Nucleobase modification by an RNA enzyme.

Ribozymes can catalyze phosphoryl or nucleotidyl transfer onto ribose hydroxyls of RNA chains. We report a single ribozyme that performs both reactions, with a nucleobase serving as initial acceptor moiety. This unprecedented combined reaction was revealed while investigating potential contributions of ribose hydroxyls to catalysis by kinase ribozyme K28. For a 58nt, cis-acting form of K28, each nucleotide could be replaced with the corresponding 2΄F analog without loss of activity, indicating that no particular 2΄OH is specifically required. Reactivities of two-stranded K28 variants with oligodeoxynucleotide acceptor strands devoid of any 2΄OH moieties implicate modification on an internal guanosine N-2, rather than a ribose hydroxyl. Product mass suggests formation of a GDP(S) adduct along with a second thiophosphorylation, implying that the ribozyme catalyzes both phosphoryl and nucleotidyl transfers. This is further supported by transfer of radiolabels into product from both α and γ phosphates of donor molecules. Furthermore, periodate reactivity of the final product signifies acquisition of a ribose sugar with an intact 2΄-3΄ vicinal diol. Neither nucleobase modification nor nucleotidyl transfer has previously been reported for a kinase ribozyme, making this a first-in-class ribozyme. Base-modifying ribozymes may have played important roles in early RNA world evolution by enhancing nucleic acid functions.

RNA-DNA Chimeras in the Context of an RNA World Transition to an RNA/DNA World.

The RNA world hypothesis posits that DNA and proteins were later inventions of early life, or the chemistry that gave rise to life. Most scenarios put forth for the emergence of DNA assume a clean separation of RNA and DNA polymer, and a smooth transition between RNA and DNA. However, based on the reality of "clutter" and lack of sophisticated separation/discrimination mechanisms in a protobiological (and/or prebiological) world, heterogeneous RNA-DNA backbone containing chimeric sequences could have been common-and have not been fully considered in models transitioning from an RNA world to an RNA-DNA world. Herein we show that there is a significant decrease in Watson-Crick duplex stability of the heterogeneous backbone chimeric duplexes that would impede base-pair mediated interactions (and functions). These results point to the difficulties for the transition from one homogeneous system (RNA) to another (RNA/DNA) in an RNA world with a heterogeneous mixture of ribo- and deoxyribonucleotides and sequences, while suggesting an alternative scenario of prebiological accumulation and co-evolution of homogeneous systems (RNA and DNA).

A Deep Cavitand Templates Lactam Formation in Water.

Cyclization reactions are common processes in organic chemistry and show familiar patterns of reaction rates vs ring size. While the details vary with the nature of bond being made and the number of unsaturated atoms, small rings typically form quickly despite angle strain, medium size rings form very slowly due to internal strains, and large rings form slowly (when they form at all) because fewer and less probable conformations bring the ends of the substrate together. High dilution is commonly used to slow the competing bi- and higher molecular processes. Here we apply cavitands to the formation of medium size lactams from ω-amino acids in aqueous (D2O) solution. The cavitands bind the amino acids in folded conformations that favor cyclization by bringing the ends closer together. Yields of a 12-membered lactam are improved 4.1-fold and 13-membered lactam 2.8-fold by the cavitand template. The results open possibilities for moving organic reactions into water even when the processes involve dehydration.

Alkyl groups fold to fit within a water-soluble cavitand.

We report here a widened, deep cavitand host that binds hydrophobic and amphiphilic guests in D2O. Small alkanes (C6 to C11) are bound in compressed conformations and tumble rapidly within the space. Longer n-alkanes (C13 to C14), n-alcohols, and α,ω-diols are taken up in folded conformations. The guests' termini are exposed to solvent while atoms near the alkane's center are buried and protected. The cavitand acts as a concave template that pushes terminal atoms of the guest closer together. The unexpected binding modes are interpreted in terms of the size and shape of the space accessible in the new cavitand.

Folded alkyl chains in water-soluble capsules and cavitands.

A deep cavitand with ionic "feet" dimerizes around hydrophobic compounds in D2O. Longer n-alkane guests, C14-C18, are encapsulated in contorted conformations and NMR is used to deduce their shapes. Competition experiments establish the driving forces involved and how they compensate for the steric clashes in the folded structures of the encapsulated alkanes. Bolaamphiphiles instead prefer to bind in the monomeric cavitand with conformations that bury the methylenes but expose the polar head groups to solvent.

Fluorous effects in amide-based receptors for anions.

