RNA-mediated synthesis of palladium nanoparticles on Au surfaces

Synthesis of fluorescent AuNCs with RNA as template

Although nucleic acids have been widely used as templates for the synthesis of nanomaterials, the synthesis of RNA-templated gold nanoclusters (AuNCs) has not been explored. In this work, we developed a simple strategy for synthesis of RNA-templated fluorescent AuNCs. We first evaluated the adsorption of different nucleoside monophosphates (NMP) on gold atoms. Our density function theory simulation and isothermal titration calorimetry measurements demonstrated that adenosine monophosphate (AMP) is a superior gold binder than other NMPs or deoxyadenosine monophosphate. Afterwards, NMP-templated synthesis of AuNCs was conducted in various pH environments, and our results indicated that bright green light-emitting AMP-templated AuNCs can be obtained at pH ∼6.0. In order to study the synthesis mechanism of AuNCs, we investigated the effects of reducing agent type and addition time, and the negative charge carried by template nucleotides on the fluorescence of AuNCs. Finally, we extended the template AMP into RNA hairpin structure, the fluorescence intensity was the highest when the cyclic bases were poly 16 A. This study opens new routes to synthesize fluorescent AuNCs using RNA templates.

Biomimetic and Bioinspired Synthesis of Nanomaterials/Nanostructures

In recent years, due to its unparalleled advantages, the biomimetic and bioinspired synthesis of nanomaterials/nanostructures has drawn increasing interest and attention. Generally, biomimetic synthesis can be conducted either by mimicking the functions of natural materials/structures or by mimicking the biological processes that organisms employ to produce substances or materials. Biomimetic synthesis is therefore divided here into "functional biomimetic synthesis" and "process biomimetic synthesis". Process biomimetic synthesis is the focus of this review. First, the above two terms are defined and their relationship is discussed. Next different levels of biological processes that can be used for process biomimetic synthesis are compiled. Then the current progress of process biomimetic synthesis is systematically summarized and reviewed from the following five perspectives: i) elementary biomimetic system via biomass templates, ii) high-level biomimetic system via soft/hard-combined films, iii) intelligent biomimetic systems via liquid membranes, iv) living-organism biomimetic systems, and v) macromolecular bioinspired systems. Moreover, for these five biomimetic systems, the synthesis procedures, basic principles, and relationships are discussed, and the challenges that are encountered and directions for further development are considered.

Aptamers and the RNA world, past and present

Aptamers and the SELEX process were discovered over two decades ago. These discoveries have spawned a productive academic and commercial industry. The collective results provide insights into biology, past and present, through an in vitro evolutionary exploration of the nature of nucleic acids and their potential roles in ancient life. Aptamers have helped usher in an RNA renaissance. Here we explore some of the evolution of the aptamer field and the insights it has provided for conceptualizing an RNA world, from its nascence to our current endeavor employing aptamers in human proteomics to discover biomarkers of health and disease.

Unusual reactivity of a silver mineralizing peptide

The ability of peptides selected via phage display to mediate the formation of inorganic nanoparticles is now well established. The atomic-level interactions between the selected peptides and the metal ion precursors are in most instances, however, largely obscure. We identified a new peptide sequence that is capable of mediating the formation of Ag nanoparticles. Surprisingly, nanoparticle formation requires the presence of peptide, HEPES buffer, and light; the absence of any one of these compromises nanoparticle formation. Electrochemical experiments revealed that the peptide binds Ag+ in a 3 Ag+:1 peptide ratio and significantly alters the Ag+ reduction potential. Alanine replacement studies yielded insight into the sequence-function relationships of Ag nanoparticle formation, including the Ag+ coordination sites and the residues necessary for Ag synthesis. In addition, the peptide was found to function when immobilized onto surfaces, and the specific immobilizing concentration could be adjusted to yield either spherical Ag nanoparticles or high aspect ratio nanowires. These studies further illustrate the range of interesting new solid-state chemistries possible using biomolecules.

RNA-poly(o-methoxyaniline) hybrid templated growth of silver nanoparticles and nanojacketing: physical and electronic properties

Three nanobiocomposites (PRAg31, PRAg11, and PRAg13; the numbers indicate the weight ratios of poly(o-methoxyaniline) (POMA) and ribonucleic acid (RNA), respectively), produced from the same amount of POMA (P) and silver nitrate (AgNO(3)) with differing proportions of RNA (R) are prepared by aging the aqueous solutions of the mixture for 3 weeks at 30 degrees C. The scanning and transmission electron microscopy (SEM and TEM) indicate Ag nanoparticle formation on the hybrid fiber surface and in the PRAg31 system the hybrid fibrils become coated with metallic Ag, the phenomenon being termed as "nanojacketting". The circular dichroism (CD) spectra indicate a small distortion of RNA conformation from A helix toward B helix. FTIR and UV-vis spectra suggest that POMA (emeraldine base, EB) being doped by Ag(+) become oxidized to its pernigraniline base (PB) form and reduce Ag(+) to metallic Ag. The Ag nanoparticles thus produced become stabilized on the fibril surface by co-ordination through nitrogen atoms of POMA (PB) chains. The much slower red shift of pi band to polaron band transition peak in PRAg31 than that of the other two nanobiocomposites is indicative of difficulty in conformational transitions of POMA chain in the "nanojacketted" hybrid fibrils. The dc-conductivity values of the nanobiocomposites are two orders higher than that of the pure POMA-RNA hybrids. The PRAg31 system exhibits rectification property in the I-V characteristic curves and a probable explanation based on the feasibility of p-n junction formation arising from the transfer of lone pair of electrons of nitrogen of POMA (p-type) to the Ag nanoparticles (n-type) has been offered.

