Hierarchical self-assembly of the DNA-grafted supramolecular polymers

Conjugation of functional entities with a specific set of optical, mechanical or biological properties to DNA strands allows engineering of sophisticated DNA-containing architectures. Among various hybrid systems, DNA-grafted polymers occupy an important place in modern materials science. In this contribution we present the non-covalent synthesis and properties of DNA-grafted linear supramolecular polymers (SPs), which are assembled in a controllable manner from short chimeric DNA-pyrene oligomers. The synthetic oligomers consist of two parts: a 10 nucleotides long DNA chain and a covalently attached segment of variable number of phosphodiester-linked pyrenes. The temperature-dependent formation of DNA-grafted SPs is described by a nucleation-elongation mechanism. The high tendency of pyrenes to aggregate in water, leads to the rapid formation of SPs. The core of the assemblies consists of stacked pyrenes. They form a 1D platform, to which the DNA chains are attached. Combined spectroscopic and microscopic studies reveal that the major driving forces of the polymerization are π-stacking of pyrenes and hydrophobic interactions, and DNA pairing contributes to a lesser extent. AFM and TEM experiments demonstrate that the 1D SPs appear as elongated ribbons with a length of several hundred nanometers. They exhibit an apparent helical structure with a pitch-to-pitch distance of 50±15 nm. Since DNA pairing is a highly selective process, the ongoing studies are aimed to utilize DNA-grafted SPs for the programmable arrangement of functional entities. For example, the addition of non-modified complementary DNA strands to the DNA-grafted SPs leads to the cooperative formation of higher-order assemblies. Also, our experiments suggest that the fluorescent pyrene core of 1D ribbons serves as an efficient donor platform for energy transfer applications.

From supramolecular sheets to fibers and back: establishing the critical parameters that govern the morphology of pyrene-based self-assembled materials

The precise arraying of functional entities in morphologically well-defined shapes remains one of the key challenges in the processing of organic molecules1. Among various π-conjugated species, pyrene exhibits a set of unique properties, which make it an attractive compound for the utilization in materials science2. In this contribution we report on properties of self-assembled structures prepared from amphiphilic pyrene trimers (Py3) consisting of phosphodiester-linked pyrenes. Depending on the geometry of a pyrene core substitution (1.6-, 1.8-, or 2.7- type, see Scheme), the thermally-controlled self-assembly allows the preparation of supramolecular architectures of different morphologies in a bottom-up approach: two-dimensional (2D) nanosheets3 are formed in case of 1.6- and 2.7-substitution4 whereas one-dimensional (1D) fibers are built from 1.8- substituted isomers. The morphologies of the assemblies are established by AFM and TEM, and the results are further correlated with spectroscopic and scattering data. Two-dimensional assemblies consist of an inner layer of hydrophobic pyrenes, sandwiched between a net of phosphates. Due to the repulsion of the negative charges, the 2D assemblies exist mostly as free-standing sheets. An internal alignment of pyrenes leads to strong exciton coupling with an unprecedented observation (simultaneous development of J- and H-bands from two different electronic transitions). Despite the similarity in spectroscopic properties, the structural parameters of the 2D aggregates drastically depend on the preparation procedure. Under certain conditions extra-large sheets (thickness of 2 nm, aspect ratio area/thickness ~107) in aqueous solution are formed4B. Finally, one-dimensional assemblies are formed as micrometer-long and nanometer-thick fibers. Both, planar and linear structures are intriguing objects for the creation of conductive nanowires that may find interest for applications in supramolecular electronics.

From supramolecular sheets to fibers and back: establishing the critical parameters that govern the morphology of pyrene-based self-assembled materials

The precise arraying of functional entities in morphologically well-defined shapes remains one of the key challenges in the processing of organic molecules1. Among various π-conjugated species, pyrene exhibits a set of unique properties, which make it an attractive compound for the utilization in materials science2. In this contribution we report on properties of self-assembled structures prepared from amphiphilic pyrene trimers (Py3) consisting of phosphodiester-linked pyrenes. Depending on the geometry of a pyrene core substitution (1.6-, 1.8-, or 2.7- type, see Scheme), the thermally-controlled self-assembly allows the preparation of supramolecular architectures of different morphologies in a bottom-up approach: two-dimensional (2D) nanosheets3 are formed in case of 1.6- and 2.7-substitution4 whereas one-dimensional (1D) fibers are built from 1.8- substituted isomers. The morphologies of the assemblies are established by AFM and TEM, and the results are further correlated with spectroscopic and scattering data. Two-dimensional assemblies consist of an inner layer of hydrophobic pyrenes, sandwiched between a net of phosphates. Due to the repulsion of the negative charges, the 2D assemblies exist mostly as free-standing sheets. An internal alignment of pyrenes leads to strong exciton coupling with an unprecedented observation (simultaneous development of J- and H-bands from two different electronic transitions). Despite the similarity in spectroscopic properties, the structural parameters of the 2D aggregates drastically depend on the preparation procedure. Under certain conditions extra-large sheets (thickness of 2 nm, aspect ratio area/thickness ~107) in aqueous solution are formed4B. Finally, one-dimensional assemblies are formed as micrometer-long and nanometer-thick fibers. Both, planar and linear structures are intriguing objects for the creation of conductive nanowires that may find interest for applications in supramolecular electronics.

