4.1 DNA Read

Question (i). The DNA responsible for encoding traits related to cognitive abilities (because maybe this can help us uncover the phenomenon of cognition, like if we align the sequences from organisms with varying stages of intelligence).

Question (ii).

Oxford Nanopore Technologies, third-generation; this enables ultra-long reads which could be beneficial since we don’t know how long our target fragment is.

Input would be genomic DNA (gDNA) extracted from brain tissues of peripheral blood samples using DNA extraction kits (like from Qiagen or whatever)

• then the quality of the DNA should be assessed (e.g. electrophoresis, spectrophotometry)
• then DNA fragmentation can be carried out if the target sequence is too long
• then we PCR the templates, purify, and attach ONT adaptors to amplicons
• then prepare the library for sequencing.

Sequencing:

• Load the prepared library onto an ONT flow cell
• Choose a sequencing device based on throughput needs
• Run

Data: raw data should be in FAST5 format (electrical signal data); they can be converted into FASTQ files with ONT software. Data from multiple species can be aligned, annotated, and functionally analyzed.

4.2 DNA Write

Question (i). I once had an idea about building release-inducible 3D DNA origami that can be used to contain insulin. These can then be put into patients with blood sugar monitoring and engineered probiotics that secrete the insulin release signal when the patient’s blood sugar is low. However, this idea remains on the paper since 1) I’m not familiar with DNA origami yet and 2) Putting probiotics in blood may cause sepsis even if we add the “don’t eat me” signal.

Question (ii). chip-based DNA synthesis, since it offers high-throughput synthesis.

• surface functionalization
• chip array layout design
• nucleotide deposition: photolithography-based synthesis
  • photomask exposes regions of the chip to light;
  • light removes a protecting group;
  • a single type of nucleotide is flowed over the chip and attaches to deprotected regions.