Self assembly of poly(o-methoxy aniline) with RNA and RNA/DNA hybrids: physical properties and conformational change of poly(o-methoxy aniline)

Biomolecular hybrids of a conducting polymer [poly(o-methoxy aniline) (POMA)] and RNA are prepared at the three different compositions by mixing aqueous solutions of diethyl, 2-hydroxy ethyl, ammonium salt of RNA (type IX from Torula Yeast) and POMA (ES, emeraldine salt; doping level [Cl]/[N]=0.52). A slow increase of pH up to 30 h of aging occurs in the mixture till it levels up. The TEM micrographs indicate a fibrillar network structure in all the hybrid compositions (POMA: RNA=1:3, 1:1, 3:1, by weight). In the complexes three types of supramolecular interactions, viz. (i) electrostatic, (ii) H-bonding and (iii) pi-pi interactions, are evident from the FTIR spectroscopy. The CD spectra indicate a small distortion of A-RNA conformation towards its B form during the hybrid formation. Time and temperature dependent UV-vis spectral studies indicate a slow red shift of the pi-band to polaron band transition peak (lambda(max)) for the uncoiling of the POMA (P) chain on the RNA (R) surface. The repulsive interaction between the radical cations of POMA (ES) absorbed on the RNA surface is attributed to the conformational change causing the uncoiling of POMA chain. UV-vis spectral study indicates that the uncoiling and attachment of POMA on RNA surface is much faster than that on DNA (D). In POMA-RNA-DNA (PRD) hybrid solutions slower red shift of lambda(max) indicates more disordered array of the phosphate groups than that in PR and PD systems. The conductivity values of the PR hybrids (10(-)(6) S/cm(-1)) are three orders higher than that of RNA, rendering the PR hybrids to be useful for fabricating good biosensors. In the PRD hybrids conductivity decreases by two orders than those of PR and PD hybrids suggesting a disorder arrangement of POMA chains in the PRD hybrids. The I-V characteristic curves of the PR and PRD hybrids indicate a semiconducting nature of the hybrids.

The dawn of the RNA World: toward functional complexity through ligation of random RNA oligomers

A main unsolved problem in the RNA World scenario for the origin of life is how a template-dependent RNA polymerase ribozyme emerged from short RNA oligomers obtained by random polymerization on mineral surfaces. A number of computational studies have shown that the structural repertoire yielded by that process is dominated by topologically simple structures, notably hairpin-like ones. A fraction of these could display RNA ligase activity and catalyze the assembly of larger, eventually functional RNA molecules retaining their previous modular structure: molecular complexity increases but template replication is absent. This allows us to build up a stepwise model of ligation-based, modular evolution that could pave the way to the emergence of a ribozyme with RNA replicase activity, step at which information-driven Darwinian evolution would be triggered.

Shape-controlled synthesis of metal nanocrystals: simple chemistry meets complex physics?

Nanocrystals are fundamental to modern science and technology. Mastery over the shape of a nanocrystal enables control of its properties and enhancement of its usefulness for a given application. Our aim is to present a comprehensive review of current research activities that center on the shape-controlled synthesis of metal nanocrystals. We begin with a brief introduction to nucleation and growth within the context of metal nanocrystal synthesis, followed by a discussion of the possible shapes that a metal nanocrystal might take under different conditions. We then focus on a variety of experimental parameters that have been explored to manipulate the nucleation and growth of metal nanocrystals in solution-phase syntheses in an effort to generate specific shapes. We then elaborate on these approaches by selecting examples in which there is already reasonable understanding for the observed shape control or at least the protocols have proven to be reproducible and controllable. Finally, we highlight a number of applications that have been enabled and/or enhanced by the shape-controlled synthesis of metal nanocrystals. We conclude this article with personal perspectives on the directions toward which future research in this field might take.

