Gamma Peptide Nucleic Acids: As Orthogonal Nucleic Acid Recognition Codes for Organizing Molecular Self-Assembly.

Nucleic acids are an attractive platform for organizing molecular self-assembly because of their specific nucleobase interactions and defined length scale. Routinely employed in the organization and assembly of materials in vitro, however, they have rarely been exploited in vivo, due to the concerns for enzymatic degradation and cross-hybridization with the host's genetic materials. Herein we report the development of a tight-binding, orthogonal, synthetically versatile, and informationally interfaced nucleic acid platform for programming molecular interactions, with implications for in vivo molecular assembly and computing. The system consists of three molecular entities: the right-handed and left-handed conformers and a nonhelical domain. The first two are orthogonal to each other in recognition, while the third is capable of binding to both, providing a means for interfacing the two conformers as well as the natural nucleic acid biopolymers (i.e., DNA and RNA). The three molecular entities are prepared from the same monomeric chemical scaffold, with the exception of the stereochemistry or lack thereof at the γ-backbone that determines if the corresponding oligo adopts a right-handed or left-handed helix, or a nonhelical motif. These conformers hybridize to each other with exquisite affinity, sequence selectivity, and level of orthogonality. Recognition modules as short as five nucleotides in length are capable of organizing molecular assembly.

Comparison of the properties of cellulose nanocrystals and cellulose nanofibrils isolated from bacteria, tunicate, and wood processed using acid, enzymatic, mechanical, and oxidative methods.

This work describes the measurement and comparison of several important properties of native cellulose nanocrystals (CNCs) and cellulose nanofibrils (CNFs), such as crystallinity, morphology, aspect ratio, and surface chemistry. Measurement of the fundamental properties of seven different CNCs/CNFs, from raw material sources (bacterial, tunicate, and wood) using typical hydrolysis conditions (acid, enzymatic, mechanical, and 2,2,6,6-tetramethylpiperidinyl-1-oxyl (TEMPO)-mediated oxidation), was accomplished using a variety of measurement methods. Atomic force microscopy (AFM), transmission electron microscopy (TEM), and 13C cross-polarization magic angle spinning (CPMAS) nuclear magnetic resonance (NMR) spectroscopy were used to conclude that CNCs, which are rodlike in appearance, have a higher crystallinity than CNFs, which are fibrillar in appearance. CNC aspect ratio distributions were measured and ranged from 148±147 for tunicate-CNCs to 23±12 for wood-CNCs. Hydrophobic interactions, measured using inverse gas chromatography (IGC), were found to be an important contribution to the total surface energy of both types of cellulose. In all cases, a trace amount of naturally occurring fluorescent compounds was observed after hydrolysis. Confocal and Raman microscopy were used to confirm that the fluorescent species were unique for each cellulose source, and demonstrated that such methods can be useful for monitoring purity during CNC/CNF processing. This study reveals the broad, tunable, multidimensional material space in which CNCs and CNFs exist.

Bionanocomposites: differential effects of cellulose nanocrystals on protein diblock copolymers.

We investigate the effects of mixing a colloidal suspension of tunicate-derived cellulose nanocrystals (t-CNCs) with aqueous colloidal suspensions of two protein diblock copolymers, EC and CE, which bear two different self-assembling domains (SADs) derived from elastin (E) and the coiled-coil region of cartilage oligomeric matrix protein (C). The resulting aqueous mixtures reveal improved mechanical integrity for the CE+t-CNC mixture, which exhibits an elastic gel network. This is in contrast to EC+t-CNC, which does not form a gel, indicating that block orientation influences the ability to interact with t-CNCs. Surface analysis and interfacial characterization indicate that the differential mechanical properties of the two samples are due to the prevalent display of the E domain by CE, which interacts more with t-CNCs leading to a stronger network with t-CNCs. On the other hand, EC, which is predominantly C-rich on its surface, does not interact as much with t-CNCs. This suggests that the surface characteristics of the protein polymers, due to folding and self-assembly, are important factors for the interactions with t-CNCs, and a significant influence on the overall mechanical properties. These results have interesting implications for the understanding of cellulose hydrophobic interactions, natural biomaterials and the development of artificially assembled bionanocomposites.

Effect of Steric Constraint at the γ-Backbone Position on the Conformations and Hybridization Properties of PNAs.

