Single-molecule DNA sequencing of widely varying GC-content using nucleotide release, capture and detection in microdroplets.

Despite remarkable progress in DNA sequencing technologies there remains a trade-off between short-read platforms, having limited ability to sequence homopolymers, repeated motifs or long-range structural variation, and long-read platforms, which tend to have lower accuracy and/or throughput. Moreover, current methods do not allow direct readout of epigenetic modifications from a single read. With the aim of addressing these limitations, we have developed an optical electrowetting sequencing platform that uses step-wise nucleotide triphosphate (dNTP) release, capture and detection in microdroplets from single DNA molecules. Each microdroplet serves as a reaction vessel that identifies an individual dNTP based on a robust fluorescence signal, with the detection chemistry extended to enable detection of 5-methylcytosine. Our platform uses small reagent volumes and inexpensive equipment, paving the way to cost-effective single-molecule DNA sequencing, capable of handling widely varying GC-bias, and demonstrating direct detection of epigenetic modifications.

Single-molecule detection of deoxyribonucleoside triphosphates in microdroplets.

A new approach to single-molecule DNA sequencing in which dNTPs, released by pyrophosphorolysis from the strand to be sequenced, are captured in microdroplets and read directly could have substantial advantages over current sequence-by-synthesis methods; however, there is no existing method sensitive enough to detect a single nucleotide in a microdroplet. We have developed a method for dNTP detection based on an enzymatic two-stage reaction which produces a robust fluorescent signal that is easy to detect and process. By taking advantage of the inherent specificity of DNA polymerases and ligases, coupled with volume restriction in microdroplets, this method allows us to simultaneously detect the presence of and distinguish between, the four natural dNTPs at the single-molecule level, with negligible cross-talk.

Orbital Crossings Activated through Electron Injection: Opening Communication between Orthogonal Orbitals in Anionic C1-C5 Cyclizations of Enediynes.

Generally, the long-range electronic communication between spatially orthogonal orbitals is inefficient and limited to field and inductive effects. In this work, we provide experimental evidence that such communication can be achieved via intramolecular electron transfer between two degenerate and mutually orthogonal frontier molecular orbitals (MOs) at the transition state. Interaction between orthogonal orbitals is amplified when the energy gap between these orbitals approaches zero, or at an "orbital crossing". The crossing between two empty or two fully occupied MOs, which do not lead to stabilization, can be "activated" when one of the empty MOs is populated (i.e., electron injection) or one of the filled MOs is depopulated (i.e., hole injection). In reductive cycloaromatization reactions, such crossings define transition states with energies defined by both the in-plane and out-of-plane π-systems. Herein, we provide experimental evidence for the utility of this concept using orbital crossings in reductive C1-C5 cycloaromatization reactions of enediynes. Communication with remote substituents via orbital crossings greatly enhances regioselectivity of the ring closure step in comparison to the analogous radical cyclizations. We also present photophysical data pertaining to the efficiency of electron injection into the benzannelated enediynes.

Five discrete multinuclear metal-organic assemblies from one ligand: deciphering the effects of different templates.

A rigid organic ligand, formed through the subcomponent self-assembly of p-toluidine and 6,6'-diformyl-3,3'-bipyridine, was employed in a systematic investigation into the synergistic and competing effects of metal and anion templation. A range of discrete and polymeric metal-organic complexes were formed, many of which represent structure types that have not previously been observed and whose formation would not be predicted on taking into account solely geometric considerations. These complex structures, capable of binding multiple guests within individual binding pockets, were characterized by NMR, ESI-MS, and single-crystal X-ray diffraction. The factors that stabilize individual complexes and lead to the formation of one over another are discussed.

Anion-induced reconstitution of a self-assembling system to express a chloride-binding Co10L15 pentagonal prism.

