BOT104 - Nucleic Acid-Based Technology 2

Outline info
Last revision date 2018-07-20 11:36:17.71
Last review date 2018-07-20 11:36:24.846

Subject Title
Nucleic Acid-Based Technology 2

Subject Description
In this second course of nucleic acid-based technology, RNA-based techniques are the focus. Students acquire both the theoretical and practical knowledge in widely used RNA-based techniques. Topics include; RNA sample extraction, purification and quantification; RNA electrophoresis; RNA transcription; Northern blotting; RNA molecule site specific labeling techniques; spectroscopic study of RNA; RNA bioinformatics; RNA inhibition (RNAi) and RNA-DNA-protein interactions. It is taught by lectures and laboratory practice with a focus on lab.

Credit Status
One credit towards the Applied Biochem Techniques (ABCT) Certificate Program (APPLIED BIOTECHNOLOGY).

Learning Outcomes
Upon successful completion of this subject the student will be able to:

  1. Explain the theoretical based of commonly used DNA- based techniques.
  2. Perform RNA isolation, extraction, purification, quantification and transcription.
  3. Perform various electrophoresis techniques
  4. Perform various RNA labeling techniques
  5. Demonstrate an understanding of studing RNA with various spectroscopic methods
  6. Perform Northern Blot
  7. Perform RNAi experiments
  8. Describe RNA bioinformatics to do simple bioinformatics studies

Cheating and Plagiarism
Each student should be aware of the College's policy regarding Cheating and Plagiarism. Seneca's Academic Policy will be strictly enforced.

To support academic honesty at Seneca College, all work submitted by students may be reviewed for authenticity and originality, utilizing software tools and third party services. Please visit the Academic Honesty site on for further information regarding cheating and plagiarism policies and procedures.

All students and employees have the right to study and work in an environment that is free from discrimination and/or harassment. Language or activities that defeat this objective violate the College Policy on Discrimination/Harassment and shall not be tolerated. Information and assistance are available from the Student Conduct Office at

Accommodation for Students with Disabilities
The College will provide reasonable accommodation to students with disabilities in order to promote academic success. If you require accommodation, contact the Counselling and Disabilities Services Office at ext. 22900 to initiate the process for documenting, assessing and implementing your individual accommodation needs.

Completion of BOT 100.

Topic Outline

Week 1: tests, exam dates and students’ presentations assignment. RNA biochemistry; RNA structure and function (review); optimization of sample collection for RNA isolation from bacteria, cell cultures and tissues; extraction and analysis. Laboratory: general guidelines for working with RNA; proper aseptic techniques to prevent RNase contamination; preparation and handling of RNase-free solutions, materials and equipment. Isolation of total RNA from an E.coli culture; storage of purified RNA samples.

Week 2: RNA visualization and electrophoretic analysis of total RNA; denatured and native agarose gel electrophoresis, principle and applications; determination of RNA purity and integrity. Laboratory: preparation of denatured agarose gel electrophoresis; sample preparation; optimized conditions for separation and visualization of RNA on ethidium bromide stained gels.

Weeks 3 and 4: RNA transcription: factors required for transcription, differences between prokaryotes and eukaryotes. “In vitro” transcription systems and commercially available vectors; description of experimental protocols. Laboratory: biosynthesis of RNA: preparation of DNA insert and vector, transcription reaction, recovery and purification of RNA transcripts; visualization and analysis.

Week 5: analysis and discussion of laboratory results; midterm test-theory and practice.

Week 6: methods of RNA labeling; RNA hybridization techniques using radioactive and non-radioactive probes. Laboratory: labeling of commercially available RNA oligonucleotides with different fluorescent dyes, preparation and purification of labeled probes.

Week 7: spectroscopic analysis of RNA; applications for quantification and quality analysis of RNA; applications of fluorescent RNA spectroscopy. Laboratory: analysis of double-labeled RNA by FRET (Fluorescence Resonance Energy Transfer).

