کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
5417510 | 1506924 | 2009 | 7 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
Computational evaluation of the stability of 2â²-O-methyl-RNA/RNA duplexes incorporating 3-deazaguanine derivatives by ab initio calculations and a molecular dynamics simulation
دانلود مقاله + سفارش ترجمه
دانلود مقاله ISI انگلیسی
رایگان برای ایرانیان
کلمات کلیدی
موضوعات مرتبط
مهندسی و علوم پایه
شیمی
شیمی تئوریک و عملی
پیش نمایش صفحه اول مقاله
چکیده انگلیسی
We evaluated the intrinsic interactions of guanine (G), 3-deazaguanine (c3G), and 2-N-acetyl-3-deazaguanine (a2c3G) with neighboring bases in the 2â²-O-methyl-RNA/RNA duplex, 5â²-(C1G2G3C4X5A6G7G8A9G10)-3â²/3â²-r(G20C19C18G17C16U15C14C13U12C11)-5â², where XÂ =Â G, c3G, or a2c3G. We calculated the energies using the subsystems that were derived from the averaged structure of the molecular dynamics (MD) trajectories of the duplexes by removing the sugar and phosphate moieties. The total energies calculated in vacuo revealed that the stability order was roughly a2c3G-CÂ >>Â G-CÂ >Â c3G-C, which was not perfectly matched with the experimentally determined stability order of G-CÂ >Â a2c3G-CÂ >>Â c3G-C probably due to lack of information on the solvent effects. The stacking interactions of c3G and its neighboring bases were smaller than those of G probably because of the larger dipole moment of c3G, whereas the stacking interaction of a2c3G was in most cases larger than those of G and c3G due to the increased overlapping area of the acetyl group and the smaller dipole moment. The data also gave an insight into the mechanism of duplex stabilization of a2c3G compared with c3G. In order to estimate the solvent effects, we also conducted ab initio calculations with some solute models.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Journal of Molecular Structure: THEOCHEM - Volume 899, Issues 1â3, 15 April 2009, Pages 54-60
Journal: Journal of Molecular Structure: THEOCHEM - Volume 899, Issues 1â3, 15 April 2009, Pages 54-60
نویسندگان
Takeshi Sasami, Ryuya Tawarada, Akihiro Ohkubo, Mitsuo Sekine, Kohji Seio,