Week 2 HW: DNA Read, Write, & Edit

PART 1: Benchling & In-Silico Gel Art

Lecture Prep Homework questions from Professor Jacobson

1. The human genome is ~3.1 billion base pairs long. DNA polymerase makes roughly one error per 10 to the five nucleotides. Without correction, this is fairly error prone as it would make roughly 30,000 errors per genome replication. Luckily, human biology has interesting error correction measures including the mismatch repair system. The mismatch repair system recognises base-base mismatches and insertion/deletion mispairs through the complexes of MutS-related proteins that recognise nicks in the DNA strands.
2. There are over a million ways to code an average human protein. Not all the possible codes can work for a protein of interest due to codon rarity and context-dependent protein production.

Homework questions from Dr. LeProust

1. The most commonly used method for oligo synthesis is solid-phase phosphoramidite synthesis.
2. It is difficult to make oligos longer than 200nt via direct synthesis due to a reduction in coupling efficiency and the buildup of truncated sequences.
3. You cannot make a 2000bp gene via direct oligo synthesis because there is a break down in sequences as we try to assemble longer ones. The longer the synthesis, the lower the yield and efficiency and the higher the truncated products generated.

Homework questions from George Church

1. The 10 essential amino acids in all animals are: Leucine (L), Lysine (K), Isoleucine (I), Valine (V), Histidine (H), Methionine (M), Phenylalanine (F), Threonine (T), Tryptophan (W), Arginine (R).