwhile the phi29 will generate double-stranded DNA through amplification primers

Usage and Biology

Fig. 1. The process of BS DNA binding to P. acne DNA
BS DNA-322 is the red line like a padlock. The black sequence represents the P. acne’s DNA specific to the binding. The red boxes represent the binding regions of the two ends of BS DNA-322 (notice that the two ends are not connected). The purple boxes represent the random sequences generated. The Blue box represents the amplification region for RCA.

BS DNA-322 would bind the bacterial DNA of P. acne and show great sensitivity and specificity. It can stably bind to the specific bacterial DNA of P. acne and quantitatively indicate the amount of P. acne in the amplification result.

Characterization

First

Fig. 2. Amplification results of P. acne bacterial DNA by BS DNA-322 under the competition of randomly generated DNA fragment of size 322.

Lane M: DNA Ladder. Lane 1: Positive control group for successful amplification, only the BS DNA-322 is used to detect P. acne DNA. Lane 2: One randomly generated DNA and BS DNA-322 (with the same concentration).

BS DNA-322 is successfully ligated and amplified in Lane 1 as all the initial DNA fragments of size 322 are extended beyond size 322. In contrast, Lane 2 shows that not all DNA fragments of 322 are extended beyond 322 because some randomly generated DNA cannot bind to P. acne DNA. It proves that BS DNA-322 can still bind to P. acne DNA under competition with randomly generated DNA of the same size.

Second

Fig. 3. real-time L-RCA for detecting P. acne.
BS DNA-322 can also work when using SYBR signals to perform real-time amplification. This can significantly reduce the time needed for detecting amplification.

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal SpeI site found at 161
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal SpeI site found at 161
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal SpeI site found at 161
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal SpeI site found at 161
  • 1000
    COMPATIBLE WITH RFC[1000]


Reference

[1]Nakamura, M., Kametani, I., Higaki, S., & Yamagishi, T. (2003). Identification of Propionibacterium acnes by polymerase chain reaction for amplification of 16S ribosomal RNA and lipase genes. Anaerobe, 9(1), 5–10. https://doi.org/10.1016/s1075-9964(03)00061-1.