Keywords
interlocked G-quadruplex
molecular mechanics
DNA
G-quadruplex oligomers
How to Cite
Abstract
The fabrication of nanostructures based on DNA as a material to build systems capable of complex functions is a frontier in continuous exploration. In this article it is reported the detailed characterization at atomic level of G-quadruplex units in order to obtain a better comprehension on how these units can self assemble into interlocked G-quadruplexes. The method used is modeling with molecular mechanics. Previously we reported the construction of interlocked G-quadruplexes by a thermal cyclic procedure (similar in implementation as the ones used in the cycling steps in a PCR protocol) parting from the sequence 5"™-TGGG-3"™. Based on our experimental data reported previously, models were built for the structures, and minimization and analyses via molecular mechanics was carried out in order to understand the factors that determine the more stable structures. It was found that the identity of the 5"™and 3"™ ends of the oligonucleotides is of the uppermost importance in the stability of the DNA assemblies in this study. Furthermore, the presence of cations in the regions of the molecule where the degree of steric hindrance allows more room for the cations could play a significant role in the dynamics of conformation of the supramolecule at those sites and possibly limiting or capping the self assembly of the structure. In summary, the results allow a better comprehension of the system at a molecular scale with the finality of developing more efficient procedures for the controlled fabrication of nanostructures based on G-quadruplex DNA.
References
Seeman, N. 2007. An overview of structural DNA nanotechnology. Molecular Biotechnology. 37 (3), 246-257.
Dutta, K.; Fujimoto, T. 2010. Development of New Functional Nanostructures Consisting of Both DNA Duplex and Quadruplex. Chem. Commun. 46 (41), 7772-7774.
Pal, S.; Deng, Z. 2010. DNA-Origami-Directed Self-Assembly of Discrete Silver-Nanoparticle Architectures. Angewandte Chemie International Edition. 49 (15), 2700-2704.
Sadhasivam, S.; Yun, K. 2010. DNA Self-Assembly: Prospectus and Its Future Application. Journal of Materials Science. 45 (10), 2543-2552.
Wilner, O. I.; Henning, A. 2010. Covalently Linked DNA Nanotubes. 10 (4), 1458-1465.
Andersen, E. S.; Dong, M. 2009. Self-Assembly of aNanoscale DNA Box with a Controllable Lid. Nature. 459 (7243), 73-76.
Dietz, H.; Douglas, S. 2009. Folding DNA into Twisted and Curved Nanoscale Shapes. Science. 325 (5941), 725-730.
Ke, Y.; Sharma, J. 2009. Scaffolded DNA Origami of a DNA Tetrahedron Molecular Container. Nano Letters. 9 (6), 2445-2447.
Pisano, S.; Varra, M. 2008. Superstructural Self-Assembly of the G-quadruplex Structure Formed by the Homopurine Strand in a DNA Tract of Human Telomerase Gene Promoter. Biophys. Chem. 136 (2-3), 159-163.
Bath, J.; Turberfield, A. J. 2007. DNA Nanomachines. Nature Nanotechnology. 2 (5), 275-284.
Lin, C.; Liu, Y. 2006. DNA Tile Based Self-assembly: Building Complex Nanoarchitectures. ChemPhysChem. 7 (8), 1641-1647.
Niemeyer, C. M.; Simon, U. 2005. DNA-Based Assembly of Metal Nanoparticles. European Journal of Inorganic Chemistry 2005 (18), 3641-3655.
Bates, P.; Mergny, J. 2007. Quartets in G-major. The First International Meeting on Quadruplex DNA. In EMBO Rep, England. Vol. 8, pp 1003-10.
Mendez, M. A.; Szalai, V. A. 2009. Fluorescence of Unmodified Oligonucleotides: A Tool to Probe G-quadruplex DNA Structure. Biopolymers. 91 (10), 841-850.
Miyoshi, D.; Karimata, H. 2007. Artificial G-wire Switches with 2, 2'-Bipyridine Units Responsive to Divalent Metal Ions. J. Am. Chem. Soc. 129, 5919-5925.
Alberti, P.; Bourdoncle, A. 2006. DNA Nanomachines and Nanostructures Involving Quadruplexes. Org. Biomol. Chem. 4, 3383-3391.
