Polyethylene can be melted and reformed into a new shape over and over again. These meltable, reshapable polymers are known as thermoplastics. Other examples include polystyrene and polypropylene. The strength of polymers also varies depending on how the molecules are arranged. To use our paperclip analogy, you may decide to have some paperclips branching off your main line. They result in a polymer with a lower density. Low-density polyethylene LDPE —the squishy material that plastic bags and wrap like the kind you might wrap your sandwich in —is an example.
The resulting polymer is stronger and has a higher density. An example is high-density polyethylene HDPE , used to make things like plastic bottles, food containers and plumbing pipes. In contrast to thermoplastic polymers are thermosetting polymers. It is useful, though, for things like car tyres, since a tyre that melts in the heat is going to make for a pretty interesting drive to the beach. Glues and electrical components are also thermosetting polymers. As well as the arrangement of molecules, the properties of a polymer are also determined by the length of the molecular chain.
In a nutshell, longer equals stronger. This is because, as a molecule gets longer, the total binding forces between molecules are greater, making the polymer chain stronger.
When more than a thousand carbon atoms line up in a chain of ethylene monomers, for example, the resulting polymer, polyethylene, is strong and flexible.
Developments in synthetic polymers go way beyond plastic bags and drink bottles. Flexible, electricity-conducting polymers may be the next big thing. Into virtual reality VR? In the not-too-distant future, you might be able to ditch the chunky goggles and pop in a pair of contact lenses instead, thanks to very thin, electricity-conducting polymer coatings. Australian scientists have also been working on lightweight, flexible solar cells which can be cheaply printed with polymer inks using a conventional printer.
Cities of the future could see a multitude of surfaces—buildings, cars, even clothing—made of this power-generating material. Thanks to a plethora of cheap, disposable products and packaging, plastics often get a bad rap pardon the pun for their impact on the environment—and rightly so. The sequence of nucleotides along the DNA molecule is a code for genes.
The genetic information stored in a molecule for DNA is a set of instructions for each organism to stay alive and grow. Proteins are biological polymers made inside cells. They are made from amino acid monomers and have a huge range of roles inside living things. Nucleotides have three components: a base, a sugar deoxyribose and a phosphate residue. The four bases are adenine A , cytosine C , guanine G and thymine T.
The sugar and phosphate create a backbone down either side of the double helix. The bases interact via hydrogen bonds with complementary bases on the other DNA strand in the helix. Her scientific interests focus on innovative synthesis concepts to achieve functional macromolecules, hybrid materials, and life-like systems to solve current challenges in biomedicine and material science.
More by Colette J. More by Meizhou Zhang. More by Pia Winterwerber. More by Yuzhou Wu. More by David Y. More by Tanja Weil. Cite this: Chem. Published by American Chemical Society. Article Views Altmetric -. Citations 1. Abstract High Resolution Image. The genetic code, one of the most prominent molecular monuments in nature, is a technological wonder from the perspective of both structural biology and macromolecular chemistry. Chemically speaking, the genetic code is a set of colossal chains of DNA in which the diversity of life is governed through the sequence information stored within the DNA nucleobases adenine, cytosine, guanine, and thymine.
Although its biological role and impact are clearly unambiguous, DNA has a different facade in the synthetic world—collectively known as DNA nanotechnology. Taking advantage of how the alignment of nucleotides can be woven differently with multiple intersecting chains not present in nature, nanoscale structures can be tailored with near limitless geometric possibilities.
From straightforward shapes such as Y-shaped DNA-crossovers and multiarm Holliday junctions to complex folding technologies such as DNA origami, these platforms have made revolutionary advances in biophysics, photonics, nanomedicine, and materials science.
The level of precision, coupled with the ease of DNA hybridization methods, has resulted in their widespread accessibility across all disciplines.
As such, significant attempts to stabilize DNA structures involving the conjugation of polymers, hydrophobic molecules, nanoparticles, or even higher ordered DNA weaving strategies have been achieved to protect the DNA phosphodiester bonds from hydrolysis.
Interestingly, these approaches very often result in the creation of novel materials with unique characteristics and structures due to the differences between the physical properties of the DNA and its attached motif. The dimensionality of structures from 1D to 3D can be customized by increasing the complexity of the DNA component, i. By exploring the influences of synthetic macro molecules on a non-natural, yet geometrically precise object, exclusive lessons on self-assembly, patterning, and interactions across 3D space can be learnt.
