Binding of cationic conjugated polymers to DNA: Atomistic simulations of adducts involving the Dickerson's dodecamer

J. Preat, E.A. Perpete, D. Zanuy, C. Aleman

Research output: Contribution to journalArticle

Abstract

We here describe the investigation at the atomistic level of the structure, stability, and dynamics of several complexes resulting from the interaction of oxidized poly(3,4-ethylenedioxythiophene) with the well-known Dickerson's dodecamer sequence. Four specific arrangements have been selected as referential structures for molecular dynamics simulations, and the resulting independent trajectories tend to converge in two distinguishable models with the strongest interactions. The first one presents a coiled DNA strand enveloping the oligomer chain, whereas in the second model, the conducting polymer chain and the disorganized DNA strand are facing side-by-side. Analysis of the intermolecular interactions indicates that the electrostatic interactions involving the negatively charged DNA phosphates and the positively charged units of the oligomer are much more frequent in the first model. In addition, aside from these electrostatic interactions, specific O•••H and S•••H hydrogen bonds, stacking, and N-H••• interactions have been detected. Among all of these four specific interactions, we show that the stacking is the most abundant and shows the best stability, whereas O•••H hydrogen bonds are also frequent with long lifetimes. At the end, we have to underline that these specific interactions are predominant for the thymine and the guanine, which is in perfect agreement with previous experimental observations.
Original languageEnglish
Pages (from-to)1298-1304
Number of pages7
JournalBiomacromolecules
Volume12
Issue number4
DOIs
Publication statusPublished - 11 Apr 2011

Fingerprint

Conjugated polymers
DNA
Coulomb interactions
Oligomers
Hydrogen bonds
Thymine
Guanine
Conducting polymers
Molecular dynamics
Phosphates
Trajectories
Computer simulation

Cite this

@article{7ee0ab85bac84f7f8fac882b8c881ab1,
title = "Binding of cationic conjugated polymers to DNA: Atomistic simulations of adducts involving the Dickerson's dodecamer",
abstract = "We here describe the investigation at the atomistic level of the structure, stability, and dynamics of several complexes resulting from the interaction of oxidized poly(3,4-ethylenedioxythiophene) with the well-known Dickerson's dodecamer sequence. Four specific arrangements have been selected as referential structures for molecular dynamics simulations, and the resulting independent trajectories tend to converge in two distinguishable models with the strongest interactions. The first one presents a coiled DNA strand enveloping the oligomer chain, whereas in the second model, the conducting polymer chain and the disorganized DNA strand are facing side-by-side. Analysis of the intermolecular interactions indicates that the electrostatic interactions involving the negatively charged DNA phosphates and the positively charged units of the oligomer are much more frequent in the first model. In addition, aside from these electrostatic interactions, specific O•••H and S•••H hydrogen bonds, stacking, and N-H••• interactions have been detected. Among all of these four specific interactions, we show that the stacking is the most abundant and shows the best stability, whereas O•••H hydrogen bonds are also frequent with long lifetimes. At the end, we have to underline that these specific interactions are predominant for the thymine and the guanine, which is in perfect agreement with previous experimental observations.",
author = "J. Preat and E.A. Perpete and D. Zanuy and C. Aleman",
note = "MEDLINE{\circledR} is the source for the MeSH terms of this document.",
year = "2011",
month = "4",
day = "11",
doi = "10.1021/bm200022n",
language = "English",
volume = "12",
pages = "1298--1304",
journal = "Biomacromolecules",
issn = "1525-7797",
publisher = "American Chemical Society",
number = "4",

}

Binding of cationic conjugated polymers to DNA : Atomistic simulations of adducts involving the Dickerson's dodecamer. / Preat, J.; Perpete, E.A.; Zanuy, D.; Aleman, C.

In: Biomacromolecules, Vol. 12, No. 4, 11.04.2011, p. 1298-1304.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Binding of cationic conjugated polymers to DNA

T2 - Atomistic simulations of adducts involving the Dickerson's dodecamer

AU - Preat, J.

AU - Perpete, E.A.

AU - Zanuy, D.

AU - Aleman, C.

N1 - MEDLINE® is the source for the MeSH terms of this document.

PY - 2011/4/11

Y1 - 2011/4/11

N2 - We here describe the investigation at the atomistic level of the structure, stability, and dynamics of several complexes resulting from the interaction of oxidized poly(3,4-ethylenedioxythiophene) with the well-known Dickerson's dodecamer sequence. Four specific arrangements have been selected as referential structures for molecular dynamics simulations, and the resulting independent trajectories tend to converge in two distinguishable models with the strongest interactions. The first one presents a coiled DNA strand enveloping the oligomer chain, whereas in the second model, the conducting polymer chain and the disorganized DNA strand are facing side-by-side. Analysis of the intermolecular interactions indicates that the electrostatic interactions involving the negatively charged DNA phosphates and the positively charged units of the oligomer are much more frequent in the first model. In addition, aside from these electrostatic interactions, specific O•••H and S•••H hydrogen bonds, stacking, and N-H••• interactions have been detected. Among all of these four specific interactions, we show that the stacking is the most abundant and shows the best stability, whereas O•••H hydrogen bonds are also frequent with long lifetimes. At the end, we have to underline that these specific interactions are predominant for the thymine and the guanine, which is in perfect agreement with previous experimental observations.

AB - We here describe the investigation at the atomistic level of the structure, stability, and dynamics of several complexes resulting from the interaction of oxidized poly(3,4-ethylenedioxythiophene) with the well-known Dickerson's dodecamer sequence. Four specific arrangements have been selected as referential structures for molecular dynamics simulations, and the resulting independent trajectories tend to converge in two distinguishable models with the strongest interactions. The first one presents a coiled DNA strand enveloping the oligomer chain, whereas in the second model, the conducting polymer chain and the disorganized DNA strand are facing side-by-side. Analysis of the intermolecular interactions indicates that the electrostatic interactions involving the negatively charged DNA phosphates and the positively charged units of the oligomer are much more frequent in the first model. In addition, aside from these electrostatic interactions, specific O•••H and S•••H hydrogen bonds, stacking, and N-H••• interactions have been detected. Among all of these four specific interactions, we show that the stacking is the most abundant and shows the best stability, whereas O•••H hydrogen bonds are also frequent with long lifetimes. At the end, we have to underline that these specific interactions are predominant for the thymine and the guanine, which is in perfect agreement with previous experimental observations.

UR - http://www.scopus.com/inward/record.url?scp=79953846747&partnerID=8YFLogxK

U2 - 10.1021/bm200022n

DO - 10.1021/bm200022n

M3 - Article

VL - 12

SP - 1298

EP - 1304

JO - Biomacromolecules

JF - Biomacromolecules

SN - 1525-7797

IS - 4

ER -