Kinetics of the Conformational Transformation between B- and A‑Forms in the Drew–Dickerson Dodecamer
Some DNA sequences in crystals and in complexes with proteins can exist in the forms intermediate between the B- and A-DNA. Based on this, it was implied that the B-to-A transition for any DNA molecule should go through these intermediate forms also in kinetics. More precisely, the helix parameter S...
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Published in | ACS omega Vol. 5; no. 51; pp. 32995 - 33006 |
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Abstract | Some DNA sequences in crystals and in complexes with proteins can exist in the forms intermediate between the B- and A-DNA. Based on this, it was implied that the B-to-A transition for any DNA molecule should go through these intermediate forms also in kinetics. More precisely, the helix parameter Slide has to change first, and the molecule should take the E-form. After that, the Roll parameter changes. In the present work, we simulated the kinetics of the B–A transition in the Drew–Dickerson dodecamer, a known B-philic DNA oligomer. We used the “sugar” coarse-grained model that reproduces ribose flexibility, preserves sequence specificity, employs implicit water and explicit ions, and offers the possibility to vary friction. As the control parameter of the transition, we chose the volume available for a counterion and considered the change from a large to a small volume. In the described system, the B-to-A conformational transformation proved to correspond to a first-order phase transition. The molecule behaves like a small cluster in the region of such a transition, jumping between the A- and B-forms in a wide range of available volumes. The viscosity of the solvent does not affect the midpoint of the transition but only the overall mobility of the system. All helix parameters change synchronously on average, we have not observed the sequence “Slide first, Roll later” in kinetics, and the E-DNA is not a necessary step for the transition between the B- and A-forms in the studied system. So, the existence of the intermediate DNA forms requires specific conditions, shifting the common balance of interactions: certain nucleotide sequence in specific solution or/and the interaction with some protein. |
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AbstractList | Some
DNA sequences in crystals and in complexes with proteins can
exist in the forms intermediate between the B- and A-DNA. Based on
this, it was implied that the B-to-A transition for any DNA molecule
should go through these intermediate forms also in kinetics. More
precisely, the helix parameter
Slide
has to change
first, and the molecule should take the E-form. After that, the
Roll
parameter changes. In the present work, we simulated
the kinetics of the B–A transition in the Drew–Dickerson
dodecamer, a known B-philic DNA oligomer. We used the “sugar”
coarse-grained model that reproduces ribose flexibility, preserves
sequence specificity, employs implicit water and explicit ions, and
offers the possibility to vary friction. As the control parameter
of the transition, we chose the volume available for a counterion
and considered the change from a large to a small volume. In the described
system, the B-to-A conformational transformation proved to correspond
to a first-order phase transition. The molecule behaves like a small
cluster in the region of such a transition, jumping between the A-
and B-forms in a wide range of available volumes. The viscosity of
the solvent does not affect the midpoint of the transition but only
the overall mobility of the system. All helix parameters change synchronously
on average, we have not observed the sequence “
Slide
first,
Roll
later” in kinetics, and the
E-DNA is not a necessary step for the transition between the B- and
A-forms in the studied system. So, the existence of the intermediate
DNA forms requires specific conditions, shifting the common balance
of interactions: certain nucleotide sequence in specific solution
or/and the interaction with some protein. Some DNA sequences in crystals and in complexes with proteins can exist in the forms intermediate between the B- and A-DNA. Based on this, it was implied that the B-to-A transition for any DNA molecule should go through these intermediate forms also in kinetics. More precisely, the helix parameter has to change first, and the molecule should take the E-form. After that, the parameter changes. In the present work, we simulated the kinetics of the B-A transition in the Drew-Dickerson dodecamer, a known B-philic DNA oligomer. We used the "sugar" coarse-grained model that reproduces ribose flexibility, preserves sequence specificity, employs implicit water and explicit ions, and offers the possibility to vary friction. As the control parameter of the transition, we chose the volume available for a counterion and considered the change from a large to a small volume. In the described system, the B-to-A conformational transformation proved to correspond to a first-order phase transition. The molecule behaves like a small cluster in the region of such a transition, jumping between the A- and B-forms in a wide range of available volumes. The viscosity of the solvent does not affect the midpoint of the transition but only the overall mobility of the system. All helix parameters change synchronously on average, we have not observed the sequence " first, later" in kinetics, and the E-DNA is not a necessary step for the transition between the B- and A-forms in the studied system. So, the existence of the intermediate DNA forms requires specific conditions, shifting the common balance of interactions: certain nucleotide sequence in specific solution or/and the interaction with some protein. Some DNA sequences in crystals and in complexes with proteins can exist in the forms intermediate between the B- and A-DNA. Based on this, it was implied that the B-to-A transition for any DNA molecule should go through these intermediate forms also in kinetics. More precisely, the helix parameter Slide has to change first, and the molecule should take the E-form. After that, the Roll parameter changes. In the present work, we simulated the kinetics of the B–A transition in the Drew–Dickerson dodecamer, a known B-philic DNA oligomer. We used the “sugar” coarse-grained model that reproduces ribose flexibility, preserves sequence specificity, employs implicit water and explicit ions, and offers the possibility to vary friction. As the control parameter of the transition, we chose the volume available for a counterion and considered the change from a large to a small volume. In the described system, the B-to-A conformational transformation proved to correspond to a first-order phase transition. The molecule behaves like a small cluster in the region of such a transition, jumping between the A- and B-forms in a wide range of available volumes. The viscosity of the solvent does not affect the midpoint of the transition but only the overall mobility of the system. All helix parameters change synchronously on average, we have not observed the sequence “Slide first, Roll later” in kinetics, and the E-DNA is not a necessary step for the transition between the B- and A-forms in the studied system. So, the existence of the intermediate DNA forms requires specific conditions, shifting the common balance of interactions: certain nucleotide sequence in specific solution or/and the interaction with some protein. |
Author | Kovaleva, Natalya A Zubova, Elena A Strelnikov, Ivan A |
AuthorAffiliation | N.N. Semenov Federal Research Center for Chemical Physics Russian Academy of Sciences |
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Snippet | Some DNA sequences in crystals and in complexes with proteins can exist in the forms intermediate between the B- and A-DNA. Based on this, it was implied that... Some DNA sequences in crystals and in complexes with proteins can exist in the forms intermediate between the B- and A-DNA. Based on this, it was implied that... |
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Title | Kinetics of the Conformational Transformation between B- and A‑Forms in the Drew–Dickerson Dodecamer |
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