The 5th and 6th bases of DNAs
Project Description

The 5th and the 6th base in DNAs

It is generally unthink of if the common four bases of DNA (A:T; C:G) were to have additional components.
In a major group of organisms, the dinoflagellates, this is exactly what happened.
Not only it happened, dinoflagellates are the major symbionts in corals, bleached during coral bleaching, the major red-tide agents and the blue-fluorescence along HKUST prominade in spring night
Dinoflagellates also hold many other records, including the largest genomes, omega-3 etc
Some suggest it is for defence of the genome, some say it is for DNA topology, 5hmu also transend the RNA: DNA pre-life world…………………….

Key questions: what do they do to the DNAs ?
How were they made ?
Are there side benefits ??

The project (2-3 students, depending on experience (e.g. computer search, molecular, or chemical training) will progress from in silico analysis of related enzymes and proteins, to experimental section.

Substantial amount of thymine (60-70%) are replaced by 5-hydroxymethyluracil (5hmu) in dinoflagellate genomes (Rae, 1973; Rae and Steele, 1978; Herzog et al., 1982). 5hmu-containing templates were read correctly (i.e. as T) by DNA polymerases tested, suggesting prevalence of the non-canonical base was unrelated to genome defense(Vilpo and Vilpo, 1995; Zhang, 1999) nor modulation of transcription rates(van Luenen et al., 2012) as in the case of Base J. Bases roll and tilt in relation to each other along the axis of the double helix, and their combined effect on torsion angles in dinucleotides are crucial parameters governing DNA conformation (Johnson et al., 2008; Lawson and Berman, 2008; Svozil et al., 2008).

Supervisor
WONG Joseph Tin Yum
Quota
3
Course type
UROP1000
UROP1100
Applicant's Roles

The project (2-3 students, depending on experience (e.g. computer search, molecular, or chemical training) will progress from in silico comparative analysis of related enzymes and proteins, to experimental section.

Applicant's Learning Objectives

in silico computor search with sequence homology, selected DNA metabolism enzymes
and higher level to gene-knockdown, algal culture and flow cytometric analysis

Complexity of the project
Challenging