Glushenkov AN, Hovorun DM. Can Nucleobase Pairs Offer a Possibility of a Direct 3D Self-assembly?
NANOSCALE RESEARCH LETTERS 2016;
11:134. [PMID:
26956603 PMCID:
PMC4783318 DOI:
10.1186/s11671-016-1347-3]
[Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 03/01/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND
The nucleobase pairs are characterized by their conformational diversity in the wild. Yet a modern nanobiotechnology utilizes their planar conformations only, developing what can be called a "planar approach". It is well established that the most energetically favorable conformations of the complementary nucleobase pairs are planar and correspond to the classical Watson-Crick nucleobase pairs.
PRESENTATION OF THE HYPOTHESIS
The point of interest lies in a study of a conformational capacity of the nucleobase pairs to expand the diversity of a spatial configuration and to produce the complex 3D objects from the non-planar conformations. If such a goal could be achieved, then that could definitely open the perspectives for a novel "stereo approach".
TESTING THE HYPOTHESIS
For the first time, basing on the first principles, we reveal an ability of the heteroassociates of the m(1)Cyt · m(1)Thy to form up to ten observable molecular complexes under standard conditions. The first three of them have population of ~90 % at standard conditions and are highly non-planar. The most energetically favorable structure has a T-shape, while the next two have an L-shape. At the same time, we show the lack of any experimental data covering a self-assembly of the m(1)Cyt · m(1)Thy base pairs.
IMPLICATIONS OF THE HYPOTHESIS
We present a theoretical evidence of the fact that the conformational capacity of the nucleobase pairs is much richer from the perspective of their self-assembly than it is considered in the modern nanobiotechnology. The capability of a modified cytosine and a modified thymine to create significantly non-planar structures opens a way for the innovative "stereo approach" to construction of the nanobiotechnological devices. We believe that a modern nanobiotechnological basis can and should be extended with the new nucleic base pairs with innate ability for non-planar structures. We would like to especially emphasize a prognostic role of our algorithm in obtaining the new results.
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