Posts Tagged ‘Biology’

Multispectral Chiral Imaging with a Metalens.

Saturday, January 6th, 2018

The title here is from an article on metalenses[1] which caught my eye.

Metalenses are planar and optically thin layers which can be manufactured using a single-step lithographic process. This contrasts with traditional lenses that are not flat and where the optical properties result from very accurately engineered curvatures, which in turn are expensive to manufacture. Metalenses can have built into them many interesting optical properties, including light polarisation and dispersion. Nanoengineering has now resulted[1] in a metalens which can simultaneously present two images of opposite helicity of an object within the same field of view.

What is the relevance to chemistry? Well, a well-known chiroptical technique is known as electronic circular dichroism (ECD). At its simplest, it probes the difference in absorption by a chiral molecule of UV and visible light with opposite circular polarisation. This difference plotted as a function of the wavelength of the light is known as the ECD response. Importantly, this response can also be calculated for either enantiomer of the chiral molecule and hence the absolute configuration can be assigned on the basis of which calculated response matches the observed spectrum. Because the difference in response to the two polarisations of the light (Δε) is actually very small, the ECD technique is intrinsically less sensitive than e.g. normal UV/Visible spectra and this requires the use of expensive instruments to record that small difference. Chiral metalenses offer an interesting future opportunity to create new forms of ECD instrument, perhaps ones that are far more sensitive. In turn, this could lower the costs of acquiring ECD functionality in the standard laboratory (see [2] for an application in teaching laboratories). Very possibly, the most expensive component would in fact then be the computational simulations required to match up with the experimental spectrum!

When metalenses were first introduced, they were only able to lens a limited range of wavelengths. In another article by the same group[3] they now announce a new generation of metalens that covers the region 470 to 670 nm. This excludes the UV regions (<300nm) or the IR regions (>1200nm). The latter covers another important chiroptical instrumental technique known as vibrational circular dichroism, or VCD. As with ECD, the VCD response of a chiral molecule can be pretty well calculated using quantum chemistry and indeed often the VCD method is the only one that can successfully be used to assign absolute molecular configurations.[4] Unfortunately, VCD instruments are even more expensive than ECD ones, again largely due to the intrinsic insensitivity and the need to accumulate data using Fourier Transform methods over many hours. Few chemistry departments have such an instrument. So I will keep an eye out for when an effective chiral metalens operating in infra-red regions is announced! The prospect of routine VCD analyses is tantalising! 

 

References

  1. M. Khorasaninejad, W.T. Chen, A.Y. Zhu, J. Oh, R.C. Devlin, D. Rousso, and F. Capasso, "Multispectral Chiral Imaging with a Metalens", Nano Letters, vol. 16, pp. 4595-4600, 2016. https://doi.org/10.1021/acs.nanolett.6b01897
  2. K.K.(. Hii, H.S. Rzepa, and E.H. Smith, "Asymmetric Epoxidation: A Twinned Laboratory and Molecular Modeling Experiment for Upper-Level Organic Chemistry Students", Journal of Chemical Education, vol. 92, pp. 1385-1389, 2015. https://doi.org/10.1021/ed500398e
  3. W.T. Chen, A.Y. Zhu, V. Sanjeev, M. Khorasaninejad, Z. Shi, E. Lee, and F. Capasso, "A broadband achromatic metalens for focusing and imaging in the visible", Nature Nanotechnology, vol. 13, pp. 220-226, 2018. https://doi.org/10.1038/s41565-017-0034-6
  4. J.I. Murray, N.J. Flodén, A. Bauer, N.D. Fessner, D.L. Dunklemann, O. Bob‐Egbe, H.S. Rzepa, T. Bürgi, J. Richardson, and A.C. Spivey, "Kinetic Resolution of 2‐Substituted Indolines by <i>N</i>‐Sulfonylation using an Atropisomeric 4‐DMAP‐<i>N</i>‐oxide Organocatalyst", Angewandte Chemie International Edition, vol. 56, pp. 5760-5764, 2017. https://doi.org/10.1002/anie.201700977

A form of life that can stably store genetic information using a six-letter, three-base-pair alphabet?

Saturday, December 2nd, 2017

For around 16 years, Floyd Romesberg’s group has been exploring un-natural alternatives (UBPs) to the Watson-Crick base pairs (C-G and A-T) that form part of the genetic code in DNA. Recently they have had remarkable success with one such base pair, called X and Y (for the press) and dNaMTP and d5SICSTP (in scholarly articles).[1],[2] This extends the genetic coding from the standard 20 amino acids to the possibility of up to 172 amino acids. Already, organisms engineered to contain X-Y pairs in their DNA have been shown to express entirely new (and un-natural) proteins.

There is also some measure of controversy. Why? Well, you might spot why with the structures of the bases as shown below.

I first note that d5SICS only has one exemplar in the Cambridge structural database (CSD), with the deoxyribose ring replaced by something quite different. The dNaM sub-structure is rather more abundant (360), although none have a deoxyribose ring attached. So we cannot really tell how these molecules might interact when adjacent (they are after all described as a base pair). But it is unlikely to be via hydrogen bonds, since d5SICS has only C-H groups, and dNaM has no acidic hydrogens either. Hence this base pair is described as being hydrophobic! I might suggest that some small molecule analogues of the two systems above are rapidly made and their crystal structures determined so that we might have at least some data about their interactions (or absence thereof).

If you were set the task of designing some un-natural base pairs to splice into DNA, I doubt you would start with the premise of dropping the complementary base pairing induced by two or three pairs of hydrogen bonds. Of course the integrity of the double helix is retained because of the C-G/A-T base pairs accompanying the hydrophobic d5SICS-dNaM ones. The controversy is about exactly how many such hydrophobic base pairs can in fact be included before the DNA structure becomes unstable to life. 

When I first came across attempts to engineer new forms of DNA (and possibly life), it was directed at replacing the pentose sugar by a hexose,[3] a project that ultimately failed because the resulting DNA was too flexible. Now we have the enthralling prospect of the discovery of many new alternatives to the standard base pairs, with biochemical consequences I cannot even begin to imagine! 

References

  1. A.W. Feldman, M.P. Ledbetter, Y. Zhang, and F.E. Romesberg, "Reply to Hettinger: Hydrophobic unnatural base pairs and the expansion of the genetic alphabet", Proceedings of the National Academy of Sciences, vol. 114, 2017. https://doi.org/10.1073/pnas.1708259114
  2. D.A. Malyshev, K. Dhami, H.T. Quach, T. Lavergne, P. Ordoukhanian, A. Torkamani, and F.E. Romesberg, "Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet", Proceedings of the National Academy of Sciences, vol. 109, pp. 12005-12010, 2012. https://doi.org/10.1073/pnas.1205176109
  3. M. Egli, P.S. Pallan, R. Pattanayek, C.J. Wilds, P. Lubini, G. Minasov, M. Dobler, C.J. Leumann, and A. Eschenmoser, "Crystal Structure of Homo-DNA and Nature's Choice of Pentose over Hexose in the Genetic System", Journal of the American Chemical Society, vol. 128, pp. 10847-10856, 2006. https://doi.org/10.1021/ja062548x