Hybrid receptors designed to recognize both the sulfonate headgroup and the fluorous tail of perfluorooctanesulfonate (CF(3)(CF(2))(7)SO(3)(-), "PFOS") were prepared by coupling fluorinated carboxylic acids onto poly(aminomethyl)benzene scaffolds. Binding to PFOS, CF(3)SO(3)(-), p-TsO(-), and Cl(-) was monitored by (1)H NMR and isothermal titration calorimetry (ITC). In chloroform solvent, hydrogen-bonding to anions is accompanied by downfield shifts in the amide NH protons of the fluorinated receptors and by evolution of heat. Association constants for 1:1 complexation (K(assoc)) are >1000 M(-1). An analogous hydrocarbon receptor binds weakly to anionic guests (K(assoc) < 50 M(-1)). Ab initio calculations indicate that the differences in 1:1 binding strengths between fluorous and nonfluorous hosts cannot be ascribed to differences in NH donor acidities.

The effects of hexafluoroisopropanol on guest binding by water-soluble capsule and cavitand hosts.

Encapsulation of amphiphilic guests in a water-soluble cavitand is enhanced by the addition of hexafluoroisopropanol (HFIP). While binding of n-alkanes in cavitands in HFIP/D2O mixtures was similar to that observed in 100% D2O, the binding of guests with terminal polar groups was quite different. Several α,ω-bolaamphiphiles: alkyldiols (C10-C12), a dinitrile (C14) and a diacid (C16) became encapsulated in HFIP/D2O solutions. As little as 15% HFIP v/v in D2O moves the guest from cavitand to the dimeric capsule. The unusual binding of polar functional groups inside the confined space is deduced from NMR COSY spectra and supported by DFT calculations. Alkane guests are also encapsulated in 100% HFIP.

Complexation of alkyl groups and ghrelin in a deep, water-soluble cavitand.

A cavitand with ionic, but nonionizable "feet" folds around hydrophobic guests in D2O. Short alkanes and ibuprofen are included and exchange rates are slow on the NMR timescale. Normal octanoyl groups show good affinity for the cavitand and the gastric peptide ghrelin is bound at low pH and physiological temperature.

Exploring Anion-Induced Conformational Flexibility and Molecular Switching in a Series of Heteroaryl-Urea Receptors.

Anion binding studies of 1,10-phenanthroline- and 2-pyridyl-substituted urea-based receptors reveal that guest-dependent conformations exist in structural variants related to a previously investigated bipyridyl-based receptor. Dynamic conformational switching persists in a monofunctional pyridyl-urea receptor, and the preorganization provided by a phenanthroline-based analogue promotes convergence of anion coordinating groups to a single guest. Despite this predisposition for anion coordination, the conformational flexibility of the bipyridyl-based receptor provides the most selective motif for H2PO4- coordination. Furthermore, the two new phenanthrolyl- and pyridyl-receptors serve as models of the bipyridyl-based receptor, elucidating accurate stepwise association constants for 1:2 host/guest binding by this receptor, and suggest that oxoanions prefer the embrace of a "U" conformation in 1:1 complexes.

Intramolecular N-H···Cl hydrogen bonds in the outer coordination sphere of a bipyridyl bisurea-based ligand stabilize a tetrahedral FeLCl2 complex.

A bipyridyl-based anion receptor is utilized as a ligand in a tetrahedral FeCl2 complex and demonstrates secondary coordination sphere influence through intramolecular hydrogen bonding to the chloride ligands as evidenced by X-ray crystallography.

Lithium-selective phosphine oxide-based ditopic receptors show enhanced halide binding upon alkali metal ion coordination.

Previous work on a ditopic receptor based on a tripodal phosphine oxide core demonstrated preferential enhancement of bromide binding over chloride or iodide in the presence of lithium cation. Current studies on an elongated receptor provide evidence that preferential bromide binding enhancement in the presence of lithium cation is common to this receptor class in general, and that lengthening of the receptor results in an overall increase in halide association. Furthermore, the extended receptor shows a strong preference for Li+ binding in solution.

Lithium cation enhances anion binding in a tripodal phosphine oxide-based ditopic receptor.

A tripodal ditopic receptor presents H-bond donors and a phosphine oxide to potential guests. In the idealized binding conformation, an endohedral P=O functionality provides enhanced halide binding in the presence of lithium with the greatest ΔΔG° observed for bromide, while minimal changes in K(a) are observed in the presence of sodium.

Hydrogen bonding vs steric gearing in a hexasubstituted benzene.

Treatment of hexakis(bromomethyl)benzene with excess NaN 3, followed by hydrogenation of the resultant polyazide, affords hexamine 3 in high yield. Coupling to six equivalents of nonanoic acid provides hexamide 5 without chromatographic purification. The NH resonance of 5 appears far downfield (approximately 9.7 ppm) in CDCl3 and is unaffected by changes in concentration or by addition of chloride or trifluoromethanesulfonate ions. DFT calculations predict that 5 exists as a bowl, with all six substituents intramolecularly H-bonded together on one side of the plane defined by the anchoring arene.