Lifetimes and Reaction Pathways of Guanine Radical Cations and Neutral Guanine Radicals in an Oligonucleotide in Aqueous Solutions

The exposure of guanine in the oligonucleotide 5′-d­(TCGCT) to one-electron oxidants leads initially to the formation of the guanine radical cation G^•+, its deptotonation product G­(-H)^•, and, ultimately, various two- and four-electron oxidation products via pathways that depend on the oxidants and reaction conditions. We utilized single or successive multiple laser pulses (308 nm, 1 Hz rate) to generate the oxidants CO₃^•– and SO₄^•– (via the photolysis of S₂O₈^2– in aqueous solutions in the presence and absence of bicarbonate, respectively) at concentrations/pulse that were ∼20-fold lower than the concentration of 5′-d­(TCGCT). Time-resolved absorption spectroscopy measurements following single-pulse excitation show that the G^•+ radical (p<i>K</i>_a = 3.9) can be observed only at low pH and is hydrated within 3 ms at pH 2.5, thus forming the two-electron oxidation product 8-oxo-7,8-dihydroguanosine (8-oxoG). At neutral pH, and single pulse excitation, the principal reactive intermediate is G­(-H)^•, which, at best, reacts only slowly with H₂O and lives for ∼70 ms in the absence of oxidants/other radicals to form base sequence-dependent intrastrand cross-links via the nucleophilic addition of N3-thymidine to C8-guanine (5′-G*CT* and 5′-T*CG*). Alternatively, G­(-H)^• can be oxidized further by reaction with CO₃^•–, generating the two-electron oxidation products 8-oxoG (C8 addition) and 5-carboxamido-5-formamido-2-iminohydantoin (2Ih, by C5 addition). The four-electron oxidation products, guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp), appear only after a second (or more) laser pulse. The levels of all products, except 8-oxoG, which remains at a low constant value, increase with the number of laser pulses

Mechanistic Aspects of Hydration of Guanine Radical Cations in DNA

The mechanistic aspects of hydration of guanine radical cations, G^•+ in double- and single-stranded oligonucleotides were investigated by direct time-resolved spectroscopic monitoring methods. The G^•+ radical one-electron oxidation products were generated by SO₄^•– radical anions derived from the photolysis of S₂O₈^2– anions by 308 nm laser pulses. In neutral aqueous solutions (pH 7.0), after the complete decay of SO₄^•– radicals (∼5 μs after the actinic laser flash) the transient absorbance of neutral guanine radicals, G­(-H)^• with maximum at 312 nm, is dominant. The kinetics of decay of G­(-H)^• radicals depend strongly on the DNA secondary structure. In double-stranded DNA, the G­(-H)^• decay is biphasic with one component decaying with a lifetime of ∼2.2 ms and the other with a lifetime of ∼0.18 s. By contrast, in single-stranded DNA the G­(-H)^• radicals decay monophasically with a ∼ 0.28 s lifetime. The ms decay component in double-stranded DNA is correlated with the enhancement of 8-oxo-7,8-dihydroguanine (8-oxoG) yields which are ∼7 greater than in single-stranded DNA. In double-stranded DNA, it is proposed that the G­(-H)^• radicals retain radical cation character by sharing the N1-proton with the N3-site of C in the [G^•+:C] base pair. This [G­(-H)^•:H⁺C ⇆ G^•+:C] equilibrium allows for the hydration of G^•+ followed by formation of 8-oxoG. By contrast, in single-stranded DNA, deprotonation of G^•+ and the irreversible escape of the proton into the aqueous phase competes more effectively with the hydration mechanism, thus diminishing the yield of 8-oxoG, as observed experimentally

Sub-10 nm Self-Assembly of Mesogen-Containing Grafted Macromonomers and Their Bottlebrush Polymers

