Big Chemical Encyclopedia

Chemical substances, components, reactions, process design ...

Articles Figures Tables About

Nucleic acid base pairs Geometry

Olson WK, Bansal M, Burley SK, Dickerson RE, Gerstein M, Harvey SC, Heinemann U, Lu X-J, Neidle S, Shakked Z, Sklenar H, Suzuki M, Tung C-S, Westhof E, Wolberger C, Berman HM. A standard reference frame for the description of nucleic acid base-pair geometry. J. Mol. Biol. 2001 313 229-237. [Pg.1510]

I. Dqbkowska, H.V. Gonzales, P. Jurecka, P. Hobza, Stabilization energies of the hydrogen-bonded and stacked stmctures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5,-d(GCGAAGC)-3 hairpin Complete basis set calculations at the MP2 and CCSD(T) levels. J. Phys. Chem. A 109, 1131-1136 (2005)... [Pg.395]

From semiempiricaF to ab initio the levels of treatment of this interaction over the years parallel the development of computational quantum chemistry. Some of the recent computations were able to optimize the molecular geometries using gradient proce-dures ° while others have fit the results of ab initio calculations on smaller systems to empirical functions so as to then study the full nucleic acid base pairs " -. There has also been work that relates the effect of adding or removing an electron to the base pair upon the nature of the interaction " -. ... [Pg.114]

If we consider studies of nucleic acids and their components, there is currently only one reliable gas phase experiment (mass-field spectroscopy) on the energetics of nucleic acid base pairs [7a]. This experiment provides interaction enthalpies of several base pairs at rather high temperatures of 350-400K. The experimental technique does not allow for the determination of the geometry of complexes, and it is even not possible to distinguish between H-bonded and stacked structures. Recent state-of-the art theoretical analysis of gas phase thermodynamics of uracil dimer indicates that this pair exists as a mixture of several H-bonded and stacked structures [8]. Furthermore, their relative populations could vary depending on experimental conditions. It is likely that... [Pg.86]

Extensive studies in the past years have provided the molecular geometries of more than 100 nucleic acid base pairs (Figure 1) and trimers which were obtained at the HF level with medium sized polarized basis sets of atomic orbitals [12g,13c,29,30,32,33,43,59] including pairs with protonated bases [32b], rare tautomers [13c,43], modified, and nonnatural bases [59]. [Pg.96]

Figure 3. Optimal geometries of ten stacked nucleic acid base pairs. ITieir structure has been obtained using an ab initio-fitted potential. The interaction energy (kcal/mol) has been evaluated at the MP2/6-31G (0.25) level. For more details see [12a]. Figure 3. Optimal geometries of ten stacked nucleic acid base pairs. ITieir structure has been obtained using an ab initio-fitted potential. The interaction energy (kcal/mol) has been evaluated at the MP2/6-31G (0.25) level. For more details see [12a].
One of the most prominent hydrogen-bonded systems is DNA. Despite numerous experimental and theoretical investigations on vibrational spectra of nucleic acid bases [7-13], information on inter- and intramolecular interactions in base pairs and DNA oligomers is still limited [14-25]. A recent example is the work on single adenine-uracil (AU) base pairs in the Watson-Crick geometry in solution, which showed an enhancement of vibrational energy... [Pg.143]

Overlap Geometry at the Intercalation Site We shall attempt to utilize the nucleic acid base and anthracycline ring proton com-plexation shifts to deduce which anthracycline aromatic ring(s) overlap with nearest neighbor base pairs in the daunomycin poly-(dA-dT) intercalation complex. It should be noted that the nonplanarity of ring A in the antibiotic requires that the aromatic portion of the anthracycline chromophore cannot intercalate with its long axis colinear to the direction of the Watson-Crick hydrogen bonds at the intercalation site as was demonstrated for proflavine-nucleic acid complexes. [Pg.268]

This article is devoted to a comprehensive review of theoretical and experimental results on excited state properties (electronic transitions, excited state geometries, charges, interaction etc.) of the natural nucleic acid bases and base pairs. It is well known that there are three important components of DNA. [Pg.253]

Thus the theoretical studies on the excited states of the nucleic acid bases and base pairs have been greatly helpful in unravelling several details regarding e nature and locations of transitions and excited state geometries and properties that were not understood earlier. However the knowledge obtained in this regard is expected to become richer in future as better computational technologies become available. [Pg.334]


See other pages where Nucleic acid base pairs Geometry is mentioned: [Pg.379]    [Pg.101]    [Pg.279]    [Pg.393]    [Pg.482]    [Pg.114]    [Pg.118]    [Pg.835]    [Pg.244]    [Pg.519]    [Pg.434]    [Pg.311]    [Pg.1924]    [Pg.76]    [Pg.390]    [Pg.400]    [Pg.410]    [Pg.179]    [Pg.7]    [Pg.388]    [Pg.688]    [Pg.124]    [Pg.122]    [Pg.31]    [Pg.56]    [Pg.68]    [Pg.296]    [Pg.7]    [Pg.364]    [Pg.92]    [Pg.249]    [Pg.331]    [Pg.248]    [Pg.10]    [Pg.36]    [Pg.89]   
See also in sourсe #XX -- [ Pg.483 ]




SEARCH



Base pairing bases

Base pairs

Base pairs, nucleic acids

Base-pairing geometry

Base-pairing, nucleic acids

Bases Base pair

Geometry nucleic acids

Nucleic acid pairing

Nucleic acids bases

© 2024 chempedia.info