Tag: DNA

Minelise’s comment on: Synthesis and Direct Observation of Thermoresponsive DNA Copolymers

By Minelise E. Rivera

MER blog image 18-05

In this paper, Li and Schroeder use single molecule techniques to have a direct observation on DNA-PNIPAM copolymers. First, they synthetized DNA-PNIPAM copolymers using a two-step strategy based on polymerase chain reaction (PCR) for generating linear DNA backbones containing dibenzocyclooctyne-dUTP, then grafted thermoresponsive side branches (PNIPAM) onto DNA backbones using copper-free click chemistry. Subsequent single molecule fluorescence spectroscopy studies unveiled more clearly the molecular heterogeneity association with the stretching and relaxing of the polymer above and below their LCST. Their results showed that intramolecular conformational dynamics of DNA-PNIPAM copolymers are affected by properties of the branches like molecular weight, density, leading to a change in transition temperatures. In other words, the single molecule technique provided a better understanding in a molecular perspective of chemically heterogeneous and stimuli-response polymers.

As I read this paper and looked for information to better understand it, I was amazed by the details with which they worked with throughout their study. I would have thought of working better with a bunch of them instead of just single molecules. It didn’t cross my mind that someone was going to, not only synthesized the molecule, but also study its characteristics. It was very interesting to learn about the methods that they used for characterization and synthesis. It got me wondering if those methods were the only ones that would work in this case and why. But, what I think that was very useful for me is that I got to understand better the importance of the LCST and the role that it played in their system. It reminded me of our project in which the SGQ self-assembles into the SHS and how it is to study it and understand its influence in the SHS as it was important for the copolymers with which it was worked with in the paper.

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Kiara’s comment on: A 2,7-diamino-1,4,8-triazanaphthalene derivative selectively binds to cytosine bulge DNA only at a weakly acidic pH

By Kiara N. Villa Del Valle

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This paper focuses reports how through a change in the pH, their compound gets protonated and through hydrogen bonds, the compound and the base binds. Lastly, the better-known DNA structure the double helix, but there are other varieties such as hairpin loops, interior loops, multi-branched loops and bulge loops. Bulge loops, are when an extra base winds up on one side of the DNA strand. This can happen when the helix missing a base or an extra one was inserted during the DNA copying process. This anomaly can cause cancer or triplet diseases. They first performed experiments to determine the pH dependence if the azaDANP. They changed the pH from 1.0 to 9.0 and it shows a hypochromic and hypsochromic shifts as the pH was changing. They also plotted the absorption in terms of the pH and determined a pKaH (pKa of the protonated form) of 4.3, a lower pKaH of 6.8 for a previously described compound. This decrease was due to the decreased basicity of the ring nitrogen by the substitution at C4-N. To get information about the azaDANP binding to the C-bulge, they simulated possible complexes between azaDANP and cytosine, it showed that the protonation likely occurs at N1 for the complex formation. They performed more experiments to measure the absorption spectra of azaDANP in presence of T, G, A and C bulged DNA, at pH 7.0 and 5.5 at room temperature. We want to focus in this, at 5.5 pH there is a new absorption band at 407 nm that in neutral pH is not observed and therefore suggesting that the formation is pH sensitive. The thermal stability of the azaDANP-C-bulge was investigated with absorption with variable temperature. We can see that the peak observed at 407 nm at 2 °C decreases as the temperature is increased to 80 °C. This shows the equilibrium of azaDANP and GCG/CC DNA to form a binary complex and, therefore, appearing to be temperature dependent.

 

Aikawa, 2017. A 2,7-diamino-1,4,8-triazanaphthalene derivative selectively binds to cytosine bulge DNA only at a weakly acidic pH

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José’s comment on: Intelligent, Biodegradable, and Self-Healing Hydrogels Utilizing DNA Quadruplexes

By José M. Martinez

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This paper is about making of a water based gel made from the supramolecular interactions of guanosine rich oligonucleotides. They attached these oligonucleotides symmetrically into the ends of PEG chains of variable lengths and conformations. This was made through High Efficiency Liquid Phase (HELP) synthesis. This synthetic strategy, as its name says, occurs in a liquid phase instead of the usual solid phase synthesis. The purpose of this is to allow them to obtain greater quantities of product more easily without risking the effectiveness. These DNA-PEG-DNA monomers have the ability, when diluted and presented with a cation (K+ or Na+), to self-assemble its DNA moieties through non-covalent interactions to for G-quadruplexes. Those strong interactions change the physical properties of the solution by forming a hydrogel. In the study, it was proven that the concentration of the cation required to trigger the self-assembly is relatively small. It is even compared to the concentration of salts found in body-related fluids like sweat, saliva, and tears. The hydrogel also has the capability to heal itself and interact by diffusion with another of the same kind. Finally, it was found that by adding a few extra nucleotides to the DNA moiety of the monomer and a matching strand for that part, the G-quadruplexes could be disassembled, returning the gel back to its liquid phase. All the previously stated properties indicate potential uses of this hydrogel for biomedical purposes.
Regarding myself, I learned mostly about the molecular aspect of gels and how they are formed. It was very interesting seeing the role that the supramolecular interactions played in the formation of this particular gel and the experiments made to investigate further into its properties.

JMM: Tanaka, 2017. Intelligent, Biodegradable, and Self-Healing Hydrogels Utilizing DNA Quadruplexes

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