Monovalent Cations Sequester within the A-Tract Minor Groove of [d(CGCGAATTCGCG)]<sub>2</sub><sup>,</sup>

Woods, Kristen Kruger; McFail-Isom, Lori; Sines, Chad C.; Howerton, Shelley B.; Stephens, Rasheeda K.; Williams, Loren Dean

doi:10.1021/ja9919579

Cited by 76 publications

(88 citation statements)

References 34 publications

(70 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The magnitude of the effect is consistent with previous experimental results on the extent and location of NH 4 ϩ binding to A4T4, T4A4, and GCA5CG (53). The ApT step represents a unique and species-dependent tight binding site for monovalent cations, which can coordinate to the two opposing T carbonyls (41,(49)(50)(51)(52)(53)55). We propose that the specific minor groove widthdependent binding of monovalent cations at the ApT step contributes to the global bend observed for A4T4.…”

Section: Global Bend Of D(caaaattttg)n and D(gttttaaaac)nsupporting

confidence: 90%

“…X-ray crystallography (49,50), molecular dynamics (51), capillary electrophoresis (52), and NMR (53) studies of DNA have shown that, in addition to waters, monovalent cations can bind specifically in the minor groove of A-tracts, although the relative occupancies remain unresolved (54). In our previous NMR studies of A4T4 and T4A4, NH 4 ϩ were found to localize in the narrowest parts of the minor grooves, resulting in a very different distribution of cation localization for the two molecules that was proposed to contribute to A-tract bending (53).…”

Section: Global Bend Of D(caaaattttg)n and D(gttttaaaac)nmentioning

confidence: 99%

See 1 more Smart Citation

DNA A-tract bending in three dimensions: Solving the dA ₄ T ₄ vs. dT ₄ A ₄ conundrum

Štefl

Ravindranathan

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

140

144

View full text Add to dashboard Cite

Section: Global Bend Of D(caaaattttg)n and D(gttttaaaac)nsupporting

confidence: 90%

Section: Global Bend Of D(caaaattttg)n and D(gttttaaaac)nmentioning

confidence: 99%

DNA A-tract bending in three dimensions: Solving the dA ₄ T ₄ vs. dT ₄ A ₄ conundrum

Štefl

Ravindranathan

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

140

144

View full text Add to dashboard Cite

“…As it is mentioned before, divalent cations have a greater tendency to orient and polarize water molecules and to resist dehydration. 24 Any change in the tendency based on the valence of the cation, besides the ionic radius, is of interest for the analysis of the displacement obtained from the IPMC. If the results from the monovalent species sustained a tendency at which the smallest cation, the lithium, showed the greatest displacements, when comparing the lithium and magnesium the results show something different.…”

Section: Graphical Results From the Solved Equationsmentioning

confidence: 99%

Modeling the displacement in three‐layer electroactive polymers using different counter‐ions by a phase transformation approach

Guzmán

Cortés

Fuentes

et al. 2009

J of Applied Polymer Sci

View full text Add to dashboard Cite

The use of three-layer electroactives polymers is becoming more widely known among researchers and engineers because of their potentials to become mechanical actuators. The up-to-date research and development in the Nafion V R /Metal composites has given some fundamentals, preparation techniques, and modeling of the phenomena regarding the deformation of the material from different scientific point of view. This gives the opportunity to propose correlations for modeling the phenomena present in these materials by different approaches. A constitutive model for the bending deformation of a Nafion V R Ionic Polymer-Metal Composite (IPMC) was formulated based on an approach that represents, analogically, a phase transformation inside the base polymer and combines it with the bending of a beam in order to predict the displacement when the material is subject to an electrical input. The model was solved and evaluated for five different types of counter-ion systems. Experimental data was used to solve the parameters within the model. The results of the solved model gave a good fitting of the experimental data and are shown for different voltage and frequency conditions in all five ionic systems.

