Molecular Methods

Aim of the course

The course is aimed to acquire a deep knowledge of advanced molecular methodologies such as deep sequencing, single molecule techniques, and gene editing methods. Special attention will be devoted to the applications of these techniques to research and to biomedical diagnosis.

Course opening:

October 2, 2023, 9:00 am

Auletta Seminari

Building of Fisiologia Generale


Every Monday and Wednesday 9:00-11:00

Runs until mid-December, 2023

To access the next sections students must register using Infostud credentials







 Program of the course


Next Generation Sequencing: methodologies and applications (Lectures 1-13, 26 h)



History of DNA sequencing

Human Genome Project 

Next Generation Sequencing (deep sequencing)

NGS Platforms and technologies 

Third Generation Sequencing




      •Whole Genome Sequencing (WGS)

      •Whole Exome Sequencing (WES)







      •Bisulfite-seq etc.

Metagenomics and microbiomics 

Towards precision medicine

NGS data analysis

Single cell sequencing

Single Molecule Techniques and Super Microscopy (Lectures 14-16, 6 h)


Studying single molecules 

      •AFM (Atomic Force Microscopy)

      •Optical Tweezers and Magnetic Tweezers

      •Single molecule FRET


From Microscopy to Nanoscopy: beyond the limits of Abbe law 

      • STED (Stimulated Emission Depletion)

      •STORM (Stochastic Optical Reconstruction Microscopy)


Advanced Tools to Target and Edit Genomes (Lectures 17-20, 8h; Laboratory Exercise, 12 h)


Gene targeting by site-specific nucleases: ZFNs (Zinc Finger Nucleases), TALENs (transcription activator-like effector nucleases)

CRISPR/CAS revolution: a simple and powerful method to edit genomes 

Applications of the CRISPR/CAS system

Future perspectives of gene and genome editing

Cloning single-guide RNA expressing vectors (Lab exercise)


There is not a specific textbook for the course. Knowledge of basic biomolecular techniques is expected to succeed in the course.

Reviews and articles, together with lectures (PDF), will be available on the course website on e-learning platform





Basic knowledge


  • Wilson and Walker’s Principles and Techniques of Biochemistry and Molecular Biology (8th edition) – Hofmann A & Clokie S, Cambridge University Press (2018)
  • Biotecnologie Molecolari, principi e tecniche (2a edizione) – Brown TA, Zanichelli 2017
  • Gene Cloning and DNA Analysis: An Introduction (7th edition) - Brown TA, Wiley & Sons (2016)
  • Biologia Molecolare del Gene (settima edizione) (cap. 7; parte 6, Appendix) – Watson et al., Zanichelli ed.
  • From Genes to Genomes – Dale JW, Von Schantz M, Plant N, Wiley-Blackwell eds.*
  • Tecniche e Metodi per la Biologia Molecolare - Amaldi F, Benedetti P, Pesole G, Plevani P, CEA-Zanichelli 2020 (disponibile anche come e-book)



Specific knowledge


  • Reviews and articles (available on the course website)
  • Next-Generation DNA Sequencing Informatics – Brown, CSHL press#
  • Atomic Force Microscopy For Biologists – Morris et al., Imperial College Press#


* Available at the Department library (Antropologia)

#  Available at the teacher’s room (Fisiologia Generale, 1° floor, Room 10)