Biochemical systems are adaptable, capable of reconstitution at all levels to achieve the functions associated with life. Synthetic chemical systems are more limited in their ability to reorganize to achieve new functions; they can reconfigure to bind an added substrate (template effect) or one binding event may modulate a receptor's affinity for a second substrate (allosteric effect). Here we describe a synthetic chemical system that is capable of structural reconstitution on receipt of one anionic signal (perchlorate) to create a tight binding pocket for another anion (chloride). The complex, barrel-like structure of the chloride receptor is templated by five perchlorate anions. This second-order templation phenomenon allows chemical networks to be envisaged that express more complex responses to chemical signals than is currently feasible.

Hybrids of amino acids and acetylenic DNA-photocleavers: optimising efficiency and selectivity for cancer phototherapy.

Hybrid agents which combine potent DNA-photocleavers with tunable amino acids or small peptides were designed to improve selectivity of Nature's most potent class of antibiotics towards cancer cells. The ability of these compounds to photocleave DNA is controlled by their incorporation into hybrid architectures with functional elements derived from natural amino acids. These conjugates are highly effective at inducing double-strand DNA cleavage and, in some cases, rival or even surpass both naturally occurring DNA cleavers and anticancer agents that are currently in clinical use. The possibility of triggering their activity in a photochemical and pH-sensitive fashion allows for a high degree of selectivity over activation. The conjugates were shown to penetrate cell membranes and induce efficient intracellular DNA cleavage. Initial in vitro tests against a variety of cancer cell lines confirm the potential of these compounds as anticancer agents at low nanomolar concentrations.

Subcomponent self-assembly and guest-binding properties of face-capped Fe4L4(8+) capsules.

A general method for preparing Fe(4)L(4) face-capped tetrahedral cages through subcomponent self-assembly was developed and has been demonstrated using four different C(3)-symmetric triamines, 2-formylpyridine, and iron(II). Three of the triamines were shown also to form Fe(2)L(3) helicates when the appropriate stoichiometry of subcomponents was used. Two of the cages were observed to have nearly identical Fe-Fe distances in the solid state, which enabled their ligands to be coincorporated into a collection of mixed cages. Only one of the cages combined a sufficiently large cavity with the sufficiently small pores required for guest binding, taking up a wide variety of guest species in size- and shape-selective fashion.

Reversible anion-templated self-assembly of [2+2] and [3+3] metallomacrocycles containing a new dicopper(I) motif.

A new dicopper(I) complex is reported that can be incorporated into extended architectures through multitopic carboxylate linkers; reversible carboxylate templation under pH control led to the formation of [2+2] and [3+3] metallomacrocycles.

C-lysine conjugates: pH-controlled light-activated reagents for efficient double-stranded DNA cleavage with implications for cancer therapy.

Double-stranded DNA cleavage of light-activated lysine conjugates is strongly enhanced at the slightly acidic pH (<7) suitable for selective targeting of cancer cells. This enhancement stems from the presence of two amino groups of different basicities. The first amino group plays an auxiliary role by enhancing solubility and affinity to DNA, whereas the second amino group, which is positioned next to the light-activated DNA cleaver, undergoes protonation at the desired pH threshold. This protonation results in two synergetic effects which account for the increased DNA-cleaving ability at the lower pH. First, lysine conjugates show tighter binding to DNA at the lower pH, which is consistent with the anticipated higher degree of interaction between two positively charged ammonium groups with the negatively charged phosphate backbone of DNA. Second, the unproductive pathway which quenches the excited state of the photocleaver through intramolecular electron transfer is eliminated once the donor amino group next to the chromophore is protonated. Experiments in the presence of traps for diffusing radicals show that reactive oxygen species do not contribute significantly to the mechanism of DNA cleavage at the lower pH, which is indicative of tighter binding to DNA under these conditions. This feature is valuable not only because many solid tumors are hypoxic but also because cleavage which does not depend on diffusing species is more localized and efficient. Sequence-selectivity experiments suggest combination of PET and base alkylation as the chemical basis for the observed DNA damage. The utility of these molecules for phototherapy of cancer is confirmed by the drastic increase in toxicity of five conjugates against cancer cell lines upon photoactivation.