In this respect, polymer chemistry plays a crucial role in conferring additional properties to the already broad repertoire of capabilities demonstrated by DNA. Here, the near limitless capacity for monomer design coupled with recent advances in radical polymerization methodologies under mild aqueous conditions offers a fertile avenue for the development of novel polymer—DNA conjugates in years to come. Hence, one can easily envision the overwhelming extent of possibilities fusing polymer-based technologies, i.
Furthermore, the influence of DNA technology on synthetic chemistry is not solely limited on the nanoscale. By mimicking how nature uses DNA as a template for the proliferation of life, synthetic molecules can be designed to assemble similarly along a chain of ssDNA thereby transferring the sequence information provided by the template DNA onto the newly formed synthetic polymer chain.
Beyond the recruitment of small molecules or polymer precursors based on the recognition of the nucleobases, DNA can be used to template polymer synthesis by functioning as a reactive center either as an initiator or a catalyst.
Exploited differently, these parts of the DNA have expanded the breadth of polymer chemistry and provided alternative routes to fabricate nanoscale architectures. Chemistries on DNA. Native DNA is a rather chemically inert structure due to the lack of functional groups and the requirement to largely conserve the base-paring region to maintain function.
Consequently, the plethora of chemistries achievable on DNA has expanded and has been reviewed recently. Specifically, we will discuss the possible techniques to install reactive handles and the challenges to adapt each chemistry for DNA synthesis.
These functional handles can be divided into different categories where the target motif can be introduced through covalent modifications or noncovalent interactions with the DNA structure Figure 1. To incorporate covalent handles on DNA, depending on where the desired modification is situated, the attachment of the reactive group can be conducted during or at the end of DNA synthesis.
For the synthesis of an oligodeoxynucleotide ODN a solid phase approach, employing phosphoramidite chemistry, is typically adopted. Phosphoramidite chemistry was first developed in the s by Caruthers and co-workers and, through the optimization and employment of a solid support, resulted in the high yielding automated system used today.
The CPG bead provides a high surface area to offer numerous attachment points in addition to a high stability to chemical environments. Once the cycles are complete, the furnished ODNs are deprotected and cleaved from the CPG using a solution of ammonia.
In this way, phosphoramidite chemistry provides an approach to synthesize any sequence of DNA up to approximately bases. For DNA—polymer conjugates, ODNs are often shorter than 30 bases; therefore, this method does not pose as a limitation to the length and sequences attainable. High Resolution Image. Importantly, phosphoramidite chemistry is not limited to natural nucleotides.
Modified phosphoramidites were developed alongside the described method producing varying nucleobase, sugar, and phosphate backbone moieties.
There are several protective groups, including dimethoxytrityl DMT for amines and 2-chlorotrityl for carboxylic acids Figure 2 B , which can be employed to incorporate these functional groups. Hydrophobic and hydrophilic linkers are available in the form of alkyl chains and ethylene glycol units, respectively, to link the described functional handles to the phosphoramidite. The incorporation of the functional groups described above into the DNA makeup provides an avenue to synthesize DNA for conjugation to preformed polymers.
Where polymerization directly from DNA is desired, the polymerization initiators, agents or monomers, must be attached prior to polymerization. Atom transfer radical polymerization ATRP initiator phosphoramidites are not available commercially; however, several can be synthesized and have been incorporated through solid phase synthesis prior to deprotection and cleavage, demonstrating a feasible method to attach initiator moieties to ODNs.
However, the attachment of reversible addition—fragmentation chain transfer RAFT agents prior to deprotection and cleavage is not possible due to its instability in ammonia. Similarly, the norbornene-phosphoramidite is also not available commercially; however, its synthesis and consequent incorporation has been established. Modifications in the base pair region may not be optimal due to conformation dynamics, 16 in addition to sterics and charge repulsion from the overall DNA structure.
Thus, to ensure the functional group is positioned externally i. These developments achieved through phosphoramidite chemistry have enabled the initial vision and future realization of covalent DNA—polymer synthesis.
For several functional groups, such as RAFT agents, the corresponding phosphoramidite is either not commercially available or is not compatible with the solid phase synthesis process. However, the chemical handles available through solid phase synthesis can be postmodified after column cleavage to position the unattainable groups.
Although the chemistry itself is simpler than the synthesis of a phosphoramidite, unprotected DNA is a polyelectrolyte and requires an aqueous solvent system e. As native DNA does not bear specific sites for chemoselective reactions, these compatible handles must be incorporated prior to column cleavage through the phosphoramidite chemistry described above. The conjugation of these functional ODNs with small molecules for example, fluorophores has enabled the establishment of common procedures and reagents for coupling in the presence of unprotected DNA.