From Ribbons to Networks: Hierarchical Organization of DNA-Grafted Supramolecular Polymers

DNA-grafted supramolecular polymers (SPs) allow the programmed organization of DNA in a highly regular, one-dimensional array. Oligonucleotides are arranged along the edges of pyrene-based helical polymers. Addition of complementary oligonucleotides triggers the assembly of individual nanoribbons resulting in the development of extended supramolecular networks. Network formation is enabled by cooperative coaxial stacking interactions of terminal GC base pairs. The process is accompanied by structural changes in the pyrene polymer core that can be followed spectroscopically. Network formation is reversible, and disassembly into individual ribbons is realized either via thermal denaturation or by addition of a DNA separator strand.

DNA Catalysis: The Chemical Repertoire of DNAzymes

Deoxyribozymes or DNAzymes are single-stranded catalytic DNA molecules that are obtained by combinatorial in vitro selection methods. Initially conceived to function as gene silencing agents, the scope of DNAzymes has rapidly expanded into diverse fields, including biosensing, diagnostics, logic gate operations, and the development of novel synthetic and biological tools. In this review, an overview of all the different chemical reactions catalyzed by DNAzymes is given with an emphasis on RNA cleavage and the use of non-nucleosidic substrates. The use of modified nucleoside triphosphates (dN*TPs) to expand the chemical space to be explored in selection experiments and ultimately to generate DNAzymes with an expanded chemical repertoire is also highlighted.

Supramolecular Polymers in DNA Nanotechnology

Creation of biocompatible functional materials is an important task in supramolecular chemistry. In this contribution, we report on noncovalent synthesis of DNA-grafted supramolecular polymers (SPs). DNA-grafted SPs enable programmed arrangement of oligonucleotides in a regular, tightly packed one-dimensional array. Further interactions of DNA-grafted SPs with complementary DNA strands leads to the formation of networks through highly cooperative G-C blunt-end stacking interactions. The structural changes in the polymeric core enable to monitor spectroscopically the stepwise formation of networks. Such stimuli-responsive supramolecular networks may lead to the development of DNA-based smart materials.

RNAs and ribonucleoproteins in recognition and catalysis.

CONTENTS. 1. Did life begin with catalytic RNA?–2. Self-splicing and self-cleaving RNAs–2.1 Self-splicing of group I introns – 2.2 Self-splicing of group II introns – 2.3 Self-cleaving RNAs–3. Splicing mediated by trans-acting factors–3.1 Group III introns – 3.2 Splicing of nuclear pre-mRNAs – 3.3 Trans-splicing – 3.4 Is nuclear pre-mRNA splicing evolutionarily related to group I and group II self-splicing?– 3.5 Non-RNA mediated splicing of tRNAs–4. Processing of ribosomal precursor RNAs–5. Processing of pre-mRNA 3′ ends–5.1 Polyadenylation – 5.2 Histone pre-mRNA 3′ processing–6. Other RNPs involved in metabolic mechanisms–6.1 5′ end processing of pre-tRNAs by RNase P – 6.2 The signal recognition particle – 6.3 Telomerase – 6.4 RNA editing in trypanosomatid mitochondria–7. Why RNA?

Supramolecular Organization of Dye Molecules in Zeolite L Channels: Synthesis, Properties, and Composite Materials

Sequential insertion of different dyes into the 1D channels of zeolite L (ZL) leads to supramolecular sandwich structures and allows the formation of sophisticated antenna composites for light harvesting, transport, and trapping. The synthesis and properties of dye molecules, host materials, composites, and composites embedded in polymer matrices, including two- and three-color antenna systems, are described. Perylene diimide (PDI) dyes are an important class of chromophores and are of great interest for the synthesis of artificial antenna systems. They are especially well suited to advancing our understanding of the structure–transport relationship in ZL because their core fits tightly through the 12-ring channel opening. The substituents at both ends of the PDIs can be varied to a large extent without influencing their electronic absorption and fluorescence spectra. The intercalation/insertion of 17 PDIs, 2 terrylenes, and 1 quaterrylene into ZL are compared and their interactions with the inner surface of the ZL nanochannels discussed. ZL crystals of about 500 nm in size have been used because they meet the criteria that must be respected for the preparation of antenna composites for light harvesting, transport, and trapping. The photostability of dyes is considerably improved by inserting them into the ZL channels because the guests are protected by being confined. Plugging the channel entrances, so that the guests cannot escape into the environment is a prerequisite for achieving long-term stability of composites embedded in an organic matrix. Successful methods to achieve this goal are described. Finally, the embedding of dye–ZL composites in polymer matrices, while maintaining optical transparency, is reported. These results facilitate the rational design of advanced dye–zeolite composite materials and provide powerful tools for further developing and understanding artificial antenna systems, which are among the most fascinating subjects of current photochemistry and photophysics.