Week 8: prediction of RNA structures, principle and applications; RNA secondary and tertiary structures and function; access to RNA structure database; bioinformatics; RNA-DNA-protein interactions. Laboratory: analysis and prediction of RNA structures using different methods and software.  

Week 9: RNA interference (RNAi) and antisense RNA (asRNA) technologies, overview; mechanisms and applications in medicine and food industry; students’ presentations.

Week 10: Final exam- theory and practice.

Mode of Instruction
Lectures, Laboratory, Tutorials, Assignment Presentations, Discussions

Prescribed Texts
to be introduced by the instructor.

Reference Material
Prescribed texts, Laboratory experiment notes in form of procedures and reports

Required Supplies
Laboratory coat, safety glasses

Promotion Policy

Grading Policy
A+ 90%  to  100%
A 80%  to  89%
B+ 75%  to  79%
B 70%  to  74%
C+ 65%  to  69%
C 60%  to  64%
D+ 55%  to  59%
D 50%  to  54%
F 0%    to  49% (Not a Pass)
EXC Excellent
SAT Satisfactory
UNSAT Unsatisfactory

For further information, see a copy of the Academic Policy, available online ( or at Seneca's Registrar's Offices.

Modes of Evaluation

  • Assignments are due at the beginning of the class on which they are due.
  • A late penalty of 10% per day is assessed for late assignments, including those not handed in at the beginning of class when due.
  • Material will not be accepted after one week following the due date and/or when the marked material is returned to students, whichever comes first.
  • Assignments are to be prepared by computer.

Absenteeism and Exams/Quizzes
  • Students should be aware that absenteeism almost guarantees an inability to achieve satisfactory grades.
  • Students who are absent for an examination due to an emergency (e.g., motor vehicle accident, hospitalization or death in the family) may provide official documentation within five days of the missed exam and be provided a deferred exam at a later date.  Official documentation includes a death notice or an original doctor’s certificate identifying the date, length of time expected absence and the specific reason for the absence.  Examinations missed without official documentation and approval result in a grade of zero.
  • There are no deferred options for missed quizzes.  The value of missed quizzes, at the discretion of the Faculty, will be added to other evaluation components.

English Proficiency
  • All written work should demonstrate the following characteristics for clarity and conciseness:
-writing is consistent with the rules of English grammar
-spelling and punctuation are correct
-sentences are structured correctly
-main ideas are supported with specific, relevant examples and reasons
-work flows logically through supporting statements/paragraphs
-work is arranged in correct format (e.g., as a report, essay)
-up to 10% of the final grade may be deducted on all work if the above English competencies are not met.

Format for Assignments
  • Students must use the standard, APA style for quoting sources.   Help is available at:

Laboratory Attendance
The laboratory component is essential and therefore it is strongly recommended that you attend all labs.  Any missed labs must be supported with a legal document with three days of the lab.  Any student who fails to attend more than 2 laboratory classes for a 10 week subject will not pass the subject.    

Laboratory Safety
Students are required to review and understand the safety procedures and guidelines outlined on the first class and sign the sheet to this effect before beginning work in the laboratory.  Students must also wear a lab coat and safety glasses when conducting experiments.
A student who arrives without the proper safety equipment will not be permitted to participant in the lab but will be asked to leave the class.  The student will receive no grade for the lab missed.

Grading is based on the following marking scheme:
Laboratory reports 20%
Assignments 10%
Midterm test 30%
Final Exam 40%

Note: Absent exams generally cannot be made up; lab mark will be pro-rated if two or few labs are missed with reasonable excuses (doctor’s notes etc.). No one shall miss more than two labs.


Other Evaluation Considerations
The student is expected to comply with the Safety Rules for working in the laboratory, sign the safety contract, and WILL NOT UNDER ANY CIRCUMSTANCES WEAR CONTACT LENSES in the laboratory. The student will know where all safety equipment is located in the laboratory and will be familiar with WHIMIS concepts and signage.


Approved by: Denis Gravelle