For instance, norbornene—tetrazine chemistry was established as an efficient self-reporting method for DNA—polymer conjugation; therefore, the modification of a reactive ODN to bear these specialized functions was desired. The examples described so far document the secondary modification of native DNA to bear functional handles for covalent conjugation of DNA with presynthesized polymers.
For polymerization to occur from DNA grafting from approach , the polymerization initiator or agent must be anchored to the DNA structure. Postmodification cannot take place on the solid support and must be conducted in solution after cleavage.
These methods demonstrated the ability to synthesize ODNs bearing a wide range of functional groups for either direct polymer conjugation or growth through RAFT polymerization, aiding the widespread development of DNA—polymer function and application. Nonetheless, the examples described here each adopt an amine-functionalized ODN and therefore do not explore the plethora of coupling chemistries available to position functional groups not available as phosphoramidites.
Through the continuous expansion of click chemistry and bioconjugation, the possibilities for ODN functionalization with synthetic macromolecules can be perpetually expanded. Additionally, in this section we have highlighted the approaches adopted for reported conjugations, which each require a functional handle from solid phase phosphoramidite synthesis.
However, the functionalization of DNA is not limited to this method. Chemical handles can also be incorporated through DNA polymerase extension with modified deoxynucleotide triphosphates dNTPs. The employment of modified dNTPs opens an alternative toolbox to incorporate non-native functional groups through enzymatic synthesis.
In addition to the portfolio of covalent chemistries available to the reactive groups of DNA, noncovalent approaches exploiting the structural elements of DNA offer an alternative route for DNA functionalization. Native dsDNA is a highly charged molecule, formed through many noncovalent interactions which can be exploited for noncovalent complexation.
These interactions present opportunities for noncovalent dynamic binding of small molecules to the major and minor groove, between base pairs and to the phosphate backbone Figure 4. Through these binding modes, there is the potential for noncovalent interactions to be used to anchor functional groups as well as to complex whole polymers. In contrast to the covalent conversions described above, noncovalent complexation is a highly dynamic assembly that does not require chemical modifications to the intrinsic DNA makeup.
The capability to employ electrostatic interactions with the charged backbone generates a simple method for cationic molecules to bind to the sterically available anionic groups on DNA. The charged backbone plays many important roles in nature, such as guiding proteins and ligands to designated positions, 22 for example through the supramolecular assembly of DNA with the positively charged histone protein. These intrinsic interactions inspired the employment of the phosphate backbone for DNA—polymer conjugate synthesis.
To afford this interaction, a reduction in ion—ion repulsion is required where stabilization with Group 1 and 2 counterions is commonly used. Thus, equally for the interaction with polymers, ion displacement must occur. A huge charge repulsion must be overcome in comparison to other biological molecules, such as proteins, which are commonly neutral or have low charge counts.
The interaction of polycationic polymers with DNA has gained interest due to the increased ambition to deliver DNA to cells as potential therapeutics.
The dissociation of DNA—polycations through the addition of counterions can probe the effect of ionic strength on the polymer interactions. Anion competitors were also studied showing the larger and less electronegative I — caused the greatest effect on polymer dissociation followed by Br — , Cl — , and F —.
Full neutralization of charge leads to DNA condensation, which, depending on the application desired, can have implications, such as steric hindrance of reactive sites. Similarly, the pH has large consequences on binding strength and, accordingly, the ability to form complexes.
Thus, the shape can dictate both the polymer packing and the condensation of DNA. An understanding of the structure and charge effects of cationic polymer binding to DNA can aid the design and choice of the respective polymer to avoid undesired structure deformation and to ensure applicability for the desired function.
Groove binders have become a major target for small molecule and protein binding for therapeutic action. Groove binders can target either the major or minor groove Figure 4 through several noncovalent interactions, consisting of hydrogen bonding and van der Waals and electrostatic interactions.
Each base pair provides a different environment through the varying electrostatic effects, groove width, and depths. Therefore, selective binding can be employed; for example, small molecule binding tends to prefer AT rich regions due to the increase in van der Waals forces provided through the deeper pocket. Specific interactions include H-bonding with the sugar C1, purine N3, and pyrimidine N1 as well as the base pairing moieties. Larger molecules, such as proteins and carbohydrates, recognize and bind in the major groove.
Although there are more donor and acceptor sites in the major groove providing the platform for stronger overall enthalpic interactions, fewer natural examples of major groove binders are described.
In this case, the noncovalent H-bonds and salt bridges allow a reversible binding and release for processes, such as transcription and gene regulation. The functional groups on the bases and ribose sugar provide several H-bond donor and acceptor sites. A detailed analysis of structure relationships has been reviewed previously by Thornton and co-workers. Proteins and aminoglycosides both offer many H-bonding sites in addition to positively charged residues to overcome repulsive forces.
