Structure and Electronic Spectra of DNA Mini-hairpins with G_n:C_nStems

Abstract

The solution structure of a synthetic DNA mini-hairpin possessing a stilbenediether linker and three G:C base pairs has been obtained using (1)H NMR spectral data and constrained torsion angle molecular dynamics. Notable features of this structure include a compact hairpin loop having a short stilbene-guanine plane-to-plane distance and approximate B-DNA geometry for the three base pairs. Comparison of the electronic spectra of mini-hairpins having one-to-four G:C base pairs and stilbenediether or hexamethyleneglycol linkers reveals the presence of features in the UV and CD spectra of the stilbene-linked hairpins that are not observed for the ethyleneglycol-linked hairpins. Investigation of the electronic structure of a stilbene-linked hairpin having a single G:C base pair by means of time-dependent density functional theory shows that the highest occupied molecular orbital, but not the lowest unoccupied molecular orbital, is delocalized over the stilbene and adjacent guanine. The calculated UV and CD spectra are highly dependent upon hairpin conformation, but reproduce the major features of the experimental spectra. These results illustrate the utility of an integrated experimental and theoretical approach to understanding the complex electronic spectra of pi-stacked chromophores.

Dynamics and Efficiency of Hole Transport in LNA:DNA Hybrid Diblock Oligomers

“…The decrease in the values of Φ cs for this series of LNA hairpins is also larger than that for the DNA hairpins. When the backbone of the G track is locked as 27,28 Molecular dynamics simulations and CD spectroscopy of the stilbene-DNA conjugate A 6 are consistent with the formation of a capped hairpin structure in which the capping group is π-stacked with the neighboring base pair. 29 A snapshot of a minimized structure obtained from a molecular dynamics simulation is shown in Figure 5.…”

Electronic excited states of guanine-cytosine hairpins and duplexes studied by fluorescence spectroscopy

“…The spectra of the longer duplexes d6 and d10 are similar to those of the corresponding hairpins; however, the CD spectrum of d2 is missing the two prominent negative bands observed for the other duplexes and hairpins. Thus, two GC pairs may be sufficient for the formation of a stable base-paired glycol-linked hairpin, 23 but not for the formation of a duplex.…”

Distance‐Dependent Electronic Interactions Across DNA Base Pairs: Charge Transport, Exciton Coupling, and Energy Transfer

“…The structures of exceptionally stable hairpins having stilbenediether (SD) linkers (Figure 1a) have been investigated by means of x‐ray crystallography (Figure 2a),10,11 solution 1 H NMR spectroscopy, and molecular modeling 12. All three methods show that the SD chromophore is π‐stacked with the adjacent base pair and that the base‐pair domains adopt B‐DNA structures with normal helical pitch and rise.…”