Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer

Sarah L. Williams, Laura K. Parkhurst, Lawrence J Parkhurst

Research output: Contribution to journalArticle

20 Citations (Scopus)

Abstract

Local DNA deformation arises from an interplay among sequence-related base stacking, intrastrand phosphate repulsion, and counterion and water distribution, which is further complicated by the approach and binding of a protein. The role of electrostatics in this complex chemistry was investigated using tethered cationic groups that mimic proximate side chains. A DNA duplex was modified with one or two centrally located deoxyuracils substituted at the 5-position with either a flexible 3-aminopropyl group or a rigid 3-aminopropyn-1-yl group. End-to-end helical distances and duplex flexibility were obtained from measurements of the time-resolved Förster resonance energy transfer between 5′- and 3′-linked dye pairs. A novel analysis utilized the first and second moments of the G(t) function, which encompasses only the energy transfer process. Duplex flexibility is altered by the presence of even a single positive charge. In contrast, the mean 5′-3′ distance is significantly altered by the introduction of two adjacently tethered cations into the double helix but not by a single cation: two adjacent aminopropyl groups decrease the 5′-3′ distance while neighboring aminopropynyl groups lengthen the helix.

Original languageEnglish (US)
Pages (from-to)1028-1035
Number of pages8
JournalNucleic acids research
Volume34
Issue number3
DOIs
StatePublished - Mar 20 2006

Fingerprint

Fluorescence Resonance Energy Transfer
Energy Transfer
Cations
DNA
Static Electricity
Carrier Proteins
Coloring Agents
Phosphates
Water

ASJC Scopus subject areas

  • Genetics

Cite this

Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer. / Williams, Sarah L.; Parkhurst, Laura K.; Parkhurst, Lawrence J.

In: Nucleic acids research, Vol. 34, No. 3, 20.03.2006, p. 1028-1035.

Research output: Contribution to journalArticle

@article{e96e0cdf7006414e9a6a8edc72475162,
title = "Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer",
abstract = "Local DNA deformation arises from an interplay among sequence-related base stacking, intrastrand phosphate repulsion, and counterion and water distribution, which is further complicated by the approach and binding of a protein. The role of electrostatics in this complex chemistry was investigated using tethered cationic groups that mimic proximate side chains. A DNA duplex was modified with one or two centrally located deoxyuracils substituted at the 5-position with either a flexible 3-aminopropyl group or a rigid 3-aminopropyn-1-yl group. End-to-end helical distances and duplex flexibility were obtained from measurements of the time-resolved F{\"o}rster resonance energy transfer between 5′- and 3′-linked dye pairs. A novel analysis utilized the first and second moments of the G(t) function, which encompasses only the energy transfer process. Duplex flexibility is altered by the presence of even a single positive charge. In contrast, the mean 5′-3′ distance is significantly altered by the introduction of two adjacently tethered cations into the double helix but not by a single cation: two adjacent aminopropyl groups decrease the 5′-3′ distance while neighboring aminopropynyl groups lengthen the helix.",
author = "Williams, {Sarah L.} and Parkhurst, {Laura K.} and Parkhurst, {Lawrence J}",
year = "2006",
month = "3",
day = "20",
doi = "10.1093/nar/gkj498",
language = "English (US)",
volume = "34",
pages = "1028--1035",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "3",

}

TY - JOUR

T1 - Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer

AU - Williams, Sarah L.

AU - Parkhurst, Laura K.

AU - Parkhurst, Lawrence J

PY - 2006/3/20

Y1 - 2006/3/20

N2 - Local DNA deformation arises from an interplay among sequence-related base stacking, intrastrand phosphate repulsion, and counterion and water distribution, which is further complicated by the approach and binding of a protein. The role of electrostatics in this complex chemistry was investigated using tethered cationic groups that mimic proximate side chains. A DNA duplex was modified with one or two centrally located deoxyuracils substituted at the 5-position with either a flexible 3-aminopropyl group or a rigid 3-aminopropyn-1-yl group. End-to-end helical distances and duplex flexibility were obtained from measurements of the time-resolved Förster resonance energy transfer between 5′- and 3′-linked dye pairs. A novel analysis utilized the first and second moments of the G(t) function, which encompasses only the energy transfer process. Duplex flexibility is altered by the presence of even a single positive charge. In contrast, the mean 5′-3′ distance is significantly altered by the introduction of two adjacently tethered cations into the double helix but not by a single cation: two adjacent aminopropyl groups decrease the 5′-3′ distance while neighboring aminopropynyl groups lengthen the helix.

AB - Local DNA deformation arises from an interplay among sequence-related base stacking, intrastrand phosphate repulsion, and counterion and water distribution, which is further complicated by the approach and binding of a protein. The role of electrostatics in this complex chemistry was investigated using tethered cationic groups that mimic proximate side chains. A DNA duplex was modified with one or two centrally located deoxyuracils substituted at the 5-position with either a flexible 3-aminopropyl group or a rigid 3-aminopropyn-1-yl group. End-to-end helical distances and duplex flexibility were obtained from measurements of the time-resolved Förster resonance energy transfer between 5′- and 3′-linked dye pairs. A novel analysis utilized the first and second moments of the G(t) function, which encompasses only the energy transfer process. Duplex flexibility is altered by the presence of even a single positive charge. In contrast, the mean 5′-3′ distance is significantly altered by the introduction of two adjacently tethered cations into the double helix but not by a single cation: two adjacent aminopropyl groups decrease the 5′-3′ distance while neighboring aminopropynyl groups lengthen the helix.

UR - http://www.scopus.com/inward/record.url?scp=33644855950&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33644855950&partnerID=8YFLogxK

U2 - 10.1093/nar/gkj498

DO - 10.1093/nar/gkj498

M3 - Article

VL - 34

SP - 1028

EP - 1035

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 3

ER -