Through this knowledge, polymer design can be molded to encompass these attributes. However, it is important to also consider the structural distortions groove binding can have on the B-DNA structure. Groove binders that possess a strong overall binding enthalpy that outweighs the conformational changes can induce a fit. While the backbone and grooves offer external interactions with DNA, the structure also offers the conformational flexibility to exploit the base pair stacking to complex small molecules within.
This extension is useful to determine binding through length changes; however, it may also alter recognition and function of DNA as a genetic material. As well as the stacking interactions, complementary dipoles can also increase association strength.
The aromatic nature provides a plethora of reaction conditions to perform substitution reactions to anchor reactive handles on the intercalator backbone. Polymerization from the functionalized acridine could then be performed followed by DNA intercalation. Intercalation was noted with each polymer—acridine conjugate; however, there was an effect on the association constant depending on the polymer employed Table 1. The authors attribute this effect to the molecular weight and structure of the polymer where varying hydrophobicity and side-chain makeup have been explored.
Specifically, a trimethylpsoralen was functionalized with a terminal amine to afford amide conjugation with an NHS polymer. So far in this section, the two examples have demonstrated the direct assembly of polymers with DNA through covalent polymer conjugation with an intercalator.
Although binding was noted in each case, a reduction in association strength was also exhibited. This was demonstrated with proflavin, an acridine derivative, which can undergo modification to produce a diazide, positioning the functional handles in the major groove.
However, by a further modification to produce methyl proflavindiazide, the binding strength is returned to the same magnitude as the unmodified proflavin.
Table 1. List of Intercalators and Their Binding Strength. In the complexation interactions described above, each mechanism is explored individually; however, for several DNA binders, multiple interactions are involved. A commonly adopted example is the combination of intercalation and groove binding of antibiotics bearing peptide groups which reside in the minor groove.
The interactions noted for intercalator—conjugate assemblies lay the foundation for intercalator—polymer design to guide the synthesis of precise polymeric nanostructures.
DNA—Polymer Synthesis. Polymerization was first noted in the s and has since developed to produce the synthetic polymers commonly used today, such as PS and Nylon Figure 6. Due to the structural prospects, diblock copolymers have gained growing interest and can be designed to form many nanostructures, such as micelles and vesicles. Through the advancements of living polymerization techniques, polymer length dispersity is now reduced and has enabled the synthesis of copolymers for lithography and many controlled nanostructures.
DNA is a highly programmable entity with a plethora of structures, providing the platform to control the synthesis of polymers as well as their spatial organization. Here, we will discuss the recent advancements, the challenges, and possible solutions to synthesize DNA—polymer conjugates.
There have been large developments in the synthesis of covalent DNA—polymer conjugates; however, several limitations have hindered progress. We will first introduce the polymerization methods employed for DNA—polymer conjugate synthesis and highlight the limitations of these methods in addition to the challenges of combining synthetic polymers with DNA. Through this discussion, we can build a greater understanding of the progress made in this field through solution- and platform-based conjugation methods which are described in this section.
There are several polymerization methods applicable to DNA—polymer conjugates, including anionic, cationic, ring-opening, and free radical polymerizations. Free radical polymerizations are most commonly adopted for linear polymer synthesis for DNA—polymer conjugates where the equilibrium required to accomplish reduced mass dispersity was first demonstrated through ATRP.
ATRP was invented in and employs an alkyl halide as the initiator along with a redox-active catalyst Figure 7 A. The first examples of ATRP required a metal catalyst, which initially led to developments involving reducing agents to reactivate the metal center to reduce the required metal concentration; however, it could not be removed entirely. Metal free ATRP was later developed and employs an organic redox-active catalyst, therefore reducing the biological toxicity of the reaction and increasing the compatibility of ATRP for DNA conjugation.
RAFT proceeds by a radical polymerization mechanism in the presence of a chain transfer agent CTA to afford the necessary equilibrium for reduced mass distribution Figure 7 B. The added chain transfer step redistributes the radical to allow an equal probability for all chains to grow. Importantly, RAFT polymerization end-group chemistry is readily available through the liberation of the thiol group in the transfer agent.
The catalyst, again, provokes challenges for purification and side reactions. The synthesis of covalently bound DNA—polymer conjugates has seen large developments, now enabling the controlled synthesis of diblock copolymers consisting of many combinations of polymers and DNA nanostructures. The synthesis of DNA—polymer conjugates can be categorized into three methods: grafting from , grafting to , and grafting through Figure 8.
