Theoretical study of peptide nucleic acid with(2'R,4'R)-prolyl-(1S,2S)-2-aminocyclobutanecarboxylic acid acid backbone binding to DNA and self-pairing
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Abstract
The binding ability of pyrrolidinyl peptide nucleic acid (PNA) binding to its complementary DNA and self-paring has been studied experimentally. However, a detailed understanding of the binding property is still unclear due to the lack of their crystallographic data. In this work, structural and energetic properties of PNA-DNA and PNA-PNA duplexes were studied using molecular dynamics (MD) simulations and quantum calculations. The studied pyrrolidinyl PNA backbone was (2¢R,4¢R)-prolyl-(1S,2S)-2-aminocyclobutanecarboxylic acid. MD simulations of three different forms (A–, B– and P–form) were performed in order to investigate the probable duplex conformation. As the results, PNA-PNA duplex exhibited the structural feature between A- and P-type conformations, while PNA-DNA double helix clearly showed the characteristic of B-form. In addition, quantum calculations revealed that the interaction of PNA-DNA duplex was larger than that of PNA-PNA duplex, indicating higher intrinsic stability of PNA-DNA compared to PNA-PNA double strand. This research may lead to a design of PNA for further applications.
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Blackburn GM, Gait MJ, Loakes D, Williams DM. Nucleic acids in chemistry and biology. 3rd ed. Cambridge: RSC Publishing; 2006.
Dahm R. Friedrich Miescher and the discovery of DNA. Dev Biol. 2005;278:274–288.
Dahm R. Discovering DNA: Friedrich Miescher and the early years of nucleic acid research. Hum Genet. 2008;122:565–581.
Nielsen PE, Egholm M, Berg RH, Buchardt O. Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 1991;254:1497–1500.
Egholm M, Buchardt O, Nielsen PE, Berg RH. Peptide nucleic acids (PNA). Oligonucleotide analogs with an achiral peptide backbone. J Am Chem Soc. 1992;114:1895–1897.
Hyrup B, Nielsen PE. Peptide nucleic acids (PNA): synthesis, properties and potential applications. Bioorg Med Chem. 1996;4:5–23.
Ray A, Nordén B. Peptide nucleic acid (PNA): its medical and biotechnical applications and promise for the future. FASEB J. 2000;14:1041–1060.
Porcheddu A, Giacomelli G. Peptide nucleic acids (PNAs), a chemical overview. Curr Med Chem. 2005;12:2561–2599.
Gambari R. Peptide nucleic acids: a review on recent patents and technology transfer. Expert Opin Ther Pat. 2014;24:267–294.
Vilaivan T, Suparpprom C, Harnyuttanakorn P, Lowe G. Synthesis and properties of novel pyrrolidinyl PNA carrying β-amino acid spacers. Tetrahedron Lett. 2001;42:5533–5536.
Vilaivan T, Srisuwannaket C. Hybridization of pyrrolidinyl peptide nucleic acids and DNA: selectivity, base-pairing specificity, and direction of binding. Org Lett. 2006;8:1897–1900.
Taechalertpaisarn J, Sriwarom P, Boonlua C, Yotapan N, Vilaivan C, Vilaivan T. DNA-, RNA- and self-pairing properties of a pyrrolidinyl peptide nucleic acid with a (2'R,4'S)-prolyl-(1S,2S)-2-aminocyclopentanecarboxylic acid backbone. Tetrahedron Lett. 2010;51:5822–5826.
Vilaivan C, Srisuwannaket C, Ananthanawat C, Suparpprom C, Kawakami J, Yamaguchi Y, Vilaivan T. Pyrrolidinyl peptide nucleic acid with α/β-peptide backbone: a conformationally constrained PNA with unusual hybridization properties. Artif DNA PNA XNA 2011;2:50–59.
Mansawat W, Vilaivan C, Balázs Á, Aitken DJ, Vilaivan T. Pyrrolidinyl peptide nucleic acid homologues: effect of ring size on hybridization properties. Org Lett. 2012;14:1440–1443.
Vilaivan T. Pyrrolidinyl PNA with alpha/beta-dipeptide backbone: from development to applications. Acc Chem Res. 2015;48:1645–1656.
Siriwong K, Chuichay P, Saen-oon S, Suparpprom C, Vilaivan T, Hannongbua S. Insight into why pyrrolidinyl peptide nucleic acid binding to DNA is more stable than the DNA·DNA duplex. Biochem Biophys Res Commun. 2008;372:765–771.
Poomsuk N, Siriwong K. Structural properties and stability of PNA with (2'R,4'R)- and (2'R,4'S)-prolyl-(1S,2S)-2-aminocyclopentanecarboxylic acid backbone binding to DNA: a molecular dynamics simulation study. Chem Phys Lett. 2013;588:237–241.
Rasmussen H, Kastrup JS, Nielsen JN, Nielsen JM, Nielsen PE. Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 Å resolution. Nat Struct Mol Biol. 1997;4:98–101.
Lu XJ, Olson WK. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res. 2003;31:5108–5121.
Case DA, Darden TA, Cheatham TE, Simmerling CL, Wang J, Duke RE, et al. AMBER 12. University of California: San Francisco; 2012.
Jorgensen W. Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water. J Am Chem Soc. 1981;103:335–340.
Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys. 1977;23:327–341.
Darden T, York D, Pedersen L. Particle mesh Ewald: an N⋅log(N) method for Ewald sums in large systems. J Chem Phys. 1993;98:10089–10092.
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Cheeseman JR, Scalmani G, et al. Gaussian 09 Revision B.01. Wallingford CT: Gaussian; 2009.
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt, DM, Meng EC, Ferrin TE. UCSF chimera-a visualization system for exploratory research and analysis. J Comput Chem. 2004;25:1605–12.
Saenger W. Principles of nucleic acid structure. New York: Springer-Verlag; 1984.