Tag Archives: Grzegorz Krzyżewski

Synthetic genetics and imprinting a sequence of a single DNA (deoxyribonucleic acid) strand

Caption: A polymer negative of a sequence of the genetic code, chemically active and able to bind complementary nucleobases, has been created by researchers from the Institute of Physical Chemistry of the Polish Academy of Sciences in Warsaw. Credit: IPC PAS, Grzegorz Krzyzewski

Those are very large hands! In any event, I think they left out the word ‘model’ when describing what the researcher is holding.

A Jan. 19, 2017 news item on phys.org announces the research from the Institute of Physical Chemistry of the Polish Academy of Sciences (IPC PAS),

In a carefully designed polymer, researchers at the Polish Academy of Sciences have imprinted a sequence of a single strand of DNA. The resulting negative remained chemically active and was capable of binding the appropriate nucleobases of a genetic code. The polymer matrix—the first of its type—thus functioned exactly like a sequence of real DNA.

A Jan. 18, 2017 IPC PAS press release, which originated the news item, provides more detail about the breakthrough and explains how it could lead to synthetic genetics,

Imprinting of chemical molecules in a polymer, or molecular imprinting, is a well-known method that has been under development for many years. However, no-one has ever before used it to construct a polymer chain complementing a sequence of a single strand of DNA. This feat has just been accomplished by researchers from the Institute of Physical Chemistry of the Polish Academy of Sciences (IPC PAS) in Warsaw in collaboration with the University of North Texas (UNT) in Denton, USA, and the University of Milan in Italy. In an appropriately selected polymer, they reproduced a genetically important DNA sequence, constructed of six nucleobases.

Typically, molecular imprinting is accomplished in several steps. The molecules intended for imprinting are first placed to a solution of monomers (i.e. the basic “building blocks” from which the future polymer is to be formed). The monomers are selected so as to automatically arrange themselves around the molecules being imprinted. Next, the resulting complex is electrochemically polymerized and then the imprinted molecules are extracted from the fixed structure. This process results in a polymer structure with molecular cavities matching the original molecules with their size and shape, and even their local chemical properties.

“Using molecular imprinting, we can produce, e.g. recognition films for chemical sensors, capturing molecules of only a specific chemical compound from the surroundings – since only these molecules fit into the existing molecular cavities. However, there’s no rose without a thorn. Molecular imprinting is perfect for smaller chemical molecules, but the larger the molecule, the more difficult it is to imprint it accurately into the polymer,” explains Prof. Wlodzimierz Kutner (IPC PAS).

Molecules of deoxyribonucleic acid, or DNA, are really large: their lengths are of the order of centimetres. These molecules generally consist of of two long strands, paired up with each other. A single strand is made up of nucleotides with multiple repetitions, each of which contains one of the nucleobases: adenine (A), guanine (G), cytosine (C), or thymine (T). The bases on both strands are not arranged freely: adenine on one strand always corresponds to thymine on the other, and guanine to cytosine. So, when we have one thread, we can always recreate its complement, which is the second strand.

The complementarity of nucleobases in DNA strands is very important for cells. Not only does it increase the permanence of the record of the genetic code (damage in one strand can be repaired based on the construction of the other), but it also makes it possible to transfer it from DNA to RNA in the process known as transcription. Transcription is the first step in the synthesis of proteins.

“Our idea was to try to imprint in the polymer a sequence of a single-stranded DNA. At the same time, we wanted to reproduce not only the shape of the strand, but also the sequential order of the constituent nucleobases,” says Dr. Agnieszka Pietrzyk-Le (IPC PAS).

In the study, financed on the Polish side by grants from the Foundation for Polish Science and the National Centre for Science, researchers from the IPC PAS used sequences of the genetic code known as TATAAA. This sequence plays an important biological role: it participates in deciding on the activation of the gene behind it. TATAAA is found in most eukaryotic cells (those containing a nucleus); in humans it is present in about every fourth gene.

A key step of the research was to design synthetic monomers undergoing electrochemical polymerization. These had to be capable of accurately surrounding the imprinted molecule in such a way that each of the adenines and thymines on the DNA strand were accompanied by their complementary bases. The mechanical requirements were also important, because after polymerization the matrix had to be stable. Suitable monomers were synthesized by the group of Prof. Francis D’Souza (UNT).

“When all the reagents and apparatus have been prepared, the imprinting itself of the TATAAA oligonucleotide is not especially complicated. The most important processes take place automatically in solutions in no more than a few dozen minutes. Finally, on the electrode used for electropolymerization, we obtain a layer of conductive polymer with molecular cavities where the nucleobases are arranged in the TTTATA sequence, that is, complementary to the extracted original”, describes doctoral student Katarzyna Bartold (IPC PAS).

Do polymer matrices prepared in this manner really reconstruct the original sequence of the DNA chain? To answer this question, at the IPC PAS careful measurements were carried out on the properties of the new polymers and a series of experiments was performed that confirmed the interaction of the polymers with various nucleobases in solutions. The results leave no doubt: the polymer DNA negative really is chemically active and selectively binds the TATAAA oligonucleotide, correctly reproducing the sequence of nucleobases.

The possibility of the relatively simple and low-cost production of stable polymer equivalents of DNA sequences is an important step in the development of synthetic genetics, especially in terms of its widespread applications in biotechnology and molecular medicine. If an improvement in the method developed at the IPC PAS is accomplished in the future, it will be possible to reproduce longer sequences of the genetic code in polymer matrices. This opens up inspiring perspectives associated not only with learning about the details of the process of transcription in cells or the construction of chemosensors for applications in nanotechnologies operating on chains of DNA, but also with the permanent archiving and replicating of the genetic code of different organisms.

