Total Pageviews

Tuesday, June 28, 2011

Interested in optical rulers? Well, which kind!?

Recently, three-dimensional plasmon rulers based on nano-rods are reported on Science. Hopefully, it will be cool weaponry for measuring the structures of the molecules in the near future. Over the past few decades, optical rulers based on different principles emerged from various branches of optical science. At the same time, researchers are trying hard to push each methodology to the limit. Optical Rulers, as a result, attract an army of researchers and spin off fruitful results. A quick summary of them seems to be a fair amount of content for everyone.

First thing first, what does an optical ruler do? Quite straightforward, it measures the dimensions of the molecular structures. For example, what is the distance between two subunits of a hemoglobin protein? What is the height of a membrane protein when measured from the membrane surface? Put into one sentence – optical rulers are aimed to map out the 3D structures of the molecules such that we can use this information to figure out the functionality of the molecules.

First ruler comes to your mind, I guess, will be the technique of X-ray diffraction. It is a true powerful optical ruler. After all, the DNA structure is solved by it, and Nobel Prize acclaims this technique for more than once. It has great resolution ~ 1Å, and you do not have put anything attached to the molecules. However, the pitfall is that, you have to crystallize the molecules which are merely impossible for some molecules, and the crystal forms of the molecules are in general, not the in vivo forms of the molecules. A report on C&EN and JACS beautifully illustrate the structure changes dramatically depending on the environment.

What is the king of in vivo optical ruler? I would say so far it is NMR. It has the resolutions of a few Å, and the algorithm is advanced so much that complex proteins are revealing their true forms (through more advanced multi-dimensional NMR). The principle is very similar to the trick we play with tuning forks. If you hit on one of the forks and bring the other replica close in, you feel the vibration on the second one and actually both will make the same tone without two touching each other. The energy (in terms of sound wave) resonates in these two forks. In NMR, intrinsic atomic spin plays the role of the tuning fork. By incorporate the isotopes (such as 1H 13C and 15N, these atoms have nonzero spins) into the amino acids of the proteins, the spins of these atoms behave like tuning forks with different tones. Imaging if there are two or more isotope atoms close to each other, the energy (in this situation, the microwave qunta) will be transferred between the isotopes (let’s say between 1H and 15N) assuming one of them is excited by microwave. NMR is specialized in measuring this energy transfer. The closer they are the more efficient energy transfer is. This efficiency drops proportional to 1/r^-6, where r is the distance between two spins. Now, if you have many of these isotope atoms located at different amino acids of a protein, you can figure out which isotopes (or more interestingly, which amino acids) are closer to each other. With the help of computer, you can infer the structures of the proteins, much like a complex trigonometry based on the relative positions of the spins.

Figure 1. A typical 2D NMR spectrum. Each blob can be thought as a sign of energy transferring between the spins of some specific hydrogen and nitrogen. By doing this kind of cross mapping, we can figure out the 3D structure of the molecules.
Two other techniques, Förster resonance energy transfer (FRET) & multi-dimensional IR spectroscopy, utilize similar principles we just described. In FRET, fluorescent dyes are attached the molecules of interest and lasers with optical frequencies are often used. If you excite one of the dye with the laser, and if the second dye is very close to the first dye, you can actually observe the light emitted from the second dye, much like the tuning fork instance we mentioned. It has the resolution of ~ nm and is widely used in biological society. On the other hand, multidimensional IR spectroscopy uses intrinsic vibrational modes of the molecules, such as the stretching mode of C=O. C=O is abundant in a protein which makes it very attractive. Through this technique, you can follow the energy is transferring from one C=O to another, and figure out the distances between two amino acids. The resolution is also in the Å scale. Another neat thing about it is that, multi-dimensional IR is able to monitor the structural change in fs to ps time scale, and this makes it very unique.

Last but not least, let’s touch the topic that initiates this short article – an optical ruler based on plasmon. As you may already learn, the plasmon is some electrons oscillating on the surface of a nano-rod. Lasers with optical frequencies are very effective in exciting these plasmon modes. Another thing you also need to know is that, plasmon modes are sensitive to the surrounding, especially when there are other nano-rods around. Again, just like the tuning fork, energy (in terms of plasmons) that locates on one nano-rod can hop onto another nano-rod. The efficiency of this hopping, and the resonant frequency of the plasmon mode are highly dependent on the overall geometry of the nano-rods and the distance among them. This is the principle we are applying. The ruler is composed of 5 nano-rods (figure 2), carefully spaced to each other. Depending on the overall geometry, the transmission spectra of the ruler is changing dramatically. This change serves as a “legend” for 3D mapping (figure 3). 

Figure 2. 3D layout of the plasmon ruler. The nano-rod in the middle has a dimension of  40*80*260 nm and is directly excited by the light source. Courtesy of N. Liu, M. Hentschel, T. Weiss, A. Alivisatos, and H. Giessen in Science 332 1407 (2011).

Figure 3. Depending on the relative position of the middle rod with respect to the other four, the transmission at certain wavelengths (as pointed out as resonance I and II) changes dramatically. This is the optical legend that can be used to infer the relative positions of the rods. Courtesy of N. Liu, M. Hentschel, T. Weiss, A. Alivisatos, and H. Giessen in Science 332 1407 (2011).
The future goal will be attaching this genre of nano-rods onto different domains of the molecules and monitoring the spectra of them. By doing so, you can figure out the distance among the rods and then map out the distances among different domains of the molecules (figure 4).

Figure 4. By attaching the nano rods (shown in yellow) onto different domains of the molecule, we can infer the 3D structure of it by interpreting the spectra of the nano rods. Courtesy of A. Mastroianni, S. Claridge, and A. Alivisatos in JACS 131 8455 (2009).
Well, next time when people are interested in optical ruler, maybe you should just say: “which kind of them are you interested!?”

The opinions expressed herein are those of the author and do not represent the Optical Society of America (OSA) or any OSA affiliate.

No comments:

Post a Comment