Exciton delocalization in a fully synthetic DNA-templated bacteriochlorin dimer

Abstract

We synthesized a de novo bacteriochlorin and created its dimer covalently attached to DNA. According to the spectral properties evaluated by modeling, the bacteriochlorin dimer showed exciton delocalization comparable to the natural Bchla dimer.

Minimizing Structural Heterogeneity in DNA Self-Assembled Dye Templating via DNA Origami-Tuned Conformations

“…Such dyes can have moieties whose water affinity and stericity play key roles in controlling dye-packing, and hence the extent of exciton delocalization, quantified as the exciton hopping parameter ( J m,n ), thoroughly described in the introduction of Mass et al J m,n and dye-packing configuration can be extracted from absorption and circular dichroism (CD) spectra using Kühn–Renger–May (KRM) exciton-vibrational dynamics theory where the transition dipole moments of dyes (hereinafter dipoles) are used. Interestingly, for LHC-derived bacteriochlorin dimer spectra, KRM modeling favorably compares to the dimer configurations and J m,n . Molecular dynamics (MD) simulations can favorably substantiate KRM models .…”

“…DNA-templated dye aggregation is used to engineer delocalized excitons, albeit template conformation can affect aggregate configuration. In general, DNA, with its well-known structure and properties, can be chemically − and physically − modified to template molecules. Furthermore, the thermal stability of DNA templates can be tuned with bridged nucleotides .…”

“…The latter naturally appears in biological processes including DNA recombination and structurally consists of four DNA duplex arms joined in a core. While duplexes control the formation of dye dimers , or cojoined dyes, , the core of a junction, such as the core of the 3-arm junction or HJ, enables systematic scalability of aggregate size. ,,− Using HJ, dyes can be singly or doubly linked to DNA. Such dyes can have moieties whose water affinity and stericity play key roles in controlling dye-packing, and hence the extent of exciton delocalization, quantified as the exciton hopping parameter ( J m,n ), thoroughly described in the introduction of Mass et al J m,n and dye-packing configuration can be extracted from absorption and circular dichroism (CD) spectra using Kühn–Renger–May (KRM) exciton-vibrational dynamics theory where the transition dipole moments of dyes (hereinafter dipoles) are used.…”

“…Molecular dynamics (MD) simulations can favorably substantiate KRM models . However, recently, ensemble-level data features were not readily interpreted as a population of aggregates with a single configuration. ,− ,,,, Instead, the features were attributed to the aggregate configurations affected by the global and local conformations of the DNA template (Scheme A,B) and dye-DNA interactions (Scheme C ), underscoring the need to investigate the heterogeneity of the template to minimize the heterogeneity of the aggregate.…”

“…Thus, methods for restricting global conformations of HJ are needed. To prevent HJ isomerization in a dimer, two arms of the HJ were immobilized in solution by unpaired thymidines . Because the J m,n was small, noncovalent interactions were argued .…”