Notice for the AFM Experiment and project for PC5213
1. Students who wish take to the experiments should see the lab officer for registration.
Attendance list must be signed during each of the lab session with the lab officer.
2. Two days per week are reserved for using the AFM. Students should try to get enough data
in the first half of the semester, so they can use the second half of the semester for discussion
of the results. The students should check the availability of the AFM with Mr. Teo and book
their experimental time slots.
3. Students who wish to take an experiment in the period other than the normal lab-hours
should obtain a special permission from both the lecturer in charge and the lab officer first
before the experiment is arranged. If the application is approved, the experiment should be
registered at least 3 days before it is taken.
4. SAFETY PRECAUTIONS:

DO NOT touch any equipment or bio-samples in the lab without permission from the
lecturers or lab-officer in charge.

Before starting any experiments, familiarize yourself with the safety rules, and the
precaution/emergency measures (such as hand/facial wash) under the supervision of
the Lab officer.
5. Students who are unable to complete the designated experiments due to the health problem
should produce a MC from their GP, and submit it to the lecturer in charge.
6. Recording experimental data

It is essential to keep a good experimental record for each experiment.

Bring your Thumb Drive for copying the data

When the experiment is completed, the note should be vetted and signed by the lecturer in
charge.
7. Experiment Report (for PC5213):
Sections:
1. Aim
2. Basic principles
3. Key experimental procedures and precautions
4. Results
5. Discussion and Conclusion (For example, discuss the data you measured; where does the
experiment error come from; how to improve the experiment; what are the possible
implications of this experiment; etc)
Sections:
1. Experiment procedure
2. Results
You should measure the equilibrium DNA conformation during your imaging. Please save both
the original data and also export the images into JPG files. In your report, you should place the
jpg images into a powerpoint file or a word file, and indicate the end-to-end distance, R, over
several specified contour length, L, for each image. You should calculate the distribution of R
under the constraint of L.
3. Discussions and Conclusion:
You will discuss the following:
How the end-to-end distance distributions reflect the bending stiffness of DNA?
Can you data be explained by assuming DNA is a semi-flexible polymer?
If it is, should it be explained by a 3-d model or a 2-d model?
What is the persistence length estimated from your data?
If anything unexpected is observed, try to give it an explanation based on the thermal statistical
theory you learnt in the class.
Your score is not determined by how perfect your images are recorded, but by how much you
understand the physics, which should be reflected in your discussion.
P.S. All the reports should not exceed 10 pages.
Notes (for PC5213):
1. On a cover page, put the experiment title, your name, matriculation number, the date you
did the experiment and the date of report submission.
2. There is no viva for the experiments.
3. All reports should be completed two weeks prior to the examination period.
Experiment marking Scheme:
Repo
rt
Discus
sion
40%
60%
8. Experiment Project report (for PC5213):
Sections:
1. Aim
2. Basic principles
3. Key experimental procedures and precautions
4. Results
5. Discussion and Conclusion (For example, discuss the data you measured; where does the
experiment error come from; how to improve the experiment; what are the possible
implications of this experiment; etc)
For the DNAs you recorded in your experiment, you will measure the bending angles over
several given contour lengths L. You should calculate the distribution of the bending angle
under the constraint of L.
You need to do the following:





Find the contour curve that fits the imaged DNA backbone the best, so you get a smooth
curve in 2-d;
From the curve you get the tangent vectors at any given points;
Get the distributions of the bending angles between any two tangent vectors which are
separated by a contour length “L”;
Compare the measured distribution with what would be expected from the traditional
semi-flexible polymer theory;
Compare the results with the most recently published results;
You will discuss the following:
How the bending angle distributions reflect the bending stiffness of DNA?
Can you data be explained by assuming DNA is a semi-flexible polymer?
At what conditions you data can be explained by a semi-flexible polymer model?
Can your data be explained a by non-harmonic elasticity model?
If anything unexpected is observed, try to give it an explanation based on the thermal statistical
theory you learnt in the class.
Project marking Scheme:
Bending angle
distribution
50%
Discussion
50%