Conformationally preorganized peptide nucleic acids (PNAs) have been synthesized through backbone modifications at the γ-position, where R = alanine, valine, isoleucine, and phenylalanine side chains. The effects of these side-chains on the conformations and hybridization properties of PNAs were determined using a combination of CD and UV-Vis spectroscopic techniques. Our results show that the γ-position can accommodate varying degrees of sterically hindered side-chains, reaffirming the bimodal function of PNAs as the true hybrids of "peptides" and "nucleic acids."

Synthesis and characterization of conformationally preorganized, (R)-diethylene glycol-containing γ-peptide nucleic acids with superior hybridization properties and water solubility.

Developed in the early 1990s, peptide nucleic acid (PNA) has emerged as a promising class of nucleic acid mimic because of its strong binding affinity and sequence selectivity toward DNA and RNA and resistance to enzymatic degradation by proteases and nucleases; however, the main drawbacks, as compared to other classes of oligonucleotides, are water solubility and biocompatibility. Herein we show that installation of a relatively small, hydrophilic (R)-diethylene glycol ("miniPEG", R-MP) unit at the γ-backbone transforms a randomly folded PNA into a right-handed helix. Synthesis of optically pure (R-MP)γPNA monomers is described, which can be accomplished in a few simple steps from a commercially available and relatively cheap Boc-l-serine. Once synthesized, (R-MP)γPNA oligomers are preorganized into a right-handed helix, hybridize to DNA and RNA with greater affinity and sequence selectivity, and are more water soluble and less aggregating than the parental PNA oligomers. The results presented herein have important implications for the future design and application of PNA in biology, biotechnology, and medicine, as well as in other disciplines, including drug discovery and molecular engineering.

2,3;5,6-Di-O-isopropyl-idene-1-O-(2-phenyl-acet-yl)-α-d-mannofuran-ose.

The title compound, C(20)H(26)O(7), was prepared by esterification of 2,3;5,6-di-O-isopropyl-idene-α-d-mannofuran-ose with phenyl-acetic acid under standard DCC/DMAP (DCC = dicyclohexylcarbodiimide and DMAP = 4-dimethylaminopyridine) con-ditions. The solid-state structure confirms the retention of the α-configuration at the anomeric C atom. The compound is characterized by a relatively rigid framework with only a few degrees of freedom. Comparison with other di-O-isopropyl-idenemannofuran-ose derivatives shows the main differences to be associated with the flexible dimethyl-dioxolane ring, and that there are only small differences for the 2,3-O-isopropyl-idene-α-d-manno-furan-ose backbone. The packing is marked by a large number of weak C-H⋯O inter-actions.

Loop and backbone modifications of peptide nucleic acid improve g-quadruplex binding selectivity.

Targeting guanine (G) quadruplex structures is an exciting new strategy with potential for controlling gene expression and designing anticancer agents. Guanine-rich peptide nucleic acid (PNA) oligomers bind to homologous DNA and RNA to form hetero-G-quadruplexes but can also bind to complementary cytosine-rich sequences to form heteroduplexes. In this study, we incorporated backbone modifications into G-rich PNAs to improve the selectivity for quadruplex versus duplex formation. Incorporation of abasic sites as well as chiral modifications to the backbone were found to be effective strategies for improving selectivity as shown by UV-melting and surface plasmon resonance measurements. The enhanced selectivity is due primarily to decreased affinity for complementary sequences, since binding to the homologous DNA to form PNA-DNA heteroquadruplexes retains high affinity. The improved selectivity of these PNAs is an important step toward using PNAs for regulating gene expression by G-quadruplex formation.

Rhodium(II)-catalyzed decomposition of 3-O-(2-diazo-2-phenylacetyl)-1,2;5,6-di-O-isopropylidene-alpha-D-allofuranose: diastereoselective ether formation.

Standard diazo transfer to 3-O-(2-phenylacetyl)-1,2;5,6-di-O-isopropylidene-alpha-d-allofuranose (2), using p-acetamidobenzenesulfonyl azide (p-ABSA, 3) and DBU as base, provides the expected 3-O-(2-diazo-2-phenylacetyl)-1,2;5,6-di-O-isopropylidene-alpha-D-allofuranose (4) as an orange syrup in 49% isolated yield. Subsequent decomposition of 4 using Rh(2)(OAc)(4) yields ether 5 in a highly diastereoselective manner and in 58% isolated yield. The X-ray crystal structure of 5 proves that both newly produced stereocenters have the (S) configuration; the conformation of the ester group at O-3 of the furanose ring of 5 is used to discuss the possible cause of the observed stereoselectivity.