Conformational analysis of canonical 2-deoxyribonucleotides. 2. Purine nucleotides.
The molecular structure of different conformers of isolated canonical purine 2'-deoxyribonucleotides 2-deoxyadenosine-5'-phosphate (pdA) and 2'-deoxyguanosine-5'-phosphate (pdG) was optimized using the B3LYP/6-31G(d) method. The results of the calculations reveal that the geometrical parameters and relative stability of the conformers significantly depend on the nature of the nucleobase, its orientation, the conformation of the furanose ring, the charge of the phosphate group and the character of the intramolecular hydrogen bonds. Analysis of the electron density distribution in purine nucleotides reveals the existence of a number of intramolecular hydrogen bonds. In general, the south conformer has a lower energy at the anti orientation of the base, and both conformers occur as the most stable for the syn orientation of the nucleobases. The results of the calculations reveal that the geometry and relative energy of the conformers of purine DNTs may be easily tuned by the charge of the phosphate group.
Shishkin
Oleg V
OV
Institute for Scintillation Materials, National Academy of Science of Ukraine, 60 Lenina Ave., Kharkiv 61001, Ukraine. shishkin@xray.isc.kharkov.com
Gorb
Leonid
L
Zhikol
Oleg A
OA
Leszczynski
Jerzy
J
D000838:Anions; D003838:Deoxyadenine Nucleotides / Q000737:chemistry; D003848:Deoxyguanine Nucleotides / Q000737:chemistry; D004355:Drug Stability; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011685:Purine Nucleotides / Q000737:chemistry*; D011742:Pyrimidine Nucleotides / Q000737:chemistry; D013816:Thermodynamics
D000838:Anions; D003838:Deoxyadenine Nucleotides; D003848:Deoxyguanine Nucleotides; D011685:Purine Nucleotides; D011742:Pyrimidine Nucleotides; C012873:2'-deoxy-5'-adenosine monophosphate; C007257:2'-deoxyguanosine 5'-phosphate