This entry is part 1 of 1 in the series "NB Chemotherapy" --

WARNING: Science Content

As with all my posts, I try to include some thought provoking science, as well as interesting water cooler talk.  Good luck.


Prerequisite Reading

Some DNA Basics

DNA Replication and Torsional Strain


Liam’s Rounds 1 and 2

The first chemotherapy drugs in Liam’s treatment were topotecan and cyclophosphamide. He received two five-day treatments with these drugs.  The first was during Aug 2014 and the second was in Sept. 2014 (separated by four weeks).

The drugs are given together for a combined treatment that offers a synergistic effect.  In his case, they proved to be very effective.  His cancer could not be found in a PET scan after just one round. (This doesn’t mean that his cancer wasn’t present, just that the much of the solid mass tumors were no longer taking up glucose … in other words – dead or dying.)


Even though chemotherapy drugs are often given in pairs to give a compounded blow to the cancer, in these blog posts I will explain the mechanism of each drug individually so that it can be digested by the audience.

Fig 1. Topotecan


Topotecan is a topoisomerase I inhibitor which is derived from a plant called the Asian “Happy Tree” (Camptotheca acuminata).[1]  Topoisomerase I, discussed in a previous blog post,  is an enzyme that relieves torsional strain ahead of the advancing DNA replication fork. Without this torsional strain relief, the DNA is too strained to be able to separate into two strands.

A chemical mechanism for how topotecan inhibits topoisomerase I is proposed in the Proceedings of the National Academy of Sciences. [2]  The authors suggest that as the one side of the DNA is pulled apart by topoisomerase I, the topotecan molecule wedges (intercalates) between the +1 and −1 bases of the duplex DNA, and is further stabilized by six different protein contacts while the DNA is open. (Think of jamming a zipper, and then sewing the thing that is lodged in the zipper in place.)

Ribbon Diagram of regular Topoisomerase I breaking one side of the DNA

Fig 2 – Ribbon Diagram of regular Topoisomerase I breaking one side of the DNA, used by permission [3] PNAS, 99, 24, pp. 15387- 15392

The intercalation of topotecan causes a shift of the downstream bases by ~3.6 Angstroms (defining the displacement that this monkey wrench causes in the system). Figures 2 and 3 show ribbon diagrams of both the regular process and the process that is poisoned by topotecan.

Ribbon Diagram of Topoisomerase I with Topotecan interfering with the process.

Fig 3 – Ribbon diagram of topoisomerase I with topotecan interfering with the process, used by permission [4] PNAS, 99, 24, pp. 15387- 15392

An article in Nature [5] provides evidence that topisomerase I is inhibited (poisoned) more readily when the forming supercoil has a positive coiling direction. Topotecan has the effect of being a monkey wrench in the topoisomerase I process.

In slightly easier to understand terms, the topotecan is just the perfect shape with just the right bonding attachments to act like something getting stuck in a zipper.  Eventually, with enough vibrations and thrashing about, the topotecan will get unstuck, but cancer is impatient with the process and typically triggers the apoptosis alarm (cell death trigger) before it can work the topotecan out of the zipper.

License Number  3681730918315, 8/4/2015, NATURE PUBLISHING GROUP LICENSE

Fig 4 – Cover art that shows a good overall picture of the topotecan poisoning process. Reprinted and adapted by permission from Macmillan Publishers Ltd: Nature, 448, 213-217, copyright 2007



  2. PNAS, 99, 24, pp. 15387- 15392 (26 Nov. 2002), “The mechanism of topoisomerase I poisoning by a camptothecin analog”PNAS Cover
  3.  Anyone may, without requesting permission, use original figures or tables published in PNAS for noncommercial and educational use (i.e., in a review article, in a book that is not for sale) provided that the original source and the applicable copyright notice are cited.
  4. See note 3
  5.  Nature 448, pp. 213-217 (12 July 2007), “Antitumour drugs impede DNA uncoiling by topoisomerase INature Artwork

DNA Replication and Torsional Strain

This entry is part 2 of 2 in the series "DNA" --

WARNING: Science Content

As with all my posts, I try to include some thought provoking science, as well as interesting water cooler talk.  Good luck.

A Schematic / Block Diagram


Many enzymes work together in the replication of DNA. The focus of this post will be on the topoisomerase enzymes and their function. In another upcoming post, I will introduce topoisomerase inhibitors. It is important to understand what is going on with these enzymes and how the topoisomerase enzymes work to relieve torsional strain during DNA replication.  

