Samir Hamdan

  Associate Professor, Bioscience ​

  Office Location: Ibn Al Haytham (Building 2) · Level 4 · Room 4221
  Email: samir.hamdan@kaust.edu.sa


Research Keywords
Single molecule imaging; single molecule enzymology; microscopy; protein structure and function; DNA replication; DNA repair; DNA recombination


Research Interests
Professor Hamdan's research interest is focused on the reconstitution, imaging and characterization of multi-protein nucleic acid binding machinaries at the single molecule level with particular focus on those involved in DNA replication, repair and recombination. Toward achieving this goal his lab uses an approach that combines conventional biochemical and biophysical tools with wide range of force and fluorescence single-molecule imaging techniques. 

The ability to observe enzymatic activities in real time at the single molecule level has profoundly changed how biochemical reactions are studied. By eliminating ensemble averaging, the distributions and fluctuations of molecular properties can be characterized, transient intermediates can be observed and identified, and catalytic mechanisms can be elucidated. Applying this multidisciplinary approach will provide a true molecular understanding of the mechanisms involved in replication, repair, and recombination. It will also extend the technique of single-molecule analysis from a few proteins to large multi-protein complexes, often containing many enzymatic activities.


Main Techniques
Single molecule (SM) imaging, SM Förster resonance energy transfer, SM force microscopy (hydrodynamic DNA flow stretching) and its combination with SM fluorescence imaging, protein expression and purification using E. coli and insect cells, bulk phase enzymology of nucleic acid binding proteins and wide range of bulk phase techniques to study protein-protein and protein-substrate interaction.

Members of the Lab

Dr Mohamed Sobhy: Research scientist focusing on developing single molecule fluorescence approaches including smFRET and applying them to diverse questions with particular focus on the mechanism of the structure specific 5’ nuclease superfamily. Dr Sobhy obtained his PhD from Pennsylvania State University (USA).

Dr Masateru Takahashi: Research scientist focusing on exploring the biotechnology potential of DNA polymerases isolated from the Red sea Brine pool microorganisms as well as the molecular mechanism of micro-RNA biogenesis. Dr Takahashi obtained his PhD from Kyushu University (Japan). 

Dr Alia Al-Kilani: Postdoctoral fellow focusing on combining SM hydrodynamic DNA flow stretching with multicolor fluorescence tracking of protein acting on DNA to investigate the mechanism of maturation of Okazaki fragment synthesis and micro-RNA biogenesis. Dr Al-Kilani obtained her PhD from University of Rennes (France).

Mohamed Salem: Third year PhD student focusing on applying SM hydrodynamic DNA flow stretching and smFRET to understand the communication between DNA replication and replication termination in the model system E. coli.

Luay Joudeh: Third year PhD student focusing on applying biochemical and divers SM imaging approaches including smFRET and combining SM hydrodynamic DNA flow stretching with multicolor fluorescence tracking of protein acting on DNA to reconstitute and understand the molecular mechanism of maturation of Okazaki fragment synthesis.

Abeer Al-Qasim: Second year PhD student focusing on applying bulk phase biochemical and biophysical techniques to achieve the in vitro reconstitution of leading strand synthesis in the model system Simian virus 40.

Fahad Rashid: Second year PhD student focusing on applying biochemical and smFRET to understand the mechanism of 5’ nucleases and their interaction with partners proteins in DNA replication and repair.

Manal Zaher: Second year PhD student focusing on applying biochemical and smFRET to investigate the mechanism of primer synthesis and handoff by DNA polymerase alpha.

Etsuko Kimura: Lab technician


Selected Publications
Iwata Y, Takahashi M, Fedoroff NV and Hamdan SM. Dissecting the Interactions of SERRATE with RNA and DICER-LIKE 1 in Arabidopsis microRNA Precursor Processing. Nucleic Acids Research. 2013, 41(19):9129-40

Sobhy MA, Joudeh L, Huang X., Takahashi M and Hamdan SM. Sequential and Multistep Substrate Interrogation Provides the Scaffold for Specificity in Human Flap Endonuclease 1. Cell Reports. 2013, 3(6): 1785-94

Jergic S, Horan NP, Elshenawy MM, Mason CE, Urathamakul T, Ozawa K, Robinson A, Goudsmits JM, Wang Y, Pan X, Beck JL, van Oijen AM, Huber T, Hamdan SM and Dixon NE. A Direct Proofreader-clamp Interaction Stabilizes the Pol III Replicase in the Polymerization Mode. EMBO J. 2013, 32(9):1322-33

Sobhy MA, Elshenawy MM, Takahashi M, Whitman BH, Walter NG and Hamdan SM. Versatile Single-molecule Multi-color Excitation and Detection Fluorescence Setup for Studying Biomolecular Dynamics. Review of Scientific Instruments Journal. 2011, 82(11): 113702-13

Hamdan SM, Loparo JJ, Takahashi M, Richardson CC, and van Oijen AM. Dynamics of DNA Replication Loops Reveal Temporal Control of Lagging-strand Synthesis. Nature. 2009, 457(7227): 336-9