Paper Citing NAMD - Abstract
Karacheytsev, Maksym V.; Gladchenko, Galina O.; Andrushchenko, Valery; Leontiev, Victor S.; Karachevtsev, Victor A.
Hybridization of Homopolynucleotides with Different Base Ordering on the Carbon Nanotube Surface
JOURNAL OF PHYSICAL CHEMISTRY C, 119:11991-12001, MAY 28 2015
Hybridization of nucleic adds on the carbon nanotube is of great interest due to its potential application in base sequencing and genetic testing. In this work, we have compared the hybridization of the two complementary homopolynucleotides poly(rI) and poly(rC) on the nanotube When either the ordered poly(rC) or disordered poly(rI) as adsorbed to the nanotube surface while the complementary homopolynucleotide was free in the suspension. The hybridization of these polymers is characterized by slower kinetics of the duplex formation on the nanotube in comparison with the case of free polymer hybridization. The hybridized duplex also shows a reduced thermostability determined from UV absorption spectra upon heating. These observations point to the defects in the structure of the duplex hybridized on the nanotube. Spectroscopic measurements and molecular dynamics simulations demonstrate that the defects of the hybridized duplex are more pronounced for the case when free poly(rC) is bound to poly(a) adsorbed to the nanotube. It is explained by a higher binding energy of the purine base (hypoxanthine) with the tube surface compared to the pyrimidine one (cytosine). Besides, a stable loop formed by poly(rI) on the nanotube significantly obstructs the hybridization with poly(rC). The strong base ordering of poly(rC) free in solution also hinders the hybridization with the adsorbed poly(rI).