Torsional Strain

When DNA is at equilibrium and not under any torsional strain, one full rotation of the double helix contains 10.6 base pairs.  When it is replicated, the entire DNA strand has to be divided into two new strands. This separation introduces a significant amount of torsional strain in the DNA coil. (Think of that handset cord on your desk phone that is completely tangled up because of all of the rotations of the handset over time.) This process of DNA entanglement is called supercoiling.  The only way to relieve the strain is to break the DNA, pass a segment through, and put it back together.  The topoisomerase enzymes do just that. They relieve the mounting torsional strain before the strain becomes so great that the replication process is halted. Still confused? Take a look at this video.

Some DNA Basics

This entry is part 1 of 2 in the series "DNA" --

WARNING: Science Content

As with all my posts, I try to include some thought provoking science, as well as interesting water cooler talk.  Good luck.

Deoxyribonucleic acid (DNA)

12 Base Pairs of DNA. For those of you not familiar with chemistry, but think you know what an atom is, each stick in this figure represents a bond between atoms. The color of the stick represents the atom that is being bonded to. If the stick line changes from one color to a different color, then you are bonding two different types of atoms together. (i.e. Grey to White = Carbon bonded to Hydrogen) You’ll also notice that some atoms bond to multiple things and others not so many. How many things it attaches to is determined by where it is on the periodic table of the elements. (Don’t worry about this, just appreciate that different atoms bond to different numbers of other atoms.)

There Is a Lot of It.

As we have mentioned before in a different post, there are about 3 billion base pairs of DNA over 46 chromosomes (23 pairs).  This count is for each cell in your body. You have about 70 trillion cells in your body. Yes, that is 70,000,000,000,000 copies of your complete DNA. (For those of you heady in math, that is 210,000,000,000,000,000,000,000 base pairs in your body right now.)

DNA Is a Storage System

DNA is an elegant storage system, and every time that I stop and think about what it is, I marvel at its simple, yet complex nature. The rotating picture to the right is 12 base pairs. The two separate helices are the attachment points of each side of the base, and the base pairs are the flat planes of atoms that connect one helix to the other. (Go ahead and take a moment and convince yourself that there are only 12 base pairs here. I know that you want to!)

The base pair that is in the center is not “technically” bonded. They are held together with a much weaker force than the standard covalent bond.  They are held together with “hydrogen bonding“.  Hydrogen bonding is an electrostatic force that only exists when hydrogen is bonded to a Flourine, Oxygen, or Nitrogen atom.  When hydrogen is taking part in hydrogen bonding, it acts like a strong magnet would if it were fastened to one piece of metal, and another piece of metal got close to it. DNA would be useless without this weak interaction.  It needs to be able to separate easily.  If it were covalently bonded across the base pairs, it would be useless.  (If you look closely at the rotating DNA picture, you will notice that the base pairs are shown with a break between them. The hydrogen bond between them is just strong enough for the base pairs to line up to one another.)


A closer look at base pairs

A Closer Look at the base pairs (Thanks to Zephyris on Wikipedia). Each of the four base pairs have names, but to keep it simple, they are abbreviated with the letters A,T,C, and G.  —“A” hydrogen bonds to “T”  — “C” hydrogen bonds to “G” — Also notice that the hydrogen bond between the base pairs is represented by a dashed line. (i.e. Not quite as strong as a regular old covalent bond)


DNA Must Break Apart

As a storage system, DNA must continually break apart in order to be read or to be duplicated.  When it is in its double helix form, it is pretty. It is in storage. It just sits there. Hydrogen bonding (which is not nearly as strong as a regular bond) can break apart easily. It can be put together easily. There are two main events that occur with DNA. Copying the DNA strand, and reading the DNA in order to produce the biological machines in the human body that are comprised of proteins.

The following videos describes how the DNA is broken apart and either copied or transcribed.

The Focus of Many Chemotherapy Agents

The main Chemotherapy drugs that are used (at least for Neuroblastoma) focus on the interruption of the copying process. An interruption of the copying process triggers the oncogenes in the cell to cause apoptosis (cell death). While healthy cells have the means and time to do their best job at repairing the cell before sounding the apoptosis alarm, cancer cells are not nearly as patient. When they discover that there is a problem with DNA replication, they will often give up… At least until they assimilate the knowledge of how to repair the DNA or the knowledge of how to keep the chemotherapy drugs out of their cell walls. This adaptation leads to the demise of the effectiveness of chemotherapy drugs in their fight against cancer.