<i>Ab initio</i> calculations on the barrier to pseudorotation of model 2′‐deoxyfuranose and 2′‐deoxy‐2′‐fluorofuranose rings

Lesyng, Bogdan; Marck, Christian; Guschlbauer, Wilhelm

doi:10.1002/qua.560280408

Cited by 9 publications

(1 citation statement)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The absence of the Bform in (dCdGfl)s requires explanation. Despite the kinetic flexibility of the 2'-deoxy-2'fluoronu cleosides [10,18] and the well known adaptability of deoxyribonucleosides, the A-form appears to dominate.…”

Section: Discussionmentioning

confidence: 99%

A → Z transition in the synthetic hexanucleotide (dCdGfl)₃

Fazakerley¹,

Uesugi²,

Izumi³

et al. 1985

FEBS Letters

View full text Add to dashboard Cite

500 MHz proton NMR and NOE measurements on (dCdGfl)j show that at very low ionic strength the hexanucleotide adopts an A-DNA conformation, whereas at high salt concentrations a Z-form is found. At intermediate salt concentrations the two species are in slow exchange on the proton NMR time scale.This transition was also observed by characteristic changes in the CD spectra.NMR NOE 2'-Deoxy-2'-ji'uoronucleoside CD Conformation

show abstract

Section: Discussionmentioning

confidence: 99%

A → Z transition in the synthetic hexanucleotide (dCdGfl)₃

Fazakerley¹,

Uesugi²,

Izumi³

et al. 1985

FEBS Letters

View full text Add to dashboard Cite

show abstract

Theoretical analysis of deoxycytidine‐5′‐phosphate protonation

Starikov¹,

Pedash

1990

Biopolymers

View full text Add to dashboard Cite

The electron density distribution in deoxycytidine-5'-monophosphate (5'-dCMP) molecule and dianion has been studied by the method of CNDO/2. The comparison between the results of calculation for the neutral molecule and the data obtained by Pearlman and Kim shows that there is a linear correlation between the atomic charges calculated using quantum chemistry and those derived from X-ray results. However, partial charges for the deoxyribose fragment are correlated in a nonlinear manner. The influence of the protons added to the cytosine and phosphate residues on the atomic charges and bond orders of deoxy-cytidine-5'-monophosphate has been analyzed here. The conclusion has been drawn that the semiempirical quantum-chemical CNDO/2 technique is applicable to the mononucleotide studies.

show abstract

Lagrangian molecular dynamics using selected conformational degrees of freedom, with application to the pseudorotation dynamics of furanose rings

1994

Self Cite

View full text Add to dashboard Cite

Using internal conformational degrees of freedom for biopolymers as natural variables, and introducing a Lagrangian dynamics approach, one can simulate time-dependent processes over a much longer time scale than in classical Newtonian molecular dynamics (MD) techniques. Two factors contribute to this: a substantial reduction in the number of degrees of freedom and a very large increase in the size of the time step. We present the Lagrangian equations of motion for repuckering transitions in model furanose (F), ribose (R), and 2'-deoxyribose (dR) ring systems using the pseudorotation phase angle as the single dynamic variable. As in most Lagrangian analyses, the effective masses for the R and dR models are dependent on conformation, and we test the behavior of this variable mass (VM) model. Since the variation in effective mass is small, the VM model is compared with a simplified constant mass (CM) model, which is shown to be an excellent approximation. The equations of motion for the CM and VM models are integrated with the leapfrog and the iterative leapfrog algorithms, respectively. The Lagrangian dynamics approach reduces the number of degrees of freedom from about 40 to 1, and allows the use of time steps on the order of 20 fs, about an order of magnitude greater than is used in conventional MD simulations.

show abstract

Ab initio calculations on the barrier to pseudorotation of model 2′‐deoxyfuranose and 2′‐deoxy‐2′‐fluorofuranose rings

Cited by 9 publications

References 27 publications

A → Z transition in the synthetic hexanucleotide (dCdGfl)₃

A → Z transition in the synthetic hexanucleotide (dCdGfl)₃

Theoretical analysis of deoxycytidine‐5′‐phosphate protonation

Lagrangian molecular dynamics using selected conformational degrees of freedom, with application to the pseudorotation dynamics of furanose rings

Contact Info

Product

Resources

About

Ab initio calculations on the barrier to pseudorotation of model 2′‐deoxyfuranose and 2′‐deoxy‐2′‐fluorofuranose rings

Cited by 9 publications

References 27 publications

A → Z transition in the synthetic hexanucleotide (dCdGfl)3

A → Z transition in the synthetic hexanucleotide (dCdGfl)3

Theoretical analysis of deoxycytidine‐5′‐phosphate protonation

Lagrangian molecular dynamics using selected conformational degrees of freedom, with application to the pseudorotation dynamics of furanose rings

Contact Info

Product

Resources

About

A → Z transition in the synthetic hexanucleotide (dCdGfl)₃

A → Z transition in the synthetic hexanucleotide (dCdGfl)₃