Magnetic structure of two- and three-dimensional supramolecular compounds

Supramolecular chiral networks of oxalato-bridged transition metals show either two- or three-dimensional structural features. The magnetic structures of such compounds have been investigated by means of elastic neutron powder diffraction.

Antibody catalysis of peptidyl-prolyl cis-trans isomerization in the folding of RNase T1

An antibody generated to an α-keto amide containing hapten 1 catalyzes the cis-trans isomerization of peptidyl-prolyl amide bonds in peptides and in the protein RNase T1. The antibody-catalyzed peptide isomerization reaction showed saturation kinetics for the cis-substrate, Suc-Ala-Ala-Pro-Phe-pNA, with a kcat/Km value of 883 s−1⋅M−1; the reaction was inhibited by the hapten analog 13 (Ki = 3.0 ± 0.4 μM). Refolding of denatured RNase T1 to its native conformation also was catalyzed by the antibody, with the antibody-catalyzed folding reaction inhibitable both by the hapten 1 and hapten analog 13. These results demonstrate that antibodies can catalyze conformational changes in protein structure, a transformation involved in many cellular processes.

Supramolecular organization of immature and mature murine leukemia virus revealed by electron cryo-microscopy: Implications for retroviral assembly mechanisms

We have used electron cryo-microscopy and image analysis to examine the native structure of immature, protease-deficient (PR−) and mature, wild-type (WT) Moloney murine leukemia virus (MuLV). Maturational cleavage of the Gag polyprotein by the viral protease is associated with striking morphological changes. The PR− MuLV particles exhibit a rounded central core, which has a characteristic track-like shell on its surface, whereas the WT MuLV cores display a polygonal surface with loss of the track-like feature. The pleomorphic shape and inability to refine unique orientation angles suggest that neither the PR− nor the WT MuLV adheres to strict icosahedral symmetry. Nevertheless, the PR− MuLV particles do exhibit paracrystalline order with a spacing between Gag molecules of ≈45 Å and a length of ≈200 Å. Because of the pleomorphic shape and paracrystalline packing of the Gag–RNA complexes, we raise the possibility that assembly of MuLV is driven by protein–RNA, as well as protein–protein, interactions. The maturation process involves a dramatic reorganization of the packing arrangements within the ribonucleoprotein core with disordering and loosening of the individual protein components.

Use of intrinsic binding energy for catalysis by an RNA enzyme

The contribution of several individual ribozyme⋅substrate base pairs to binding and catalysis has been investigated using hammerhead ribozyme substrates that were truncated at their 3′ or 5′ ends. The base pairs at positions 1.1–2.1 and 15.2–16.2, which flank the conserved core, each contribute 104-fold in the chemical step, without affecting substrate binding. In contrast, base pairs distal to the core contribute to substrate binding but have no effect on the chemical step. These results suggest a “fraying model” in which each ribozyme⋅substrate helix can exist in either an unpaired (“open”) state or a helical (“closed”) state, with the closed state required for catalysis. The base pairs directly adjacent to the conserved core contribute to catalysis by allowing the closed state to form. Once the number of base pairs is sufficient to ensure that the closed helical state predominates, additional residues provide stabilization of the helix, and therefore increase binding, but have no further effect on the chemical step. Remarkably, the >5 kcal/mol free energy contribution to catalysis from each of the internal base pairs is considerably greater than the free energy expected for formation of a base pair. It is suggested that this unusually large energetic contribution arises because free energy that is typically lost in constraining residues within a base pair is expressed in the transition state, where it is used for positioning. This extends the concept of “intrinsic binding energy” from protein to RNA enzymes, suggesting that intrinsic binding energy is a fundamental feature of biological catalysis.

The antibody catalysis route to the total synthesis of epothilones

An efficient monoclonal aldolase antibody that proceeds by an enamine mechanism was generated by reactive immunization. Here, this catalyst has been used in the total synthesis of epothilones A (1) and C (3). The starting materials for the synthesis of these molecules have been obtained by using antibody-catalyzed aldol and retro-aldol reactions. These precursors were then converted to epothilones A (1) and C (3) to complete the total synthesis.