Zombies and knots

Constructing the Jones polynomial to save the world

Day 0: smalltowns-ville, IA:

A man picks up his daily slice of breakfast pizza from his local gas station. What he doesn’t know is that it’s his last. By mid-day he feels terrible, by the time he’s ready to go home for dinner he’s already feasting on brains.

Day 4: CDC Headquarters

The Z-virus has spread midwest-wide. You’re working at the CDC as an expert in microscopy. You’re working frantically to get any information on the Z-virus you can. In furtherance of that goal, you decide to image the DNA of the Z-Virus.

DNA knot as seen under the electron microscope. - Image Credit: Javier Arsuaga, CC BY-ND

DNA

Deoxyribonucleic acid (abbreviated DNA) is the molecule that carries genetic information for the development and functioning of an organism.

DNA is made of two linked strands that wind around each other to resemble a twisted ladder — a shape known as a double helix.

Deoxyribonucleic acid (DNA). (n.d.). Genome.gov. https://www.genome.gov/genetics-glossary/Deoxyribonucleic-Acid. Accessed 3 October 2023

фосфатдезоксирибозаосновная цепь Phosphat-Deoxyriboserückgrat Khung xươngPhosphat-deoxyribosePhosphate-deoxyribosebackbone Аденин Adenin AđêninAdenine Цитозин Cytosin XitôzinCytosine Гуанин Guanin GuaninGuanine Тимин Thymin TiminThymine O O P O O O OH O O O P O O OH NH2 N N N N H2N N N N N NH2 N N O H2N N N O O NH N O O HN N O O N NH N N NH2 O N HN N N H2N 3'-конец 3′ Ende Đầu 3'3′ end 5'-конец 5′ Ende Đầu 5'5′ end 3'-конец 3′ Ende Đầu 3'3′ end 5'-конец 5′ Ende Đầu 5'5′ end
Each strand has a backbone. Attached to each sugar is one of four bases: adenine (A), cytosine (C), guanine (G) or thymine (T). The two strands are connected by chemical bonds between the bases: adenine bonds with thymine, and cytosine bonds with guanine.

Deoxyribonucleic acid (DNA). (n.d.). Genome.gov. https://www.genome.gov/genetics-glossary/Deoxyribonucleic-Acid. Accessed 3 October 2023

Photo by Madprime (talk · contribs) - This vector image was created with Inkscape ., CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=1848174

Macro Structure

Circular DNA

Dulbecco and Vogt (1963) and Weil and Vinograd (1963) discovered that double-stranded DNA of the polyoma virus is circular.

Vologodskii, A. V. (n.d.). Circular DNA. In Cyclic Polymers (pp. 47-83). Kluwer Academic Publishers. https://doi.org/10.1007/0-306-47117-5_2

“Supercoiled” DNA

Vinograd, J., Lebowitz, J., Radloff, R., Watson, R., & Laipis, P. (1965) discover that double-stranded DNA can “supercoil”.

Vinograd, J., Lebowitz, J., Radloff, R., Watson, R., & Laipis, P. (1965). The twisted circular form of polyoma viral DNA. In Proceedings of the National Academy of Sciences (Vol. 53, Issue 5, pp. 1104-1111). Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.53.5.1104