Dynamic cross-linking is retained in duplex DNA after multiple exchange of strands

Vinylidene-quinone methides, photochemical generation and β-silicon effect on reactivity

Irradiation of 2-alkynylphenols resulted in the generation of vinylidene-quinone methides (QMs), which were detected by laser flash photolysis in organic solvents and aqueous acetonitrile. QMs' spectroscopic properties and electrophilicity were both significantly affected by β-silicon effect. The hydration of the alkynyl moiety (22 and 900 M(-1) s(-1)for QM-1 and QM-2, in aqueous acetonitrile) was an acid- and base-catalyzed process. The addition of amines was fast (9.2 × 10(3) M(-1) s(-1) < k(2) < 1.3 × 10(8) M(-1) s(-1)), yielding ketimines, with primary amines.

Experimental approaches to identify cellular G-quadruplex structures and functions

Guanine-rich nucleic acids can fold into non-canonical DNA secondary structures called G-quadruplexes. The formation of these structures can interfere with the biology that is crucial to sustain cellular homeostases and metabolism via mechanisms that include transcription, translation, splicing, telomere maintenance and DNA recombination. Thus, due to their implication in several biological processes and possible role promoting genomic instability, G-quadruplex forming sequences have emerged as potential therapeutic targets. There has been a growing interest in the development of synthetic molecules and biomolecules for sensing G-quadruplex structures in cellular DNA. In this review, we summarise and discuss recent methods developed for cellular imaging of G-quadruplexes, and the application of experimental genomic approaches to detect G-quadruplexes throughout genomic DNA. In particular, we will discuss the use of engineered small molecules and natural proteins to enable pull-down, ChIP-Seq, ChIP-chip and fluorescence imaging of G-quadruplex structures in cellular DNA.

Inducible alkylation of DNA by a quinone methide-peptide nucleic acid conjugate

The reversibility of alkylation by a quinone methide intermediate (QM) avoids the irreversible consumption that plagues most reagents based on covalent chemistry and allows for site specific reaction that is controlled by the thermodynamics rather than kinetics of target association. This characteristic was originally examined with an oligonucleotide QM conjugate, but broad application depends on alternative derivatives that are compatible with a cellular environment. Now, a peptide nucleic acid (PNA) derivative has been constructed and shown to exhibit an equivalent ability to delivery the reactive QM in a controlled manner. This new conjugate demonstrates high selectivity for a complementary sequence of DNA even when challenged with an alternative sequence containing a single T/T mismatch. Alternatively, alkylation of noncomplementary sequences is only possible when a template strand is present to colocalize the conjugate and its target. For efficient alkylation in this example, a single-stranded region of the target is required adjacent to the QM conjugate. Most importantly, the intrastrand self-adducts formed between the PNA and its attached QM remained active and reversible over more than 8 days in aqueous solution prior to reaction with a chosen target added subsequently.

Hydrogen peroxide inducible DNA cross-linking agents: targeted anticancer prodrugs

The major concern for anticancer chemotherapeutic agents is the host toxicity. The development of anticancer prodrugs targeting the unique biochemical alterations in cancer cells is an attractive approach to achieve therapeutic activity and selectivity. We designed and synthesized a new type of nitrogen mustard prodrug that can be activated by high level of reactive oxygen species (ROS) found in cancer cells to release the active chemotherapy agent. The activation mechanism was determined by NMR analysis. The activity and selectivity of these prodrugs toward ROS was determined by measuring DNA interstrand cross-links and/or DNA alkylations. These compounds showed 60-90% inhibition toward various cancer cells, while normal lymphocytes were not affected. To the best of our knowledge, this is the first example of H(2)O(2)-activated anticancer prodrugs.

Applications of ortho-quinone methide intermediates in catalysis and asymmetric synthesis

Ortho-quinone methides are important synthetic intermediates and widely implicated in biological processes. In this Synopsis, recent advances concerning the synthesis and utility of these intermediates are discussed with a particular emphasis on metal-catalyzed formation of quinone methide intermediates. Additionally, applications of these intermediates as partners in asymmetric synthesis will be discussed including methods we have developed that involve the enantioselective Pd-catalyzed formation of ortho-quinone methides and the trapping of aforementioned intermediates with diverse nucleophiles.

Quinone methide generation via photoinduced electron transfer

Photochemical activation of water-soluble 1,8-naphthalimide derivatives (NIs) as alkylating agents has been achieved by irradiation at 310 and 355 nm in aqueous acetonitrile. Reactivity in aqueous and neat acetonitrile has been extensively investigated by laser flash photolysis (LFP) at 355 nm, as well as by steady-state preparative irradiation at 310 nm in the presence of water, amines, thiols, and ethyl vinyl ether. Product distribution analysis revealed fairly efficient benzylation of the amines, hydration reaction, and 2-ethoxychromane generation, in the presence of ethyl vinyl ether, resulting from a [4 + 2] cycloaddition onto a transient quinone methide. Remarkably, we found that the reactivity was dramatically suppressed under the presence of oxygen and radical scavengers, such as thiols, which was usually associated with side product formation. In order to unravel the mechanism responsible for the photoreactivity of these NI-based molecules, a detailed LFP study has been carried out with the aim to characterize the transient species involved. LFP data suggest a photoinduced electron transfer (PET) involving the NI triplet excited state (λ(max) 470 nm) of the NI core and the tethered quinone methide precursor (QMP) generating a radical ions pair NI(•-) (λ(max) 410 nm) and QMP(•+). The latter underwent fast deprotonation to generate a detectable phenoxyl radical (λ(max) 390 and 700 nm), which was efficiently reduced by the radical anion NI(•-), generating detectable QM. The mechanism proposed has been validated through a LFP investigation at 355 nm exploiting an intermolecular reaction between the photo-oxidant N-pentylnaphthalimide (NI-P) and a quaternary ammonium salt of a Mannich base as QMP (2a), in both neat and aqueous acetonitrile. Remarkably, these experiments revealed the generation of the model o-QM (λ(max) 400 nm) as a long living transient mediated by the same reactivity pathway. Negligible QM generation has been observed under the very same conditions by irradiation of the QMP in the absence of the NI. Owing to the NIs redox and recognition properties, these results represent the first step toward new molecular devices capable of both biological target recognition and photoreleasing of QMs as alkylating species, under physiological conditions.

Few constraints limit the design of quinone methide-oligonucleotide self-adducts for directing DNA alkylation

Nucleotide sequences minimally containing adenosine, cytosine or guanosine are sufficient to form intrastrand oligonucleotide quinone methide self-adducts reversibly for subsequent alkylation of complementary DNA. The general lack of sequence restrictions should now allow for alkylation of most any target of interest although reaction is most efficient when the self-adducts contain guanine residues and do not form hairpin structures.