2‐Phenanthrenyl–DNA: Synthesis, Pairing, and Fluorescence Properties

Abstract

Three 2′‐phenanthrenyl‐C‐deoxyribonucleosides with donor (phenNH2), acceptor (phenNO2), or no (phenH) substitution on the phenanthrenyl core were synthesized and incorporated into oligodeoxyribonucleotides. Duplexes containing either one or three consecutive phenR residues, which were located opposite each other, were formed. Within these residues, the phenR residues are expected to recognize each other through interstrand stacking interactions, in much the same way as described previously for biphenyl DNA. The thermal, thermodynamic, and fluorescence properties of such duplexes were determined by UV melting analysis and fluorescence spectroscopy. Depending on the nature of the substituent, the thermal stability of single‐modified duplexes can vary between −2.7 to +11.3 °C in Tm and that of triple‐modified duplexes from +7.8 to +11.1 °C. Van′t Hoff analysis suggested that the observed higher thermodynamic stability in phenH‐ and phenNO2‐containing duplexes is of enthalpic origin. A single phenH or phenNO2 residue in a bulge position also stabilizes a corresponding duplex. If a phenNO2 residue is placed in a bulge position next to a base mismatch this can lead, in a sequence‐dependent manner, to duplex destabilization. The phenNO2 residue was found to be a highly efficient (10–100‐fold) quencher of phenH and phenNH2 fluorescence if placed in the opposite position to the fluorophores. When phenH and phenNH2 residues were placed opposite each other, efficient quenching of phenH and enhancement of phenNH2 fluorescence was found, which is an indicator for electron‐ or energy‐transfer processes between the aromatic units.

Fluorescent Analogs of Biomolecular Building Blocks: Design, Properties, and Applications

“…It was used to explore environmental and dynamics features of DNA oligonucleotides 428,444–452. A phenanthrenyl nucleoside, recently reported by Leumann, was used to explore electron transfer in DNA 453,454…”

Modulation of Excess Electron Transfer through LUMO Gradients in DNA Containing Phenanthrenyl Base Surrogates

“…This effect was observed in earlier studies with non-hydrogen bonding base surrogates and was found to be an enthalpy driven process induced by the increased hydrophobic interactions of such base surrogates. [11,15] An expected decrease in stability was observed for duplexes containing electron donating groups and vice versa a stabilization of duplexes containing electron withdrawing groups. Circular dichroism (CD) spectroscopy revealed that the secondary structure of natural DNA is not disturbed by the phenanthrenyl or pyrenyl modifications.…”

“…The synthesis of the NH2 phen and phen phosphoramidites applicable for automated DNA synthesis was performed according to published procedures. [11] The introduction of a cyano group required a palladium catalyzed substitution of the In order to study the EET properties through phenanthrenyl base surrogates a α-C-nucleosidic dimethylamino-pyrene (C-AP) was synthesized that could intercalate well against an abasic site, which enables an efficient photo induced electron injection due to the close proximity to the phenanthrenyl stack. [12] The synthesis involved a nucleosidation of the chloro Hofer sugar and a Gilman cuprate [13] of the 6-bromo-N,N-dimethylpyren-1-amine, which was received from bromination, nitrification, reduction and dimethylation of the amine function of the pyrene (see Scheme S1 and Scheme S2 in ESI).…”

Synthesis and Properties of Oligonucleotides Containing Novel Fluorescent Biaryl Units

“…The sample temperature was increased by 0.5°C min -1 . The thermodynamic parameters of the duplexes on duplex formation were determined by calculations based on the slope of a 1/T m vs. ln(C T /4) plot, where C T (2,4,6,10,16,26,44,70,120, and 200 µ) is the total concentration of single strands.…”