Playing the notes of DNA with light: extremely high frequency nanomechanical oscillations

Abstract

We use a double nanohole (DNH) optical tweezer with two trapping lasers beating to excite the vibrational modes of single-stranded DNA (ssDNA) fragments in the extremely high frequency range. We find the resonant vibration frequency of a 20 base ssDNA to be 40 GHz. We show that the change in the resonant frequency for different lengths of the DNA strand is in good agreement with one dimensional lattice vibration theory. Thus the DNH tweezer system could distinguish between different lengths of DNA strands with resolution down to a few bases. By varying the base sequence and length, it is possible to adjust the resonance frequency vibration spectrum. The technique shows the potential for use in sequencing applications if we can improve the resolution of the present system to detect changes in resonant frequency for a single base change in a given sequence. The technique is single-molecule and label-free as compared to the existing methods used for DNA characterization like gel electrophoresis.

Plasmonic optical tweezers based on nanostructures: fundamentals, advances and prospects

“…Two years later, the same research group distinguished the bound and unbound forms of a single protein [136], the binding of zipping and unzipping of single DNA [31] and the single protein binding kinetics of a single human albumin [130]. Kontala et al used a double nanoaperture POT with two trapping lasers beating to excite the vibration modes of single-stranded DNA fragments in the 10-100 GHz frequency range [137]. This approach established the ability to characterize small DNA strands with resolution of a few base pairs and has the potential to be extended further for exact base sequence determination [137].…”

“…Kontala et al used a double nanoaperture POT with two trapping lasers beating to excite the vibration modes of single-stranded DNA fragments in the 10-100 GHz frequency range [137]. This approach established the ability to characterize small DNA strands with resolution of a few base pairs and has the potential to be extended further for exact base sequence determination [137]. Recently, Hacohen et al developed a double nanohole of 90 nm radius and 35 nm line slot based on a 100-nm gold layer in order to analyze the protein composition of unpurified heterogeneous medium, that is, egg white [134].…”

Nano-bio-optomechanics: nanoaperture tweezers probe single nanoparticles, proteins, and their interactions

“…By scanning the frequency, a spectrum of the vibrational resonances of the ssDNA can be achieved (see Figure 2). We noted changes in the resonance frequency with length of the ssDNA and found good agreement with a linear chain oscillator model [21]. We referred to this process as extraordinary acoustic Raman (EAR) because of its single molecule sensitivity and ability to access low wavenumbers with high resolution.…”

Radiofrequency and microwave interactions between biomolecular systems

“…Actually, several experiments [29-31, 31, 32] and theoretical arguments [33][34][35][36] favor the possibility of underdamped vibrational modes of large biomolecular structures within the higher radiofrequency and THz regions. Prospective research lies in experimental quantification of damping of the radiofrequency vibrational modes using sophisticated spectroscopy techniques such as those exploiting high resolution Brillouin scattering [37], inelastic slow neutron scattering [38], nonlinear optical Kerr-effect pump-probe spectroscopy [32], extraordinary acoustic Raman spectroscopy [39,40] and others.…”