Posted by jing0021 on April 16, 2008 11:22 PM|Permalink
Comments
Questions for Meng and the rest of the class:
1. Equation (1) in the paper does not seem right and is inconsistent with Figure 6. Clarify.
2. Based on the typical plot of a sensogram, how does one determine y in equation 1.
3. The paper mentions that the Western method is more 'sensitive' than ELISA and the SPR method. [See paragraph before discussion]. Is this statement correct?
1. After rededucing and refering to article about this equation, I think the equation should be either y=(free ssDNA)/[Kd+(free ssDNA)], in which y is the degree of saturation; or y=Bmax(free ssDNA)/[Kd+(free ssDNA)], in which y means the number of bounded DNA-protein.
2. In Figure 6, one can determine the degree of saturation by getting the ratio of concerned RU compared with the saturation RU.
3. As to sensitivity, I think they mean the limit of detection. Information from Figure 7 tells us we can get reliable response with Western blott even the sample is 1200 times diluted; however, in ELISA, there is a saturation problem when concentration is really low; and in aptamer-SPR biosensor RU will be too low to detect such low concentration.
More clarification on equation 1 and figure 6:
Equation 1 should be y=(free ssDNA)/[Kd+(free ssDNA)]. Y is the saturation degree, meaning the fraction of bounded protein to the total amount of protein added. Free ssDNA means the DNA on immobilized on gold chip without binding to protein.
This equation can be rewrite in another form y=[ free protein]/(Kd+[free protein]). Y is the saturation degree, meaning the fraction of bounded DNA on the gold chip. Free protein means the protein not bounded with ssDNA which is detectable.
In my opinion, Figure 6 is more likely to be based on the second equation, in which Y can be found by the RU to the saturation RU.
Question 2. This question refers to a sensogram not to the response units. In order words if you were doing an SPR experiment, what wiuld be the typical shape of a sensogram? How would you get from that sensogram the data for your equation?
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Comments
Questions for Meng and the rest of the class:
1. Equation (1) in the paper does not seem right and is inconsistent with Figure 6. Clarify.
2. Based on the typical plot of a sensogram, how does one determine y in equation 1.
3. The paper mentions that the Western method is more 'sensitive' than ELISA and the SPR method. [See paragraph before discussion]. Is this statement correct?
Posted by: Edgar Arriaga | April 22, 2008 10:28 PM
1. After rededucing and refering to article about this equation, I think the equation should be either y=(free ssDNA)/[Kd+(free ssDNA)], in which y is the degree of saturation; or y=Bmax(free ssDNA)/[Kd+(free ssDNA)], in which y means the number of bounded DNA-protein.
2. In Figure 6, one can determine the degree of saturation by getting the ratio of concerned RU compared with the saturation RU.
3. As to sensitivity, I think they mean the limit of detection. Information from Figure 7 tells us we can get reliable response with Western blott even the sample is 1200 times diluted; however, in ELISA, there is a saturation problem when concentration is really low; and in aptamer-SPR biosensor RU will be too low to detect such low concentration.
Posted by: Meng Jing | April 23, 2008 04:57 PM
More clarification on equation 1 and figure 6:
Equation 1 should be y=(free ssDNA)/[Kd+(free ssDNA)]. Y is the saturation degree, meaning the fraction of bounded protein to the total amount of protein added. Free ssDNA means the DNA on immobilized on gold chip without binding to protein.
This equation can be rewrite in another form y=[ free protein]/(Kd+[free protein]). Y is the saturation degree, meaning the fraction of bounded DNA on the gold chip. Free protein means the protein not bounded with ssDNA which is detectable.
In my opinion, Figure 6 is more likely to be based on the second equation, in which Y can be found by the RU to the saturation RU.
Posted by: Meng Jing | April 24, 2008 11:04 AM
Question 2. This question refers to a sensogram not to the response units. In order words if you were doing an SPR experiment, what wiuld be the typical shape of a sensogram? How would you get from that sensogram the data for your equation?
Posted by: Edgar Arriaga | April 26, 2008 09:34 AM