Base-Directed Formation of Fluorescent Silver Clusters

Small silver clusters that form with short oligonucleotides are distinguished by their strong fluorescence. Previous work showed that red and blue/green emitting species form with the cytosine oligonucleotide dC₁₂. To understand how the bases and base sequence influence cluster formation, the blue/green emitting clusters that form with the thymine-containing oligonucleotides dT12, dT₄C₄T₄, and dC₄T₄C₄ are discussed. With dT₁₂ and dT₄C₄T₄, variations in the solution pH establish that the clusters associate with the N3 of thymine. The small clusters are bound to the larger DNA template, as demonstrated by fluorescence anisotropy, circular dichroism, and fluorescence correlation spectroscopy (FCS) studies. For dT₄C₄T₄, FCS studies showed that approximately 50% of the strands are labeled with the fluorescent clusters. Absorption spectra and the gas dependence of the fluorescence show that nonfluorescent clusters also form following the reduction of the silver cation - oligonucleotide conjugates. Fluorescent cluster formation is favored by oxygen, thus indicating that the DNA-bound clusters are partially oxidized. To elaborate the sequence dependence of cluster formation, dC₄T₄C₄ was studied. Cluster formation depends on the oligonucleotide concentration, and higher concentrations favor a red emitting species. A blue/green emissive species dominates at lower concentrations of dC₄T₄C₄, and it has spectroscopic, physical, and chemical properties that are similar to those of the clusters that form with dT₁₂ and dT₄C₄T₄. These results suggest that cytosine- and thymine-containing oligonucleotides stabilize a preferred emissive silver cluster.

Interfacial and solvent effects govern the formation of tris(dibenzylidenacetone)dipalladium(0) microstructures

Organometallic palladium adducts have application as catalysts and as precursors for nanoparticle synthesis. Herein, we study the spontaneous formation of molecular crystals of the organometallic reagent tris(dibenzylidenacetone)dipalladium(0) (Pd(2)(DBA)(3)) in THF/H(2)O binary solvent systems. We report structural and chemical characterization of the resulting diverse structures with shapes including hexagonal platelets, rods, cubes, and stars. Optical microscopy, transmission electron microscopy, scanning electron microscopy, and energy-dispersive spectroscopy were used to determine representative structures and corresponding compositions when formed either in a binary solution or upon evaporation on a surface. The difference in Pd(2)(DBA)(3) particle morphology was attributed to differences in the surface tension of growing crystalline faces. The formation of a majority of rods or hexagonal platelets in solution was shown to be determined by the ratio of THF to H(2)O in the solvent, whereas supersaturation effects and interfacial surface tension played a major role in creating the shape of particles formed upon evaporation of Pd(2)(DBA)(3) droplets on a surface.

Nucleic acid and nucleotide-mediated synthesis of inorganic nanoparticles

Since the advent of practical methods for achieving DNA metallization, the use of nucleic acids as templates for the synthesis of inorganic nanoparticles (NPs) has become an active area of study. It is now widely recognized that nucleic acids have the ability to control the growth and morphology of inorganic NPs. These biopolymers are particularly appealing as templating agents as their ease of synthesis in conjunction with the possibility of screening nucleotide composition, sequence and length, provides the means to modulate the physico-chemical properties of the resulting NPs. Several synthetic procedures leading to NPs with interesting photophysical properties as well as studies aimed at rationalizing the mechanism of nucleic acid-templated NP synthesis are now being reported. This progress article will outline the current understanding of the nucleic acid-templated process and provides an up to date reference in this nascent field.

Structure and activity of apoferritin-stabilized gold nanoparticles

A simple method for synthesizing gold nanoparticles stabilized by horse spleen apoferritin (HSAF) is reported using NaBH(4) or 3-(N-morpholino)propanesulfonic acid (MOPS) as the reducing agent. AuCl(4)(-) reduction by NaBH(4) was complete within a few seconds, whereas reduction by MOPS was much slower; in all cases, protein was required during reduction to keep the gold particles in aqueous solution. Transmission electron microscopy (TEM) showed that the gold nanoparticles were associated with the outer surface of the protein. The average particle diameters were 3.6 and 15.4 nm for NaBH(4)-reduced and MOPS-reduced Au-HSAF, respectively. A 5-nm difference in the UV-Vis absorption maximum was observed for NaBH(4)-reduced (530 nm) and MOPS-reduced Au-HSAF (535 nm), which was attributed to the greater size and aggregation of the MOPS-reduced gold sample. NaBH(4)-reduced Au-HSAF was much more effective than MOPS-reduced Au-HSAF in catalyzing the reduction of 4-nitrophenol by NaBH(4), based on the greater accessibility of the NaBH(4)-reduced gold particle to the substrate. Rapid reduction of AuCl(4)(-) by NaBH(4) was determined to result in less surface passivation by the protein. Methods for studying ferritin-gold nanoparticle assemblies may be readily applied to other protein-metal colloid systems.

Selection of biomolecules capable of mediating the formation of nanocrystals

Biopolymers in the biosphere are well known to mediate the formation of a wide array of inorganic materials, such as bone, shells, lenses, and magnetic particles to name a few. Recently, in vitro experiments with biopolymers such as peptides, RNA, and DNA have shown that templating by these macromolecules can yield a variety of materials under mild reaction conditions. The primary sequence of the biopolymer can be viewed as a proteomic or genomic signature for the templating of an inorganic material from defined metal precursors and reaction conditions. Together with the rapid advances in inorganic particle synthesis by other combinatorial methods, these bioinspired in vitro materials experiments may provide additional insights into possible inorganic materials yet to be discovered and subsequently synthesized by conventional methods. Some of the concepts important to understanding the crystallization phenomena occurring during biopolymer mediation are discussed. A simple kinetic model is provided in the context of known biopolymer-mediated inorganic crystallizations.