Leiden University Scholarly Publications

Persistent URL of this record https://hdl.handle.net/1887/3281818

In Collections

This item can be found in the following collections:

Zuiddam, M. (2022)

Freedom of additional signals on genes: on the combination of DNA mechanics, genetics and translation speed

Doctoral Thesis
DNA carries various forms of information. Out of these forms of information the most well-known is classical genetic information. Throughout this dissertation we discuss what is often referred to as the second layer of information on DNA: DNA mechanics. A sequence consisting of only A’s and T’s will bend differently from a sequence of G’s and C’s. An important consequence of this mechanical layer of information is the positioning of nucleosomes. Nucleosomes consist of 147 base pairs of DNA wrapped around a protein core, like a string around a spool. By either allowing or restricting access to a binding site, a nucleosome may serve as an on/off switch, of which the location is extremely important. A third layer of information on DNA is translation speed. Translation speed refers to the rate at which a protein is created, and it depends on the codons used in a genetic sequence. The research in this thesis investigates how these layers of information are multiplexed. It uses...Show moreDNA carries various forms of information. Out of these forms of information the most well-known is classical genetic information. Throughout this dissertation we discuss what is often referred to as the second layer of information on DNA: DNA mechanics. A sequence consisting of only A’s and T’s will bend differently from a sequence of G’s and C’s. An important consequence of this mechanical layer of information is the positioning of nucleosomes. Nucleosomes consist of 147 base pairs of DNA wrapped around a protein core, like a string around a spool. By either allowing or restricting access to a binding site, a nucleosome may serve as an on/off switch, of which the location is extremely important. A third layer of information on DNA is translation speed. Translation speed refers to the rate at which a protein is created, and it depends on the codons used in a genetic sequence. The research in this thesis investigates how these layers of information are multiplexed. It uses multiple novel approaches, one of them being the use of weighted graphs consisting of all possible DNA sequences to find the very best and very worst nucleosome-attracting sequences. 

Show less
DNA mechanics
Nucleosomes
Genomics
Graph Theory
Transfer matrix calculations
All authors
Zuiddam, M.
Supervisor
Schiessel, H.
Committee
Lesne, A.; Carlon, E.; Noort, S.J.T. van; Giomi, L.; Aarts, J.
Qualification
Doctor (dr.)
Awarding Institution
Leiden Institute of Physics (LION), Faculty of Science, Leiden University
Date
2022-04-06
Title of host publication
Casimir PhD Series
ISBN (print)
9789085935124

Publication Series

Name
2022-01