MCAT Chem/Phys Question of the Day

Poly(rI)·poly(rC) duplex formation demonstrates reduced thermodynamic stability when one strand remains adsorbed to single-walled carbon nanotube surfaces. Previous work by Chen et al. (2019) established that nucleotide adsorption occurs through π-π stacking between aromatic bases and nanotube sidewalls.

The hybridization of poly(rC) strands pre-adsorbed to SWNT surfaces with free poly(rI) in solution was monitored using UV-visible spectroscopy. SWNTs (0.5 mg/mL) were dispersed in 10 mM phosphate buffer (pH 7.2) containing 0.1 M NaCl through bath sonication for 45 minutes at 4°C. Poly(rC) (average length 340 nucleotides) was added to achieve a final concentration of 0.47 μM and incubated for 24 hours at room temperature. Unbound polymer was removed by centrifugation at 16,000 × g for 30 minutes. The poly(rC)-SWNT complex was resuspended in fresh buffer to an optical density of 0.85 at 800 nm.

Hybridization kinetics were measured following addition of poly(rI) (0.47 μM final concentration) to the poly(rC)-SWNT suspension. Absorption spectra were recorded at 260 nm using a Cary 5000 spectrophotometer equipped with a temperature-controlled cuvette holder. Control experiments utilized free poly(rC) and poly(rI) at identical concentrations. Hyperchromicity was calculated as (A₂₆₀,final - A₂₆₀,initial)/A₂₆₀,initial × 100%. The melting temperature (Tm) was determined from the first derivative of melting curves obtained by heating samples from 20°C to 95°C at 0.5°C/min.

Free poly(rI)·poly(rC) duplex formation reached equilibrium within 8.3 minutes, exhibiting a hyperchromic coefficient of 24.7 ± 0.6% and Tm of 61.2°C. Surface-mediated hybridization required 187 minutes to reach 90% completion, with a reduced hyperchromic coefficient of 16.4 ± 0.8%. The Tm decreased to 48.3°C for the surface-bound duplex. Molecular dynamics simulations using AMBER force fields revealed that cytosine bases maintain partial π-stacking with the nanotube surface even after Watson-Crick base pairing with poly(rI). The average tilt angle between cytosine rings and the nanotube axis measured 23.7° in the duplex compared to 8.4° for single-stranded poly(rC).

These observations indicate that competition between base-nanotube interactions and complementary base pairing reduces both hybridization kinetics and duplex stability. The persistent π-π stacking constrains the sugar-phosphate backbone geometry, preventing optimal base pair formation.

Adapted from Maksym V Karachevtsev, Galyna O Gladchenko, Victor S Leontiev et al., Hybridization of poly(rI) with poly(rC) adsorbed to the carbon nanotube surface.