Biomolecular Technology (2008/2009)

Course Not running, not visible

Course code
4S00175
Credits
8
Coordinator
Massimo Delledonne
Teaching is organised as follows:
Unit Credits Academic sector Period Academic staff
Modulo 1 - Teoria 1 AGR/07-AGRICULTURAL GENETICS 1° Sem Massimo Delledonne
Modulo 1 - Laboratorio 3 AGR/07-AGRICULTURAL GENETICS 1° Sem Massimo Delledonne
Modulo 2 - Teoria 1 BIO/11-MOLECULAR BIOLOGY 1° Sem Barbara Molesini
Modulo 2 - Laboratorio 3 BIO/11-MOLECULAR BIOLOGY 1° Sem Barbara Molesini

Learning outcomes

Module: Modulo 2 - Teoria
-------
This course aimed to study in detail the hybridization between nucleic acids and the PCR that are at the basis of many methods for molecular analysis.


Module: Modulo 1 - Teoria
-------



Module: Modulo 1 - Laboratorio
-------



Module: Modulo 2 - Laboratorio
-------
Southern-blot (based on hybridization between nucleic acids) and RT-PCR (based on PCR) performed on transgenic and wild-type plants, will allow the student to apply the knowledges acquired.

Syllabus

Module: Modulo 2 - Teoria
-------
NUCLEIC ACID HYBRIDIZATION
1.INTRODUCTION TO NUCLEIC ACID HYBRIDIZATION: FORCES STABILIZING DNA STRUCTURE, STABILITY OF NUCLEIC ACIDS, EFFECTS OF pH, EFFECTS OF TEMPERATURE, MELTING TEMPERATURE Tm, FACTOR AFECTING Tm
2.TYPES OF HYBRIDIZATIONS
3. SOLUTION HYBRIDIZATION: REASSOCIATION OF DNA, FACTORS AFFECTING REASSOCIATION/HYBRIDIZATION (FACTORS AFFECTING RATE OF HYBRIDS FORMATION AND STABILITY OF HYBRIDS)
4.FILTER HYBRIDIZATION: TYPES AND PROPERTIES OF SUPPORT, TRANSFER OF NUCLEIC ACID TO FILTER, FIXING THE DNA TO THE MEMBRANE, SCREENING OF RECOMBINANT LIBRERIES, DOT/SLOT BLOT AND REVERSE DOT/BLOT, SOUTHERN BLOT, NORTHERN BLOT (RNA EXTRACTION AND GEL ELECTROPHORESIS OF RNA SAMPLES)
5.CHOICE OF PROBES: DNA OR RNA ? RADIOACTIVE AND NONRADIOACTIVE PROBES, DIRECT AND INDIRECT LABELING, LABELING, UNIFORM LABELING OF THE PROBE (NICK-TRANSLATION, RANDOM PRIMED LABELING, PCR-MEDIATED LABELING, RUN-OFF TRANSCRIPTION, CHEMICAL METHODS), END LABELING (T4 POLYNUCLEOTIDE KINASE, FILL-IN BY KLENOW, DNA TAILING BY TERMINAL DEOXYNUCLEOTIDYL TRANSFERASE), DETECTION OF RADIOCTIVE HYBRIDS (AUTORADIOGRAPHY), DETECTION OF NONRADIOCTIVE HYBRIDS (ALKALINE PHOSPHATASE, HORSERRADISH PEROXIDASE, CHROMOGENIC SUBSTRATES, CHEMIOLUMINESCENT SUBSTARTES)
6.SPECIFIC APPLICATIONS OF FILTER HYBRIDIZATION: DNA MAPPING, DETECTION OF RELATED SEQUENCES, DNA FINGERPRINTING BY HYBRIDIZATION, DETECTION OF MUTATIONS, DETECTION OF METHYLATIONS


PCR
1.WHAT IS PCR?
2.REAGENTS: EFFICIENCY, SPECIFICITY, FIDELITY
3.PCR CYCLE. FINAL NUMBER OF COPIES OF THE TARGET SEQUENCE
4) 4.AMPLIFYING THE CORRECT PRODUCT: DETECTION AND ANALYSIS OF PCR PRODUCTS, HOW TO AVOID CONTAMINATION (URACIL N-GLYCOSYLASE, UV, ENZYMATIC TREATMENT), HOT START, NESTED PCR
5.TECHNIQUES AND APPLICATIONS: 5’RACE-PCR AND 3’RACE-PCR, RT-PCR,PCR MUTAGENESIS (DELETION OF SEQUENCES, BASE SUBSTITUTIONS, INSERTION MUTAGENESIS), MODIFICATION OF PCR PRODUCTS(INTRODUCTION OF RESTRICTION SITES, ADDING PROMOTERS AND RIBOSOME-BINDING SITES), JOINING OVERLAPPING PCR PRODUCTS, QUANTITATIVE PCR


Module: Modulo 1 - Teoria
-------



Module: Modulo 1 - Laboratorio
-------



Module: Modulo 2 - Laboratorio
-------
1) SOUTHERN BLOT ANALYSIS OF TRANSGENIC PLANTS: GENOMIC DNA EXTRACTION, QUANTIFICATION, RESTRICTION DIGESTION, ELECTROPHORESIS OD DIGESTED DNA, CAPILLARY BLOTTING, FIXING THE DNA TO THE MEBRANE, LABELING NONRADIOACTIVE PROBE, PREHYBRIDIZATION, HYBRIDIZATION, WASHING, DETECTION OF HYBRIDS BY CHEMIOLUMINESCENT SUBSTRATE

2) RT-PCR: RNA EXTRACTION, QUANTIFICATION, DNase TREATMENT, SYNTHESIS OF cDNA, PCR

Assessment methods and criteria

Module: Modulo 2 - Teoria
-------
written examination


Module: Modulo 1 - Teoria
-------



Module: Modulo 1 - Laboratorio
-------



Module: Modulo 2 - Laboratorio
-------
Delivery of a detailed report regarding the experiments performed in the laboratory.

Studying