| Course Name | Functional Oligonucleotides |
| Code | Semester | Theory (hour/week) | Application/Lab (hour/week) | Local Credits | ECTS |
|---|---|---|---|---|---|
| BEN 520 | Fall/Spring | 3 | 0 | 3 | 7.5 |
| Prerequisites | None | |||||
| Course Language | English | |||||
| Course Type | Elective | |||||
| Course Level | Second Cycle | |||||
| Mode of Delivery | - | |||||
| Teaching Methods and Techniques of the Course | ||||||
| Course Coordinator | ||||||
| Course Lecturer(s) | - | |||||
| Assistant(s) | - | |||||
| Course Objectives | The objective of the course is to provide the ability to work with tools that target or exploit oligonucleotides. |
| Learning Outcomes | The students who succeeded in this course;
|
| Course Description | The course contains introduction of functional oligonucleotides starting with types of synthetic and natural oligonucleotides. In the proceedings, the course covers 3-dimentional topology, and forces that apply to form the topology. The areas and methods of applications are discussed over recent publications. The course also covers the process of artificial oligonucleotide synthesis, the chemical modifications used and the effect of these modifications with examples in order to provide the ability to choose correct modifications for different applications. |
| Related Sustainable Development Goals | |
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| Core Courses | |
| Major Area Courses | X | |
| Supportive Courses | ||
| Media and Managment Skills Courses | ||
| Transferable Skill Courses |
| Week | Subjects | Required Materials |
| 1 | Introduction and definitions | |
| 2 | DNA, RNA, LNA, XNA, PNA primary structure | Anosova, I., et al. (2016) 10.1093/nar/gkv1472 |
| 3 | Hydrogen bonds, Van der Waals interactions, electrostatic interactions | Fedor Kouzine, David Levens & Laura Baranello (2014) 10.4161/nucl.28909 |
| 4 | Secondary structure, B-form, Z-form, A-form, G-quadruplex, Triplex, H-junction | Fedor Kouzine, David Levens & Laura Baranello (2014) 10.4161/nucl.28909 |
| 5 | Methods for detection, permeability, fluorescence, phosphorescence, radioactive labelling | Boutorine AS, et al. (2013) 10.3390/molecules181215357 |
| 6 | Artificial oligonucleotide synthesis | Andrei Laikhter and Klaus D. Linse, (2014) |
| 7 | Midterm I | |
| 8 | Laboratory techniques, FISH, smFISH, qPCR | Kwon, S. (2013) 10.5483/BMBRep.2013.46.2.016 |
| 9 | Fluorescent group modifications | Juskowiak, B. (2011) 10.1007/s00216-010-4304-5 |
| 10 | Permeability enhancing modifications | Sandeep Verma and Fritz Eckstein (1998) |
| 11 | Nuclease resistive modifications | Sandeep Verma and Fritz Eckstein (1998) |
| 12 | Midterm II | |
| 13 | Case study I | Osman Doluca, et al. (2013) 10.1002/cplu.201300310 |
| 14 | Case study II | Osman Doluca, Jamie M Withers, Vyacheslav V. Filichev (2013) 10.1021/cr300225q |
| 15 | Review of the semester | |
| 16 | Final Exam |
| Course Notes/Textbooks | Listed articles |
| Suggested Readings/Materials | http://fbio.uh.cu/sites/genmol/adic/na_arch.htm https://www.atdbio.com/content/18/Synthesis-and-properties-of-fluorescent-oligonucleotides http://www.glenresearch.com/Catalog/index1.php |
| Semester Activities | Number | Weigthing |
| Participation | 1 | 20 |
| Laboratory / Application | ||
| Field Work | ||
| Quizzes / Studio Critiques | ||
| Portfolio | ||
| Homework / Assignments | ||
| Presentation / Jury | ||
| Project | ||
| Seminar / Workshop | ||
| Oral Exam | ||
| Midterm | 2 | 40 |
| Final Exam | 1 | 40 |
| Total |
| Weighting of Semester Activities on the Final Grade | 3 | 60 |
| Weighting of End-of-Semester Activities on the Final Grade | 1 | 40 |
| Total |
| Semester Activities | Number | Duration (Hours) | Workload |
|---|---|---|---|
| Course Hours (Including exam week: 16 x total hours) | 16 | 3 | 48 |
| Laboratory / Application Hours (Including exam week: 16 x total hours) | 16 | ||
| Study Hours Out of Class | 15 | 6 | 90 |
| Field Work | |||
| Quizzes / Studio Critiques | |||
| Portfolio | |||
| Homework / Assignments | |||
| Presentation / Jury | |||
| Project | |||
| Seminar / Workshop | |||
| Oral Exam | |||
| Midterms | 2 | 21 | |
| Final Exams | 1 | 45 | |
| Total | 225 |
| # | Program Competencies/Outcomes | * Contribution Level | ||||
1 | 2 | 3 | 4 | 5 | ||
| 1 | To be able to have adequate knowledge in Mathematics, Life Sciences and Bioengineering; to be able to use theoretical and applied information in these areas to model and solve Bioengineering problems. | X | ||||
| 2 | To be able to use scientific methods to complete and apply information from uncertain, limited or incomplete data; to be able to combine and use information from related disciplines. | X | ||||
| 3 | To be able to design and apply theoretical, experimental and model-based research; to be able to solve complex problems in such processes. | X | ||||
| 4 | Being able to utilize Natural Sciences and Bioengineering principles to design systems, devices and processes. | X | ||||
| 5 | To be able to follow and apply new developments and technologies in the field of Bioengineering. | X | ||||
| 6 | To be able to work effectively in multi-disciplinary teams within the discipline of Bioengineering; to be able to exhibit individual work. | X | ||||
| 7 | To be able to have the knowledge about the social, environmental, health, security and law implications of Bioengineering applications, to be able to have the knowledge to manage projects and business applications, and to be able to be aware of their limitations in professional life. | |||||
| 8 | To be able to have the social, scientific and ethical values in the stages of collection, interpretation, dissemination and application of data related to the field of Bioengineering. | |||||
| 9 | To be able to prepare an original thesis/term project in accordance with the criteria related to the field of Bioengineering. | |||||
| 10 | To be able to follow information about Bioengineering in a foreign language and to be able to participate in discussions in academic environments. | X | ||||
| 11 | To be able to improve the acquired knowledge, skills and qualifications for social and universal purposes regarding the studied area. | X | ||||
| 12 | To be able to recognize regional and global issues/problems, and to be able to develop solutions based on research and scientific evidence related to Bioengineering. | X | ||||
*1 Lowest, 2 Low, 3 Average, 4 High, 5 Highest
