Australian Journal of Chemistry Australian Journal of Chemistry Society
An international journal for chemical science
RESEARCH ARTICLE

Density Functional Computations on 6-Aminouracil: Effect of Amino Group in the 6th Position on the Watson–Crick Base Pair Uridine–Adenosine

M. Alcolea Palafox A D and V. K. Rastogi B C D
+ Author Affiliations
- Author Affiliations

A Nofima AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, 1430 Ås, Norway.

B Internet Lab, R.D. Foundation Group of Institutions, NH-58, Kadrabad, Modinagar (Ghaziabad), India.

C Indian Spectroscopy Society, KC 68/1, Old Kavinagar, Ghaziabad-201 002, India.

D Corresponding authors: alcolea@ucm.es; v_krastogi@rediffmail.com

Australian Journal of Chemistry 69(8) 881-889 https://doi.org/10.1071/CH15793
Submitted: 2 July 2015  Accepted: 22 February 2016   Published: 29 March 2016

Abstract

The predicted infrared and Raman spectra of 6-aminouracil in the solid state by density functional theory methods were analyzed and compared with the experimental spectra. The effect of amino substitution in the sixth position of uridine on the stability of the Watson–Crick (WC) base pairs with deoxyadenosine was evaluated. Different WC pairs of 5-aminouridine, 6-aminouridine, and uridine with deoxyadenosine were simulated, and the counterpoise-corrected interaction energies were determined. 6-Aminouridine produces a stronger WC pair than that involving uridine, and its high dipole moment facilitates interaction with water molecules.


References

[1]  C. Bayrak, J. Biol. Chem. 2012, 40, 419.

[2]  S. Aruna, G. Shanmugam, Indian J. Chem. 1986, 25A, 256.
         | 1:CAS:528:DyaL28XktFyhs7w%3D&md5=70c9cb82e87c405eeb8cc36fe5dad858CAS |

[3]  V. Gerhardt, M. Bolte, Acta Crystallogr., Sect. C: Cryst. Struct. Commun. 2013, 69, 1402.
         | CrossRef | 1:CAS:528:DC%2BC3sXhslWlsrfK&md5=cfde576d5f1a17ccae3d1880b31aff99CAS |

[4]  G. Paragi, E. Szájli, F. Bogár, L. Kovács, C. F. Guerra, F. M. Bickelhaupt, New J. Chem. 2008, 32, 1981.
         | CrossRef | 1:CAS:528:DC%2BD1cXhtlaqsbfF&md5=66f1522b2ff0f7580d04c407ff1c56c7CAS |

[5]  M. A. V. Ribeiro da Silva, L. M. P. F. Amaral, P. Szterner, J. Chem. Thermodyn. 2011, 43, 1763.
         | CrossRef | 1:CAS:528:DC%2BC3MXovFaqsbk%3D&md5=b1b46e4a588dffb472d0b9ce232843d9CAS |

[6]  C. E. Müller, Tetrahedron Lett. 1991, 32, 6539.
         | CrossRef |

[7]  A. A. Mustafa, A. A. Alhaider, A. A. Hijazi, Pharm. Res. 1989, 6, 394.
         | CrossRef | 1:CAS:528:DyaL1MXkvV2ktbg%3D&md5=016342e62309254fe350dcd25b741d97CAS | 2748529PubMed |

[8]  I. Bernier, J. Henichart, V. Warin, C. Trentesaux, J. C. Jardillier, J. Med. Chem. 1985, 28, 497.
         | CrossRef | 1:CAS:528:DyaL2MXht1Gitbg%3D&md5=a4f622269344629fc49e900033c2b8afCAS |

[9]  P. G. Kjellin, C. G. Persson, Eur. Patent 10531 1980.

[10]  E. Chmiel-Szukiewicz, J. Appl. Polym. Sci. 2006, 100, 715.
         | CrossRef | 1:CAS:528:DC%2BD28XitVOltLk%3D&md5=0baca104927c33c08de2ebb8d61e0b4aCAS |

[11]  P. M. Tarantino, P. M. Tarantino, J. Med. Chem. 1999, 42, 2035.
         | CrossRef | 1:CAS:528:DyaK1MXivVarsbg%3D&md5=9a048bd29c15b77e6536ed2512185e03CAS | 10354411PubMed |

[12]  P. Langen, G. Etzold, D. Bärwolff, B. Preussel, Biochem. Pharmacol. 1967, 16, 1833.
         | CrossRef | 1:CAS:528:DyaF2sXkvFOiu7s%3D&md5=ad3c9a3e5416efad8e79e0fd14edfd84CAS | 6053224PubMed |

[13]  C. D. Mol, A. S. Arvai, G. Slupphaug, B. Kavli, I. Alseth, H. E. Krokan, J. Tainer, Cell 1995, 80, 869.
         | CrossRef | 1:CAS:528:DyaK2MXkslOmtbs%3D&md5=955c9ec7972c27e15093eefcd6e6e149CAS | 7697717PubMed |

