Category Archives: RSC

Stability of Unnatural DNA – @PCCP #CompChem


As is the case of proteins, the functioning of DNA is highly dependent on its 3D structure and not just only on its sequence but the difference is that protein tertiary structure has an enormous variety whereas DNA is (almost) always a double helix with little variations. The canonical base pairs AT, CG stabilize the famous double helix but the same cannot be guaranteed when non-canonical -unnatural- base pairs (UBPs) are introduced.

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Figure 1

When I first took a look at Romesberg’s UBPS, d5SICS and dNaM (throughout the study referred to as X and Y see Fig.1) it was evident that they could not form hydrogen bonds, in the end they’re substituted naphtalenes with no discernible ways of creating a synton like their natural counterparts. That’s when I called Dr. Rodrigo Galindo at Utah University who is one of the developers of the AMBER code and who is very knowledgeable on matters of DNA structure and dynamics; he immediately got on board and soon enough we were launching molecular dynamics simulations and quantum mechanical calculations. That was more than two years ago.

Our latest paper in Phys.Chem.Chem.Phys. deals with the dynamical and structural stability of a DNA strand in which Romesberg’s UBPs are introduced sequentially one pair at a time into Dickerson’s dodecamer (a palindromic sequence) from the Protein Data Bank. Therein d5SICS-dNaM pair were inserted right in the middle forming a trisdecamer; as expected, +10 microseconds molecular dynamics simulations exhibited the same stability as the control dodecamer (Fig.2 left). We didn’t need to go far enough into the substitutions to get the double helix to go awry within a couple of microseconds: Three non-consecutive inclusions of UBPs were enough to get a less regular structure (Fig. 2 right); with five, a globular structure was obtained for which is not possible to get a proper average of the most populated structures.

X and Y don’t form hydrogen bonds so the pairing is pretty much forced by the scaffold of the rest of the DNA’s double helix. There are some controversies as to how X and Y fit together, whether they overlap or just wedge between each other and according to our results, the pairing suggests that a C1-C1′ distance of 11 Å is most stable consistent with the wedging conformation. Still much work is needed to understand the pairing between X and Y and even more so to get a pair of useful UBPs. More papers on this topic in the near future.

Unnatural DNA and Synthetic Biology


Ever since I read the highly praised article by Floyd Romesberg in Nature back in 2013 I got really interested in synthetic biology. In said article, an unnatural base pair (UBP) was not only inserted into a DNA double strand in vivo  but the organism was even able to reproduce the UBPs present in subsequent generations.

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Romesberg’s Nucleosides. No Hydrogen bonding is formed between them!

Inserting new unnatural base pairs in DNA works a lot like editing a computer’s code. Inserting a couple UBPs in vitro is like inserting a comment; it wont make a difference but its still there. If the DNA sequence containing the UBPs can be amplified by molecular biology techniques such as PCR it means that a polymerase enzyme is able to recognize it and place it in site, this is equivalent to inserting a ‘hello world’ section into a working code; it will compile but it’s pretty much useless. Inserting these UBPs in vivo means that the organism is able to thrive despite the large deformation in a short section of its genetic code, but having it replicated by the chemical machinery of the nucleus is an amazing feat that only a few molecules could allow.

The ultimate goal of synthetic biology would be to find a UBP which codes effectively and purposefully during translation of DNA.This last feat would be equivalent to inserting a working subroutine in a program with a specific purpose. But not only could the use of UBPs serve for the purposes of expanding the genetic code from a quaternary (base four) to a senary (base six) system: the field of DNA origami could also benefit from having an expansion in the chemical and structural possibilities of the famous double helix; marking and editing a sequence would also become easier by having distinctive sections with nucleotides other than A, T, C and G.

It is precisely in the concept of double helix that our research takes place since the available biochemical machinery for translation and replication can only work on a double helix, else, the repair mechanisms get activated or the DNA will just stop serving its purpose (i.e. the code wont compile).

My good friend, Dr. Rodrigo Galindo and I have worked on the simulation of Romesberg’s UBPs in order to understand the underlying structural, dynamical and electronic causes that made them so successful and to possibly design more efficient UBPs based on a set of general principles. A first paper has been accepted for publication in Phys.Chem.Chem.Phys. and we’re very excited for it; more on that in a future post.

New paper in PCCP: CCl3 reduced to CH3 through σ-holes #CompChem


I found it surprising that the trichloromethyl group could be chemically reduced into a methyl group quite rapidly in the presence of thiophenol, but once again a failed reaction in the lab gave us the opportunity to learn some nuances about the chemical reactivity of organic compounds. Even more surprising was the fact that this reduction occured through a mechanism in which chlorine atoms behave as electrophiles and not as nucleophiles.

We proposed the mechanism shown in figure 1 to be consistent with the 1H-NMR kinetic experiment (Figure 2) which shows the presence of the intermediary sulfides and leads to the observed phenyl-disulfide as the only isolable byproduct. The proposed mechanism invokes the presence of σ-holes on chlorine atoms to justify the attack of thiophenolate towards the chlorine atom leaving a carbanion behind during the first step. The NMR spectra were recorded at 195K which implies that the energy barriers had to be very low; the first step has a ~3kcal/mol energy barrier at this temperature.

 

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Figure 1 – Calculated mechanism BMK/6-31G(d,p) sigma holes are observed on Cl atoms

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1H NMR of the chemical reduction of the trichloromethyl group. Sulfide 4 is the only observed byproduct

To calculate these energy barriers we employed the BMK functional as implemented in Gaussian09. This functional came highly recommended to this purpose and I gotta say it delivered! The optimized geometries of all transition states and intermediaries were then taken to an MP2 single point upon which the maximum electrostatic potential on each atom (Vmax) was calculated with MultiWFN. In figure 3 we can observe the position and Vmax value of σ-holes on chlorine atoms as suggested by the mapping of electrostatic potential on the electron density of various compounds.

We later ran the same MP2 calculations on other CCl3 groups and found that the binding to an electron withdrawing group is necessary for a σ-hole to be present. (This fact was already present in the literature, of course, but reproducing it served us to validate our methodology.)

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Figure 3 – Sigma holes found on other CCl3 containing compounds

We are pleased to have this work published in PhysChemChemPhys. Thanks to Dr. Moisés Romero for letting us into his laboratory and to Guillermo Caballero for his hard work both in the lab and behind the computer; Guillermo is now bound to Cambridge to get his PhD, we wish him every success possible in his new job and hope to see him again in a few years, I’m sure he will make a good job at his new laboratory.

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