show abstract

“…The role of ions in DNA bending 13,177 was inspired in part by a combination of MD modeling studies, 10,135 crystal structures, 132,178,179 and NMR studies 128 and figures strongly in the bending polaron model 12 and a recent description of DNA curvature proposed by Hud and Plavec, 16 described above. The MD provides leading results, but at the same time it is clear that the motions of environmental ions are slow to converge.…”

Section: Discussionmentioning

confidence: 99%

Molecular dynamics simulations of DNA curvature and flexibility: Helix phasing and premelting

et al. 2004

View full text Add to dashboard Cite

Recent studies of DNA axis curvature and flexibility based on molecular dynamics (MD) simulations on DNA are reviewed. The MD simulations are on DNA sequences up to 25 base pairs in length, including explicit consideration of counterions and waters in the computational model. MD studies are described for ApA steps, A-tracts, for sequences of A-tracts with helix phasing. In MD modeling, ApA steps and A-tracts in aqueous solution are essentially straight, relatively rigid, and exhibit the characteristic features associated with the B'-form of DNA. The results of MD modeling of A-tract oligonucleotides are validated by close accord with corresponding crystal structure results and nuclear magnetic resonance (NMR) nuclear Overhauser effect (NOE) and residual dipolar coupling (RDC) structures of d(CGCGAATTCGCG) and d(GGCAAAAAACGG). MD simulation successfully accounts for enhanced axis curvature in a set of three sequences with phased A-tracts studied to date. The primary origin of the axis curvature in the MD model is found at those pyrimidine/purine YpR "flexible hinge points" in a high roll, open hinge conformational substate. In the MD model of axis curvature in a DNA sequence with both phased A-tracts and YpR steps, the A-tracts appear to act as positioning elements that make the helix phasing more precise, and key YpR steps in the open hinge state serve as curvature elements. Our simulations on a phased A-tract sequence as a function of temperature show that the MD simulations exhibit a premelting transition in close accord with experiment, and predict that the mechanism involves a B'-to-B transition within A-tracts coupled with the prediction of a transition in key YpR steps from the high roll, open hinge, to a low roll, closed hinge substate. Diverse experimental observations on DNA curvature phenomena are examined in light of the MD model with no serious discrepancies. The collected MD results provide independent support for the "non-A-tract model" of DNA curvature. The "junction model" is indicated to be a special case of the non-A-tract model when there is a Y base at the 5' end of an A-tract. In accord with crystallography, the "ApA wedge model" is not supported by MD.

show abstract

Monovalent Cations Sequester within the A-Tract Minor Groove of [d(CGCGAATTCGCG)]₂^,

Cited by 76 publications

References 34 publications

DNA A-tract bending in three dimensions: Solving the dA ₄ T ₄ vs. dT ₄ A ₄ conundrum

DNA A-tract bending in three dimensions: Solving the dA ₄ T ₄ vs. dT ₄ A ₄ conundrum

Modeling the displacement in three‐layer electroactive polymers using different counter‐ions by a phase transformation approach

Molecular dynamics simulations of DNA curvature and flexibility: Helix phasing and premelting

Contact Info

Product

Resources

About

Monovalent Cations Sequester within the A-Tract Minor Groove of [d(CGCGAATTCGCG)]2,

Cited by 76 publications

References 34 publications

DNA A-tract bending in three dimensions: Solving the dA 4 T 4 vs. dT 4 A 4 conundrum

DNA A-tract bending in three dimensions: Solving the dA 4 T 4 vs. dT 4 A 4 conundrum

Modeling the displacement in three‐layer electroactive polymers using different counter‐ions by a phase transformation approach

Molecular dynamics simulations of DNA curvature and flexibility: Helix phasing and premelting

Contact Info

Product

Resources

About

Monovalent Cations Sequester within the A-Tract Minor Groove of [d(CGCGAATTCGCG)]₂^,

DNA A-tract bending in three dimensions: Solving the dA ₄ T ₄ vs. dT ₄ A ₄ conundrum

DNA A-tract bending in three dimensions: Solving the dA ₄ T ₄ vs. dT ₄ A ₄ conundrum