Hydrogen-bonded nucleic acid base pairs containing unusual base tautomers: complete basis set calculations at the MP2 and CCSD(T) levels - PubMed
Save Email
Send to
Display options
Full text links Cite
Display options
## Abstract
The total interaction energies of altogether 15 hydrogen-bonded nucleic acid base pairs containing unusual base tautomers were calculated. The geometry properties of all selected adenine-thymine and guanine-cytosine hydrogen-bonded base pairs enable their incorporation into DNA. Unusual base pairing patterns were compared with Watson-Crick H-bonded structures of the adenine-thymine and guanine-cytosine pairs. The complete basis set (CBS) limit of the MP2 interaction energy and the CCSD(T) correction term, determined as the difference between the CCSD(T) and MP2 interaction energies, was evaluated. Extrapolation to the MP2 CBS limit was done using the aug-cc-pVDZ and aug-cc-pVTZ results, and the CCSD(T) correction term was determined with the 6-31G*(0.25) basis set. Final interaction energies were corrected while taking into account both tautomeric penalization determined at the CBS level and solvation/desolvation free energies. The situation for the
imino-tautomer of adenine (A*) with T ( 32 ). F . Structure of a wobble G·T mismatched base pair ( 33 , 34 ). Figure 5.
Open in a new tab
Helical parameters for dinucleotides and base pairs within the asymmetric junction. The helical rise ( A ) and twist ( B ) between dinucleotides, and propeller twist ( C ) and shear for base pairs ( D )were calculated using the 3DNA software ( 51 ). The semi-continuous double helices (Duplex 1 and Duplex 2) of the junction are as labeled in Fig. 1 . The location of the highly sheared A2·T9 and C7·G4 base pairs in Duplex1, along with the junction crossover are as indicated. The average B-factors ( Fig. 6 ) for the atoms in the bases and in the backbone of each nucleotide along the four chains show that the bases at the wobbled A2·T9 positions are not as well structured as the bases of other nucleotides, particularly compared to those at the junction. This is consistent with this A2·T9 base pair having only a single hydrogen bond, and the A2 base being displaced from the stacked bases of the flanking base pairs. An alternative interpretation may be that the bases are statically disordered and represents an average of two or more conformations of the nucleotides—this could also account for the higher B-factors for the A2·T9 bases. Multiple conformations of bases and deoxyribose backbones have been seen in ultra-high resolution structures of DNA duplexes ( 30 ) and the current structure at 1.9 Å resolution would not be able to resolve these alternative positions. However, positional disorder along the base planes that would result in the large shear displacements of the bases would also be reflected in correlated disorder and, consequently, higher B-factors for at least the C1' carbon of the associated backbone atoms, which is not observed. The backbone atoms of A2·T9 are as well structured as those of other nucleotides in the structure, indicating that the conformation and positions of the phosphodeoxyribose atoms are very well defin
Tautomerism in nucleic acid bases and base pairs: a brief overview - Shukla - 2013 - WIREs Computational Molecular Science - Wiley Online Library
Opens in a new windowOpens an external websiteOpens an external website in a new window
Close this dialog
This website utilizes technologies such as cookies to enable essential site functionality, as well as for analytics, personalization, and targeted advertising.To learn more, view the following link:[Privacy Policy](https://www.wiley.com/privacy)
Close Cookie Preferences
[](https://wires.onlinelibrary.wiley.com/)
[](https://wires.onlinelibrary.wiley.com/)
**
Search withinThis JournalWIREs JournalsWiley Online Library
* Search term
[Advanced Search](https://wires.onlinelibrary.wiley.com/search/advanced?publication=17590884)[Citation Search](https://wires.onlinelibrary.wiley.com/search/advanced?publication=17590884#citation)
* Search term
[Advanced Search](https://wires.onlinelibr
Everything we examined (3) — 2 independent sources
This check searched the claim as stated. It did not run a separate search for evidence against it.