DNA Melting Report Requirements

Format

• One group member must submit a single PDF file no more than 20 MB to Stellar before the deadline.
• The name of the submitted file must consist of the last name of each group member separated by underscores: <LastName1>_<LastName2>_<LastName2>.pdf
• Include computer code in an appendix at the end of the file. Do not submit code separately.
• All plots must be presented properly, including a descriptive title, axis labels, and legend.
• Begin the report with a cover page the lists the full names of all group members, your assigned DNA sample number, the type of investigation (length/ionic strength/complementarity), and a haiku about DNA melting curves.

Failure to follow the format guidelines will result in ridiculously large grade penalties

Report outline

1. Abstract:

• • In one paragraph of less than six sentences, summarize the investigation you undertook and key results.

1. Raw data

• • Plot all of your group's raw data, fluorescence vs. temperature, on the smallest number of axes that clearly convey the dataset. Include only data datasets generated by your own group.
  • On similary-grouped sets of axes, plot ΔdsDNA fraction/Δtemperature.

1. Model parameters

   Develop a model for the melting experiment and use nonlinear regression to determine best-fit parameters.

• • Use the smallest possible number of plots to compare the model with best-fit parameters to your data and a simulated result obtained from DINAmelt or another melting curve simulator.
  • Include a table of estimated thermodynamic parameters, ΔH, ΔS, and T_m. Use multiple methods to find T_m.

1. Unknown sample determination

• • Plot results for unknown sample, including other samples for comparison.
  • Identify your unknown sample and state your level of confidence in the answer.
  • Use the smallest possible number of plots to compare the unknown sample to the corresponding known sample.

1. Comparative data analysis

• • Compare your data to results from other groups.

1. Analysis

• • Use bullet points to explain your data analysis methodology.

1. Discussion

   Compare your results to theoretical models and/or other group's datasets.

2. Sources of error: Provide a detailed discussion of error sources. Indicate whether each source causes a systematic or random distortion in the data. (The uncertainty from a random error decreases with additional experimental runs; systematic error does not.) Consider all possible sources of error including all aspects of your instrument, the oligo design, the dye used, the experimental methodology, and the analysis methodology.
3. Instrument documentation

   Block diagram and schematics

   Include component values, relevant distances, and possibly a photograph or two. It is not necessary to document construction details, but do show your work in determining your component values, distances, etc.

   Signal to noise results

   Design evolution

   Give a bullet point summary of changes you made to your instrument design to address problems in the lab.

Lab manual sections

• Lab Manual:Measuring DNA Melting Curves
• DNA Melting: Simulating DNA Melting - Basics
• DNA Melting Part 1: Measuring Temperature and Fluorescence
• DNA Melting Report Requirements for Part 1
• DNA Melting: Simulating DNA Melting - Intermediate Topics
• DNA Melting Part 2: Lock-in Amplifier and Temperature Control
• DNA Melting Report Requirements for Part 2