Grafting from occurs when the polymerization initiator is covalently bound to the DNA followed by in situ polymerization, whereas for grafting to , the polymer and DNA parts are presynthesized prior to conjugation. Grafting through encompasses the polymerization of macromonomers bearing a polymerizable group to synthesize polymers with defined side chains. Each approach bears advantages— grafting from exhibits the greatest attachment chemistry and therefore largest density, 68 whereas grafting to allows thorough polymer characterization prior to conjugation and polymer choice is broader the polymerization occurs in the absence of DNA—the reaction can occur in larger scales, in many solvents, and using different monomers.
Grafting through is employed less frequently; however, it can efficiently synthesize many brush or hyperbranched structures. Nonetheless, each approach has drawbacks to either the yield or breadth of polymer conjugates achievable. These drawbacks can be accounted for by both the use of DNA in this system and also the polymerization conditions. Through the advancement of the polymerization methods described above, polymer synthesis, itself, is a highly established technique, which has been optimized for many monomer and polymer types.
In parallel, the expansion of bioorthogonal chemistry has provided a plethora of conjugation reactions between modified DNA and a variety of molecules, providing ample resources for DNA to polymer conjugation reactions. However, for DNA—polymer conjugates, there are several limitations due to the combination of these two materials in one reaction pot because they can each provide contrasting properties. In the approaches discussed here, DNA is present either in the conjugation reaction grafting to or in the polymerization reaction grafting from.
DNA is a highly ionic molecule requiring an aqueous environment which is readily compatible with hydrophilic monomers and polymers; however, hydrophobic monomers and polymers require a solvent mixture to enable solubility. Organic solvents are commonly poor liquids for DNA, altering hydrogen bonding, polarity, and hydrophobicity. Similarly, the grafting from approach also favors hydrophilic monomers. An example employing DMSO as the solvent to polymerize methyl acrylate established a method for successful polymerization.
In addition to solvent compatibility, both blocks of the DNA—polymer conjugate are flexible polymers and can therefore shield the reactive moiety. Steric effects are observed when coupling to all forms of DNA—ss, ds, and nanostructures—although the effects are different for the solution-based ss and ds and solid support nanostructures and DNA origami forms.
Additionally, the sequence of ssDNA requires a fine design to ensure the secondary structures do not hinder the reactive site. This also applies to dsDNA where the duplex may be in equilibrium with higher ordered structures. In both ss- and dsDNA, the sequence can be designed and modeled to ensure that inhibitory secondary structures are avoided. Conjugation to DNA origami presents the greatest hindrance for conjugation. The DNA origami not only burdens the reaction center with steric hindrance, it also, where multiple sites are present on one structure, reduces the distribution of reaction sites in solution and requires a higher local concentration on the origami.
This causes drawbacks for both approaches; however, grafting from is deemed preferable to synthesize DNA origami—polymer conjugates as the steric hindrance is reduced. In this case, the larger polymers may shield the reactive handle and therefore reduce the reaction process. Although the limitations described so far are mainly attained from the grafting to approach, the grafting from technique performs the polymerization in the presence of DNA, which produces additional challenges.
When handling DNA, small volumes are typically employed due to limited resources reactive group-bearing oligos are commonly produced in microgram quantities ; thus, when grafting from , small volumes are also adopted for the polymerization process.
The approximate length of polymers can be controlled by the monomer to transfer agent or initiator ratio; however, oxygen is a radical scavenger and can therefore quench the initiated or transferred radical, altering the ratio. Radical polymerization in the absence of DNA i. The most effective method to remove dissolved oxygen is through N 2 purging. Similarly, the freeze—pump—thaw technique, whereby the solution is frozen before a vacuum is applied to reduce the dissolved oxygen solubility, can take place in larger volumes, i.
However, this technique is again problematic when performing the polymerization in small volumes, i. Volume loss may compromise reproducibility due to the effects residual oxygen will have on the polymer length and yield.
Additionally, DNA degradation can occur when the sample is subjected to repeated freezing and thawing—tension forces are generated from ice crystals and may lead to strand breakage. Glucose oxidase, an enzyme that converts oxygen to hydrogen peroxide, can perform successful enzyme degassing for RAFT polymerization in an open, low volume vessel grafting from ODNs.
However, purification to remove the enzyme is required after the reaction if downstream processes are desired. There are also other challenges associated with the reduced concentrations available when working with DNA.
Again, polymerization in isolation from DNA can be performed as optimized; however, when reactions with DNA for conjugation or polymerizations from DNA are required, optimal concentrations may not be possible with the limited amount of DNA Table 2. This is more notable when grafting from DNA origami.
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