Here’s a link to and a citation for the paper,

Programmed transfer of sequence information into molecularly imprinted polymer (MIP) for hexa(2,2’-bithien-5-yl) DNA analog formation towards single nucleotide polymorphism (SNP) detection by Katarzyna Bartold, Agnieszka Pietrzyk-Le, Tan-Phat Huynh, Zofia Iskierko, Marta I. Sosnowska, Krzysztof Noworyta, Wojciech Lisowski, Francesco Maria Enrico Sannicolo, Silvia Cauteruccio, Emanuela Licandro, Francis D’Souza, and Wlodzimierz Kutner. ACS Appl. Mater. Interfaces, Just Accepted Manuscript
DOI: 10.1021/acsami.6b14340 Publication Date (Web): January 10, 2017

Copyright © 2017 American Chemical Society

This paper is behind a paywall.

Carbon dioxide as a source for new nanomaterials

Polish researchers have made a startling suggestion (from a Jan. 23, 2014 news item on Nanowerk),

In common perception, carbon dioxide is just a greenhouse gas, one of the major environmental problems of mankind. For Warsaw chemists CO2 became, however, something else: a key element of reactions allowing for creation of nanomaterials with unprecedented properties.

In reaction with carbon dioxide, appropriately designed chemicals allowed researchers from the Institute of Physical Chemistry of the Polish Academy of Sciences (IPC PAS) in Warsaw and the Faculty of Chemistry, Warsaw University of Technology, (WUT) for production of unprecedented nanomaterials.

Here’s an image the researchers use to illustrate their work,

Yellow tennis balls, spatially integrated in an adamant-like structure, symbolise crystal lattice of the microporous material resulting from self-assembly of nanoclusters. Orange balls imitate gas molecules that can adsorb in this material. The presentation is performed by Katarzyna Sołtys, a doctoral student from the Institute of Physical Chemistry of the Polish Academy of Sciences in Warsaw. (Source: IPC PAS, Grzegorz Krzyżewski).

Yellow tennis balls, spatially integrated in an adamant-like structure, symbolise crystal lattice of the microporous material resulting from self-assembly of nanoclusters. Orange balls imitate gas molecules that can adsorb in this material. The presentation is performed by Katarzyna Sołtys, a doctoral student from the Institute of Physical Chemistry of the Polish Academy of Sciences in Warsaw. (Source: IPC PAS, Grzegorz Krzyżewski).

The Jan. 23, 2014 IPC news release, which originated the news item, describes the work in more detail,

Carbon dioxide (CO2) is a natural component of Earth’s atmosphere. It is the most abundant carbon-based building block, and is involved in the synthesis of glucose, an energy carrier and building unit of paramount importance for living organisms.

“Carbon dioxide has been for years used in industrial synthesis of polymers. On the other hand, there has been very few research papers reporting fabrication of inorganic functional materials using CO2”, says Kamil Sokołowski, a doctoral student in IPC PAS.

Prof. Lewiński’s [Janusz Lewiński (IPC PAS, WUT)] group has shown that appropriately designed precursor compounds in reaction with carbon dioxide lead to fabrication of a microporous material (with pore diameters below 2 nm) resulting from self-assembly of luminescent nanoclusters. Novel microporous material, composed of building blocks with zinc carbonate core encapsulated in appropriately designed organic shell (hydroxyquinoline ligands), is highly luminescent, with photoluminescence quantum yield significantly higher than those of classical fluorescent compounds used in state-of-the-art OLEDs.

“Using carbon dioxide as a building block we were able to construct a highly porous and really highly luminescent material. Can it be used for construction of luminescent diodes or sensing devices? The discovery is new, the research work on the novel material is in progress, but we are deeply convinced that the answer is: yes”, says Sokołowski.

Already now it can be said that the novel material enjoys considerable interest. Polish and international patent applications were filed for the invention and the implementation work in cooperation with a joint venture company is in progress.

The design of precursors was inspired by nature, in particular by the binding of carbon dioxide in enzymatic systems of carbonic anhydrase, an enzyme responsible for fast metabolism of CO2 in human body. Effective enzyme activity is based on its active centre, where a hydroxyzinc (ZnOH) type reaction system is located.

“A hydroxyzinc reaction system occurs also in molecules of alkylzinc compounds, designed by us and used for fixation of carbon dioxide”, explains Sokołowski and continues: “These compounds are of particular interest for us, because in addition to hydroxyl group they contain also a reactive metal-carbon bond. It means that both the first and the second reaction system can participate in consecutive chemical transformations of such precursors”.

The research related to the chemistry of alkylhydroxyzinc compounds has an over 150 years of history and its roots are directly connected to the birth of organometallic chemistry. It was, however, only in 2011 and 2012 when Prof. Lewiński’s group has presented the first examples of stable alkylhydroxyzinc compounds obtained as a result of rationally designed synthesis.

The strategy for materials synthesis using carbon dioxide and appropriate alkylhydroxyzinc precursors, discovered by the researchers from Warsaw, seems to be a versatile tool for production of various functional materials. Depending on the composition of the reagents and the process conditions, a mesoporous material (with pore diameter from 2 to 50 nm) composed of zinc carbonate nanoparticles or multinuclear zinc nanocapsules for prospective applications in supramolecular chemistry can be obtained in addition to the material described above.

Further research of Prof. Lewiński’s group has shown that the mesoporous materials based on ZnCO3-nanoparticles can be transformed into zinc oxide (ZnO) aerogels. Mesoporous materials made of ZnO nanoparticles with extended surface can be used as catalytic fillings, allowing for and accelerating reactions of various gaseous reagents. Other potential applications are related to semiconducting properties of zinc oxide. That’s why the novel materials can be used in future in photovoltaic cells or as a major component of semiconductor sensing devices.

Good luck to the researchers as they find ways to turn a greenhouse gas into something useful.