Question

The sample results are given as: Detected Relative Intensity Trial 1 Trial 2 Trial 3 0 nM 0.556 0.603 0.509 5 nM 0.524 0.538 0.519 10 nM 0.454 0.469 0.467 20 nM 0.223 0.311 0.358 50 nM 0.079 0.074 0.080 Blank / Blocked 0.055 0.055 0.054 Please answer ONLY the following questions and submit a document file online: 1. Based on the given data, plot the data as the optical absorbance of supernatant against the target $T_c$ concentrations, with the baseline signal level eliminated. The each point you plot should specific the average absorbance (A, no unit) for a particular $T_c$ concentration (C, unit: nM). Please add an error bar as the standard error for each average point. 2. Please compute the fitting line in the plot (for question 1) as a linear equation, i.e. $A = k1 cdot C + k0$, where $k1$ and $k0$ are the constants you need to figure out. 3. What is the 95% confidence interval for $k0$? And what is the 95% confidence interval for $k1$? 4. Consider that you need to design the most 'stable' pair of probes (P1 and P2) for a new target DNA sequence T: 5'-ACTTGTGTCTCGTTTCTTCGATCCAAAGCG-3' Please provide a pair the sequences of P1 and P2, and the changes in the hybridization energy of T before/after binding for each of the P1 and P2 you pick. Please explain why your choice can achieve the most stable pair of probes.

          The sample results are given as:
Detected Relative Intensity
Trial 1 Trial 2 Trial 3
0 nM
0.556
0.603
0.509
5 nM
0.524
0.538
0.519
10 nM
0.454
0.469
0.467
20 nM
0.223
0.311
0.358
50 nM
0.079
0.074
0.080
Blank /
Blocked
0.055
0.055
0.054
Please answer ONLY the following questions and submit a document file online:
1. Based on the given data, plot the data as the optical absorbance of supernatant
against the target $T_c$ concentrations, with the baseline signal level eliminated. The
each point you plot should specific the average absorbance (A, no unit) for a
particular $T_c$ concentration (C, unit: nM). Please add an error bar as the standard
error for each average point.
2. Please compute the fitting line in the plot (for question 1) as a linear equation, i.e.
$A = k1 cdot C + k0$, where $k1$ and $k0$ are the constants you need to figure out.
3. What is the 95% confidence interval for $k0$? And what is the 95% confidence
interval for $k1$?
4. Consider that you need to design the most 'stable' pair of probes (P1 and P2) for a
new target DNA sequence T:
5'-ACTTGTGTCTCGTTTCTTCGATCCAAAGCG-3'
Please provide a pair the sequences of P1 and P2, and the changes in the
hybridization energy of T before/after binding for each of the P1 and P2 you pick.
Please explain why your choice can achieve the most stable pair of probes.

The sample results are given as:
Detected Relative Intensity
Trial 1 Trial 2 Trial 3
0 nM
0.556
0.603
0.509
5 nM
0.524
0.538
0.519
10 nM
0.454
0.469
0.467
20 nM
0.223
0.311
0.358
50 nM
0.079
0.074
0.080
Blank /
Blocked
0.055
0.055
0.054
Please answer ONLY the following questions and submit a document file online:
1. Based on the given data, plot the data as the optical absorbance of supernatant
against the target Tc concentrations, with the baseline signal level eliminated. The
each point you plot should specific the average absorbance (A, no unit) for a
particular Tc concentration (C, unit: nM). Please add an error bar as the standard
error for each average point.
2. Please compute the fitting line in the plot (for question 1) as a linear equation, i.e.
A = k1 cdot C + k0, where k1 and k0 are the constants you need to figure out.
3. What is the 95% confidence interval for $k0$? And what is the 95% confidence
interval for k1?
4. Consider that you need to design the most 'stable' pair of probes (P1 and P2) for a
new target DNA sequence T:
5'-ACTTGTGTCTCGTTTCTTCGATCCAAAGCG-3'
Please provide a pair the sequences of P1 and P2, and the changes in the
hybridization energy of T before/after binding for each of the P1 and P2 you pick.
Please explain why your choice can achieve the most stable pair of probes.

Added by Sandra R.

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