Krishnan-Ghosh, Y.; Liu, D. 2004. Formation of an Interlocked Quadruplex Dimer by D (GGGT). J Am Chem Soc. 126, 11009-11016.
Lu, X. -J.; Olson, W. K. 2008. 3dna: A Versatile, Integrated Software System for the Analysis, Rebuilding and Visualization of Three-Dimensional Nucleic-Acid Structures. 3 (7), 1213-1227.
Parkinson, G. N.; Lee, M. 2002. Crystal Structure of Parallel Quadruplexes from Human Telomeric DNA. Nature. 417, 876-880.
Haider, S.; Parkinson, G. 2002. Crystal Structure of the Potassium Form of an Oxytricha Nova G-quadruplex. J. Mol. Biol. 320, 189-200.
Lim, K. W.; Alberti, P. 2009. Sequence Variant (CTAGGG) n in the Human Telomere Favors a G-quadruplex Structure containing a G: C: G: C Tetrad. Nucleic Acids Research. 37 (18), 6239-6248.
Viladoms, J.; Escaja, N. 2010. Self-Association of Cyclic Oligonucleotides through G: T: G: T Minor Groove Tetrads. Tetrahedron Young Investigator Award 2010: Professor Seeberger, Tetrahedron. 2010, 18 (11), 40674073.
Webba daSilva, M. 2003. Association of DNA Quadruplexes through G: C: G: C Tetrads. Solution Structure of D (GCGGTGGAT). Biochemistry 42 (49), 14356-14365.
Escaja, N.; Pedroso, E. 2000. Dimeric Solution Structure ofTwo Cyclic Octamers: Four-stranded DNA Structures Stabilized by A: T: A: T and G: C: G: C Tetrads. J. Am. Chem. Soc. 122, 12732-12742.
Gu, J.; Leszczynski, J. 2000. Structures and Properties of the Planar G: C: G: C Tetrads: Ab initio HF and DFT Studies. J. Phys. Chem. A. 104, 7353-7358.
Gray, D. M.; Wen, J. 2007. Measured and Calculated CD Spectra of G-quartets Stacked with the Same or Opposite Polarities. Chirality.
Nagatoishi, S.; Tanaka, Y. 2007. Circular Dichroism Spectra Demonstrate Formation of the Thrombinbinding DNA Aptamer G-quadruplex under Stabilizing-Cation-Deficient Conditions. Biochem Biophys Res Commun. 352 (3), 812-7.
Fasman, G. D. 1996. Circular Dichroism and the Conformational Analysis of Biomolecules. Plenum Press: New York. p ix, 738 p.
Hud, N. V; Schultze, P. 1999. Binding Sites and Dynamics of Ammonium Ions in a Telomere Repeat DNA Quadruplex. J. Mol. Biol. 285, 233-243.
Hud, N. V; Schultze, P. 1998. Ammonium Ion as an NMR Probe for Monovalent Cation Coordination Sites of DNA Quadruplexes. Journal of the American Chemical Society. 120 (25), 6403-6404..
vanMourik, T.; Dingley, A. J. 2005. Characterization of the Monovalent Ion Position and Hydrogen-bond Network in Guanine Quartets by DFT Calculations of NMR Parameters. Chemistry. 11 (20), 6064-79.
Andreatta, D.; Sen, S. 2006. Ultrafast Dynamics in DNA: "Fraying" at the End of the Helix. 128 (21), 6885-6892.
Copyright notice
Authors who publish in the journal ACI Avances en Ciencias e Ingenierías accept the following terms:
- The authors will retain their copyright and guarantee the journal the right of first publication of their work, which will be simultaneously subject to the Creative Commons Attribution License that allows third parties to share the work provided that its author and its first publication in this journal is indicated.
- Authors may adopt other non-exclusive license agreements for the distribution of the published version of the work, thereby being able to publish it in a monographic volume or reproduce it in other ways, provided that the initial publication in this journal is indicated.
- Authors are permitted and advised to disseminate their work over the Internet:
- Before submission to the journal, authors can deposit the manuscript in pre-publication files/repositories (preprint servers/repositories), including arXiv, bioRxiv, figshare, PeerJ Preprints, SSRN, and others, which can produce interesting exchanges and increase citations of the published work (see The effect of open access).
- After submission, it is recommended that authors deposit their article in their institutional repository, personal website, or scientific social network (such as Zenodo, ResearchGate or edu).