[14]  D. Dobritzsch, G. Scheider, K. Schnackeerz, Y. Lingvist, EMBO J. 2001, 20, 650.
         | CrossRef | 1:CAS:528:DC%2BD3MXhsVyhsbY%3D&md5=4b40aca77091d4bfcc29ee7ff4d1959bCAS | 11179210PubMed |

[15]  (a) N. R. Jena, V. Gaur, P. C. Mishra, Phys. Chem. Chem. Phys. 2015, 17, 18111.
         | CrossRef | 1:CAS:528:DC%2BC2MXhtVSqt7%2FK&md5=d6b7be9d935435843ea2eaaa74737559CAS | 26099851PubMed |
      (b) N. R. Jena, M. Bansal, Phys. Biol. 2011, 8, 046007.
         | CrossRef |
      (c) P. Sharma, A. Mitra, S. Sharma, H. Singh, D. Bhattacharyya, J. Biomol. Struct. Dyn. 2008, 25, 709.
         | CrossRef |
      (d) J. Šponer, J. Leszczynski, P. Hobza, J. Biomol. Struct. Dyn. 1996, 14, 117.
         | CrossRef |
      (e) O. O. Brovarets, D. M. Hovorun, J. Biomol. Struct. Dyn. 2014, 32, 127.
         | CrossRef |
      (f) O. O. Brovarets, D. M. Hovorun, J. Biomol. Struct. Dyn. 2013, 31, 913.
         | CrossRef |

[16]  W. J. Hehre, L. Radom, P. R. Schleyer, J. A. Pople, Ab Initio Molecular Orbital Theory 1986 (Wiley & Sons: New York, NY).

[17]  J. M. Seminario, P. Politzer, in Modern Density Functional Theory: A Tool for Chemistry (Eds J. M. Seminario, P. Politzer) 1995, Vol. 2 (Elsevier: Amsterdam).

[18]  (a) A. D. Becke, J. Chem. Phys. 1992, 97, 9173.
         | CrossRef | 1:CAS:528:DyaK3sXmslamsw%3D%3D&md5=1e1f4f033a920dde129be1a4752aa7f5CAS |
      (b) A. D. Becke, J. Chem. Phys. 1993, 98, 5648.
         | CrossRef |

[19]  C. Lee, W. Yang, R. G. Parr, Phys. Rev. B 1988, 37, 785.
         | CrossRef | 1:CAS:528:DyaL1cXktFWrtbw%3D&md5=1446c2427b0599ea3e79a7334c6afa9cCAS |

[20]  M. Alcolea Palafox, Int. J. Quantum Chem. 2000, 77, 661.
         | CrossRef |

[21]  Y. Zhao, D. G. Truhlar, J. Chem. Phys. 2006, 125, 194101.
         | CrossRef | 17129083PubMed |

[22]  M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery Jr, J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, Ö. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, D. J. Fox, Gaussian 09, Revision D.01 2009 (Gaussian, Inc.: Wallingford, CT).

[23]  V. Arjunan, S. Senthilkumari, P. Ravindran, S. Mohan, J. Mol. Struct. 2014, 1064, 15.
         | CrossRef | 1:CAS:528:DC%2BC2cXksFyksLY%3D&md5=e25298cf46c8925b8e05ca910d10a6caCAS |

[24]  S. Ortiz, M. Alcolea Palafox, V. K. Rastogi, T. Akitsu, I. Hubert Joe, S. Kumar, Spectrochim. Acta, Part A 2013, 110, 404.
         | CrossRef | 1:CAS:528:DC%2BC3sXnsVGjtr8%3D&md5=df36d6dea742455d8a11dfdd9e1e7b2bCAS |

[25]  V. Arjunan, S. Thillai Govindaraja, S. Subramanian, S. Mohan, J. Mol. Struct. 2013, 1037, 73.
         | CrossRef | 1:CAS:528:DC%2BC3sXjs1Cgsro%3D&md5=e5bea2698e968b62b81fa9677b97fc18CAS |

[26]  D. Kattan, M. Alcolea Palafox, S. Kumar, D. Manimaran, H. Joe, V. K. Rastogi, Spectrochim. Acta, Part A 2014, 123, 89.
         | CrossRef | 1:CAS:528:DC%2BC2cXislKnt7c%3D&md5=325ec0931f49967a9feaa252674e821aCAS |

