Probing the local structure and dynamics of nucleotides using vibrationally enhanced alkynyl stretching

Monitoring the site-specific local structure and dynamics of polynucleotides and DNA is important for understanding their biological functions. However, structurally characterizing these biomolecules with high time resolution has been known to be experimentally challenging. In this work, several 5-silylethynyl-20-deoxynucleosides and 5-substituted phenylethynyl-2'-deoxynucleosides on the basis of deoxycytidine (dC) and deoxythymidine (dT) were synthesized, in which the alkynyl group shows intensified CRC stretching vibration with infrared transition dipole moment magnitude close to that of typical C=O stretching, and exhibits structural sensitivities in both vibrational frequency and spectral width. In particular, 5-trimethylsilylethynyl-2'-dC ((TMS)EdC, molecule 1a) was examined in detail using femtosecond nonlinear IR spectroscopy. The solvent dependent CRC stretching frequency of 1a can be reasonably interpreted mainly as the hydrogen-bonding effect between the solvent and cytosine base ring structure. Transient 2D IR and pump-probe IR measurements of 1a carried out comparatively in two aprotic solvents (DMSO and THF) and one protic solvent (MeOH) further reveal solvent dependent ultrafast vibrational properties, including diagonal anharmonicity, spectral diffusion, vibrational relaxation and anisotropy dynamics. These observed sensitivities are rooted in an extended pi-conjugation of the base ring structure in which the C equivalent to C group is actively involved. Our results show that the intensified C equivalent to C stretching vibration can potentially provide a site-specific IR probe for monitoring the equilibrium and ultrafast structural dynamics of polynucleotides.

Automated summary

This study focuses on improving the time resolution of structural analysis on biomolecules by synthesizing several 5-silylethynyl and 5-substituted phenylethynyl modified nucleosides. The results show that these compounds can serve as structurally sensitive infrared probes for monitoring the dynamic behaviors of polynucleotides.