White phosphorus is air-stable within a self-assembled tetrahedral capsule.

The air-sensitive nature of white phosphorus underlies its destructive effect as a munition: Tetrahedral P4 molecules readily react with atmospheric dioxygen, leading this form of the element to spontaneously combust upon exposure to air. Here, we show that hydrophobic P4 molecules are rendered air-stable and water-soluble within the hydrophobic hollows of self-assembled tetrahedral container molecules, which form in water from simple organic subcomponents and iron(II) ions. This stabilization is not achieved through hermetic exclusion of O2 but rather by constriction of individual P4 molecules; the addition of oxygen atoms to P4 would result in the formation of oxidized species too large for their containers. The phosphorus can be released in controlled fashion without disrupting the cage by adding the competing guest benzene.

DNA damage-site recognition by lysine conjugates.

Simple lysine conjugates are capable of selective DNA damage at sites approximating a variety of naturally occurring DNA-damage patterns. This process transforms single-strand DNA cleavage into double-strand cleavage with a potential impact on gene and cancer therapy or on the design of DNA constructs that require disassembly at a specific location. This study constitutes an example of DNA damage site recognition by molecules that are two orders of magnitude smaller than DNA-processing enzymes and presents a strategy for site-selective cleavage of single-strand nucleotides, which is based on their annealing with two shorter counterstrands designed to recreate the above duplex damage site.

Two-photon excitation of substituted enediynes.

Electronic spectroscopy of nine benzannelated enediynes and a related fulvene was studied under one-photon and two-photon excitation conditions. We utilize measured absorbance and emission spectra and time-resolved fluorescence decays of these molecules to calculate their radiative lifetimes and fluorescence quantum yields. The fluorescence quantum yields for the other compounds were referenced to the fluorescence quantum yield of compound 3 and used to determine relative two-photon absorption cross-sections. Further insight into experimental studies has been achieved using time-dependent density functional (TD-DFT) computations. The probability of two-photon absorption (TPA) increases noticeably for excitation to the higher excited states. The photophysical properties of benzannelated enediynes are sensitive to substitutions at both the core and the periphery of the enediyne chromophore. Considerably enhanced two-photon absorption is observed in an enediyne with donor substitution in the middle and acceptor substitution at the termini. Excited states with B symmetry are not active in TPA spectra. From a practical point of view, this study extends the range of wavelengths applicable for activation of the enediyne moiety from 350 to 600 nm and provides a rational basis for future studies in this field. Our theoretical computations confirmed that lowest energy TPA in benzannelated enediynes involves different orbitals than lowest energy one-photon absorbance and provided further support to the notion that introduction of donor and acceptor substituents at different ends of a molecule increases TPA.

Synthesis of selectively deuterated fulvenes and indenes from enediynes.

A facile enediyne--> fulvene--> indene transformation provides a route to all possible isotopomers of substituted fulvenes and indenes.

Control of kinetics and thermodynamics of [1,5]-shifts by aromaticity: a view through the prism of Marcus theory.

The effects of aromatic stabilization on the rates of [1,5]-hydrogen shifts in a series of carbo- and heterocyclic dihydroaromatic compounds were estimated by B3LYP/6-31G computations. The aromatic stabilization energy of the product is directly translated into increased exothermicity of these reactions. Relative trends for a significant range of endothermic and exothermic [1,5]-shifts with different intrinsic activation energies are reliably described by Marcus theory. The effects of aromaticity or antiaromaticity are very large and can lead to dramatic acceleration or deceleration of [1,5]-hydrogen shifts and even to complete disappearance of the reaction barrier. Not only the activation energy but the shape and position of the reaction barrier can be efficiently controlled by changes in the aromaticity of the products, making these systems interesting models for studying hydrogen tunneling. Marcus theory can also be applied successfully to other pericyclic shifts such as [1,5]-shifts which involve chlorine and methyl transfer.