[27]  (a) M. Alcolea Palafox, P. Posada-Moreno, A. L. Villarino-Marín, C. Martinez-Rincon, I. Ortuño-Soriano, I. Zaragoza-García, J. Comput.-Aided Mol. Des. 2011, 25, 145.
         | CrossRef | 1:CAS:528:DC%2BC3MXhsVeqtLc%3D&md5=7849f12680af9601b9e14959f438662cCAS | 21181429PubMed |
      (b) T. Zhou, D. Huang, A. Caflisch, Curr. Top. Med. Chem. 2010, 10, 33.
         | CrossRef |
      (c) M. P. Gleeson, D. Gleeson, J. Chem. Inf. Model. 2009, 49, 670.
         | CrossRef |
      (d) N. R. Jena, P. C. Mishra, J. Mol. Model. 2007, 13, 267.
         | CrossRef |
      (e) M. C. Alvarez-Ros, M. Alcolea Palafox, Pharmaceuticals 2014, 7, 695.
         | CrossRef |

[28]  M. Alcolea Palafox, V. K. Rastogi, Spectrochim. Acta, Part A 2002, 58, 411.
         | CrossRef |

[29]  J. E. Carpenter, F. Weinhold, J. Mol. Struct.: THEOCHEM 1988, 169, 41.
         | CrossRef |

[30]  G. Kerestztury, in Handbook of Vibrational Spectroscopy (Eds J. M. Chalmers, P. R. Griffths) 2002, Vol. 1, pp. 71–87 (Wiley-VCH: Weinheim).

[31]  M. Alcolea Palafox, N. Iza, M. de la Fuente, R. Navarro, J. Phys. Chem. B 2009, 113, 2458.
         | CrossRef |

[32]  S. F. Boys, F. Bernardi, Mol. Phys. 1970, 19, 553.
         | CrossRef | 1:CAS:528:DC%2BD2sXht1alt7fM&md5=531add8a3739ea622eed7d96a639ebd5CAS |

[33]  M. Alcolea Palafox, N. Iza, Phys. Chem. Chem. Phys. 2010, 12, 881.
         | CrossRef | 1:CAS:528:DC%2BC3cXjslWgtg%3D%3D&md5=107549d7f5341da8937f5185edc62de6CAS | 20066373PubMed |

[34]  M. Alcolea Palafox, J. Talaya, J. Phys. Chem. B 2010, 114, 15199.
         | CrossRef | 1:CAS:528:DC%2BC3cXhtlKjsbjI&md5=a2c45207944a964e868fe166649b3210CAS | 21038904PubMed |

[35]  S. Ortiz, M. C. Alvarez-Ros, M. Alcolea Palafox, V. K. Rastogi, V. Balachandran, S. K. Rathor, Spectrochim. Acta, Part A 2014, 130, 653.
         | CrossRef | 1:STN:280:DC%2BC2cjlsFOluw%3D%3D&md5=7fb68219d30a69ff90815192a8cfa494CAS |

[36]  M. Alcolea Palafox, G. Tardajos, A. Guerrero-Martínez, V. K. Rastogi, S. P. Ojha, W. Kiefer, Chem. Phys. 2007, 340, 17.
         | CrossRef | 1:CAS:528:DC%2BD2sXht1Gns7jO&md5=f636d393bc4619e3122b3d25215ac4e7CAS |

[37]  M. Alcolea Palafox, N. Iza, M. Gil, J. Mol. Struct.: THEOCHEM 2002, 585, 69.
         | CrossRef |

[38]  F. Peral, D. Troitino, J. Mol. Struct.: THEOCHEM 2010, 944, 1.
         | CrossRef | 1:CAS:528:DC%2BC3cXitFylsrw%3D&md5=8dba56fd3a2468880772e2a721c4f9e9CAS |

[39]  D. K. Jain, V. Jain, G. N. Singh, K. M. Sonawane, Asian J. Phys. 2000, 9, 487.
         | 1:CAS:528:DC%2BD3cXls12hurk%3D&md5=d16ff6c01ef46aaa9730cf2e9657b2b8CAS |

[40]  V. K. Rastogi, C. Singh, V. Jain, M. Alcolea Palafox, J. Raman Spectrosc. 2000, 31, 1005.
         | CrossRef | 1:CAS:528:DC%2BD3cXosVOht7g%3D&md5=e1a34821a085309c7331cd2b54275b3cCAS |

[41]  V. K. Rastogi, V. Jain, R. A. Yadav, C. Singh, M. Alcolea Palafox, J. Raman Spectrosc. 2000, 31, 595.
         | CrossRef | 1:CAS:528:DC%2BD3cXlvFCmsLg%3D&md5=ecd217a5249a8070cc8cbc01dfd6b854CAS |

[42]  S. Aruna, G. Shanmugam, Spectrochim. Acta, Part A 1985, 41, 531.
         | CrossRef |

[43]  W. Saenger, Principles of Nucleic Acid Structure 1984 (Springer Verlag: New York, NY).



Rent Article (via Deepdyve) Supplementary MaterialSupplementary Material (85 KB) Export Citation