Discovery of Liquid Crystals in Short DNA

Original paper: End-to-End Stacking and Liquid Crystal Condensation of 6- to 20- Base Pair DNA Duplexes

Ever since its discovery, scientists have known that the DNA molecule is present in every life form. It carries the genetic information of all living organisms and many viruses. Today, however, we will strip DNA of its genetic importance and look at it from a different perspective. We will discuss why DNA attracts attention even outside of the biological context: What is the connection between DNA and liquid crystals? What are end-to-end stacking interactions and why are they important? If you want to get answers on these questions (and many more), keep reading.

The chemical structure of DNA is intimately related to its geometry and physico-chemical properties. In water-based solutions, DNA is negatively charged. Since like charges repel, one DNA molecule pushes others away, effectively claiming  some  volume of space for itself [1]. Because electric repulsion decreases with distance, two DNA molecules cannot feel any kind of interactions when they are far away from each other. These features make it possible, together with DNA’s rod-like geometry, to model short DNA fragments (in this context, the term “DNA fragment” refers to an individual DNA molecule that’s much shorter than the length of a gene [2]) in a simplified way, as a hard repulsive rod (Fig.1.).

Fig. 1. Structure of double-stranded DNA. Hydrophilic sugar-phosphate backbone is on the ‘outer’ side of the molecule, while hydrophobic nitrogenous bases are found on the ‘inner’ side. However, for simplicity, short DNA fragment is often modeled simply as hard repulsive rod (blue cylinder).

In the 1940s, researchers found that DNA molecules, when placed in solutions of water and salt, form liquid crystal (LC) phases. We all know the three phases of matter: gas, liquid and solid. LCs are substances that don’t fall into any of these categories. They are an intermediate phase that has properties of liquids as well as those of solid crystals — LCs can flow like liquids, but there is still some degree of order between the molecules. There are many types of liquid crystalline phases, the simplest of which is called the nematic phase. In the nematic phase, rod-like molecules (the “hard rods” of DNA in this case) point in the same direction on average [3]. This property gives nematic liquid crystals the ability to show colorful LC textures under a microscope equipped with a polarized light source (Fig. 2. b) [4].

According to theory, repulsive hard rods show the transition from a disordered fluid phase (called the isotropic phase) to the nematic LC phase only if they are sufficiently long and thin [1]. Almost 50 years later, Bolhuis and Frenkel confirmed this prediction by computer simulation [5].

In case of DNA, simulations predict that one shouldn’t expect to observe LCs for DNA fragments shorter than approximately 9 nm. So, when the authors of today’s paper observed LC textures in very short DNA fragments–  from approximately 2 to 7 nm — under a polarized-light microscope, it came as a real surprise.

Fig. 2. a) With increasing concentration, a substance which shows liquid crystal behavior can undergo transitions between isotropic, nematic and columnar phase. b) Colorful textures of nematic liquid crystals visible under the microscope.

To understand this result,  let’s look in more detail at why hard rods in a solution begin to point in the same direction as their  concentration increases. In 1949, Lars Onsager published a paper in which he explained the entropic [1] origin of isotropic-nematic phase transition for hard rods. Entropy is usually understood as a measure of disorder. How then can the formation of liquid crystals lead to the increase of the total entropy in the system? To answer this question, we should understand the entropy as a measure of the number of possible configurations a system can have at a given state. According to Onsager, there is a balance between two contributions to the total entropy: while the number of different orientations available to each rod decreases in the process of ordering (decreased number of possible configurations), the centers of rods are able to move around more freely (Fig. 3.). The net effect is an increased number of possible configurations, which leads to an increase of total entropy in the system [6].

Fig.3. Rods in a) parallel orientation and b) perpendicular orientation In the situation in (a), the rods are unable to rotate, but can translate (move in the way that all points of the rods move in the same direction and the same distance) freely, while in (b) the rods can rotate more feely but their translation is restricted.

The authors found that LC phases of short DNA share all the basic features of LC phases observed in long DNA fragments. As well as forming a nematic phase [3] at lower concentrations, with increasing concentration they undergo a transition to the columnar phase, where the molecules lie on top of each other in layers within which they often form hexagonal structure, as shown in Fig 2. a).

But how can LC ordering happen in  solutions of short DNA? It turns out that our simplified picture of DNA as a negatively charged rod was a bit too simple. To understand why, we need to learn a little more about the physico-chemical properties of the DNA molecule.  As shown in Fig. 1, the inside of DNA is made up of chemicals called nitrogenous bases. Like cooking oil or the surface of a teflon pan, these ‘water-fearing’ hydrophobic molecules tend to minimize their contact with water. However, at the terminal end of a short piece of DNA, some of the nitrogenous bases will be exposed to water. This is unavoidable — unless another DNA terminal end happens to be nearby. In that case, the ends tend to stick together to minimize their contact area with the surrounding water. This attraction between terminal ends of DNA is called the end-to-end stacking interaction and causes the formation of long, thin rods. And, as we already discussed, these rods are exactly the shape that gives rise to Onsager’s nematic phase.

If the main driving force for the formation of LCs in short DNA fragments is end-to-end stacking of terminal ends, the absence of these interactions should prevent LC ordering in the system. To disrupt end-to-end stacking interactions, authors chemically modify  their DNA fragments to disturb the attractive interactions between the terminal ends. By doing this, they can prevent the formation of LC phases in short DNA duplexes [7]. This experiment serves as another confirmation that end-to-end stacking interactions are indeed necessary to drive short DNA fragments to the formation of more ordered phases.

Fig 4. End-to-end stacking of short DNA molecules  and the formation of nematic and columnar liquid crystal phases.

The research presented in this post provides a deeper understanding of the interactions that drive self-assembly of DNA and identifies a new type of interaction: hydrophobic end-to-end stacking between terminal ends of DNA. Identifying end-to-end stacking interactions represents another step towards better understanding of DNA as a generic (instead of genetic) building material and deciphering all of its unique properties.

[1] L. Onsager, Ann. N.Y. Acad. Sci. 51 (1949) 627-659

[2] For comparison, the smallest human genes, which are made up from DNA, are ‘only’ a few hundred nanometers long, while others are nearly a millimeter; every human cell contains approximately 2 meters of DNA in total.

[3] Double-stranded DNA is a chiral molecule with helical structure. For this reason, the nematic phase formed in solutions of DNA is called a  chiral nematic, and has different properties from a “plain-vanilla” nematic phase. However, this distinction is not relevant for us in this post.

[4]  Liquid crystals have the ability to change the direction of light polarization. This ability is called birefringence and it is responsible for the colorful textures of liquid crystals which we can observe under a microscope equipped with a polarized light source, but is also basic operating principle of modern TV and computer screens: Liquid Crystal Displays (LCDs).

[5] P. Bolhuis, D. Frenkel, J. Chem. Phys. 106 (1997) 666

[6] For further reading on this topic see: D. Frenkel, Nature materials 14 (2015) 9-12.

[7] M. Nakata, G. Zanchetta, B. D. Chapman, C. D. Jones, J. O. Cross, R. Pindak, T. Bellini, N. A. Clark, Science 318 (2007) 1276-1279

2 Replies to “Discovery of Liquid Crystals in Short DNA”

    1. These DNA origami rods are much stiffer and longer then rods in Nakata’s paper but it is indeed very interesting approach to the engineering of liquid crystals. Maybe it could be one of our future posts. 🙂 Thank you for your comment!

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