We explore the morphology and phase behavior of branched diblock macromonomers and their polymers. A series of macromonomers was synthesized based on a disubstituted norbornene. The first branch consists of polydimethylsiloxane (PDMS) while the second branch is a quasi-mesogenic structure incorporating one or more cyanobiphenyl (CB) moieties. Bottlebrush polymers with varying degrees of polymerization were prepared by “graft-through” ring-opening metathesis of the macromonomers. The molecules in the resulting library of macromonomers and bottlebrush polymers self-assemble to form classically observed microphase-separated structures, including spheres, hexagonally packed cylinders, bicontinuous gyroid, and lamellae. The systematic variation of molecular structure, molecular weight of each branch, and degree of polymerization of the polymers results in a diverse set of structures and properties. We report the observation of well-ordered lamellae and cylinders with <i>d</i>-spacings as low as 6.1 and 8.0 nm, respectively. The system displays an asymmetric phase diagram, with large deviations from the canonical phase behavior of linear coil–coil diblocks. Hexagonally packed cylinders and lamellae are observed at remarkably small mass fractions of the mesogen-containing block of 0.07 and 0.21, respectively. The samples are highly birefringent, and polarized optical microscopy revealed the formation of well-developed textures in microphase-separated states formed by cooling samples through the order–disorder transition. The textures are reminiscent of the classic fan-like or focal-conic textures observed in small molecule liquid crystal mesophases, highlighting the formation of unusually large and well-ordered grains of the microphase-separated PDMS and CB microdomains. Apparent crystallization of the CB units in systems with two or three CB moieties per monomer results in distortion of the microphase-separated structure. The small <i>d</i>-spacings and large grain sizes observed here highlight the versatility and potential utility of this molecular architecture for designing and engineering new functional materials

Stereocomplexation of Helical Polycarbodiimides Synthesized from Achiral Monomers Bearing Isopropyl Pendants

A high level of the permanent asymmetry was built into the poly­(<i>N</i>-methyl-<i>N</i>′-(2-isopropyl-6-methylphenyl)­carbodiimide) system by introducing a bulky, substituted phenyl group which revealed a very interesting phenomenological behavior upon heating. This polymer undergoes <i>P</i>/<i>M</i> racemization upon thermal annealing, thus leading to the formation of a stereocomplexed structure. Predominantly <i>P</i> and <i>M</i> helices have been obtained through helix sense selective polymerization by using chiral BINOL-Ti­(IV) diisopropoxide initiator with achiral <i>N</i>-methyl-<i>N</i>′-(2-isopropyl-6-methylphenyl)­carbodiimide monomer. Upon thermal annealing, the specific optical rotation (SOR) of the single-handed polymer begins to decrease but never reaches zero. The SOR plateaus at a large value (−286° for <i>M</i> helices or +283° for <i>P</i> helices), and shortly thereafter the polymer forms a precipitate. The process that polymer undergoes is attributed to stereocomplexation between two complementary strands via racemization. Inspired by the phenomena analogous to classical leucine zippers with isobutyl termini (interlocking motifs), a unique polycarbodiimide scaffold bearing isopropyl pendant groups was designed to play a vital role in the aggregation process with a calculated energy barrier of around 19 ± 0.4 kcal/mol. To investigate the effect of regioregularity in isopropyl groups, a series of isomeric polymers bearing isopropyl segments at the <i>ortho</i>, <i>meta</i>, and <i>para</i> positions have been synthesized, and their self-assembly behavior has been studied by using AFM, SEM, <i>p</i>-XRD, and TEM analytical techniques. To take advantage of both isopropyl zipping motif and increased solubility in organic solvents imparted by octadecyl lateral chains, a new block copolymer, poly­(<i>N</i>-methyl-<i>N</i>′-(2-isopropyl-6-methylphenyl)­carbodiimide)-<i>b</i>-poly­(<i>N</i>-phenyl-<i>N</i>′-octadecyl­carbodiimide) (<b>P-1,2</b>), was designed. The first block, containing the substituted aryl functional group, contributes to the stereocomplexation phenomena, while the second block copolymer, composed of the octadecyl group, imparts solubility and morphological attributes. This unique polymeric scaffold exhibits interesting morphologies such as spherical particles, capsules, wrinkled surface patterns, and fiber-like motifs, which may be associated with supramolecular aggregation. Detailed stereocomplex formation studies will bestow new possibilities in diverse areas, including drug delivery applications, catalysis, and chiral separations