TY - JOUR
T1 - Polyelectrolyte properties of single stranded DNA measured using SAXS and single-molecule FRET
T2 - Beyond the wormlike chain model
AU - Meisburger, Steve P.
AU - Sutton, Julie L.
AU - Chen, Huimin
AU - Pabit, Suzette A.
AU - Kirmizialtin, Serdal
AU - Elber, Ron
AU - Pollack, Lois
PY - 2013/12
Y1 - 2013/12
N2 - Nucleic acids are highly charged polyelectrolytes that interact strongly with salt ions. Rigid, base-paired regions are successfully described with wormlike chain models, but nonbase-paired single stranded regions have fundamentally different polymer properties because of their greater flexibility. Recently, attention has turned to single stranded nucleic acids due to the growing recognition of their biological importance, as well as the availability of sophisticated experimental techniques sensitive to the conformation of individual molecules. We investigate polyelectrolyte properties of poly(dT), an important and widely studied model system for flexible single stranded nucleic acids, in physiologically important mixed mono- and divalent salt. We report measurements of the form factor and interparticle interactions using SAXS, end-to-end distances using smFRET, and number of excess ions using ASAXS. We present a coarse-grained model that accounts for flexibility, excluded volume, and electrostatic interactions in these systems. Predictions of the model are validated against experiment. We also discuss the state of all-atom, explicit solvent molecular dynamics simulations of poly(dT), the next step in understanding the complexities of ion interactions with these highly charged and flexible polymers. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 1032-1045, 2013.
AB - Nucleic acids are highly charged polyelectrolytes that interact strongly with salt ions. Rigid, base-paired regions are successfully described with wormlike chain models, but nonbase-paired single stranded regions have fundamentally different polymer properties because of their greater flexibility. Recently, attention has turned to single stranded nucleic acids due to the growing recognition of their biological importance, as well as the availability of sophisticated experimental techniques sensitive to the conformation of individual molecules. We investigate polyelectrolyte properties of poly(dT), an important and widely studied model system for flexible single stranded nucleic acids, in physiologically important mixed mono- and divalent salt. We report measurements of the form factor and interparticle interactions using SAXS, end-to-end distances using smFRET, and number of excess ions using ASAXS. We present a coarse-grained model that accounts for flexibility, excluded volume, and electrostatic interactions in these systems. Predictions of the model are validated against experiment. We also discuss the state of all-atom, explicit solvent molecular dynamics simulations of poly(dT), the next step in understanding the complexities of ion interactions with these highly charged and flexible polymers. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 1032-1045, 2013.
KW - ion-DNA interactions
KW - single stranded DNA
KW - small angle X-ray scattering
UR - http://www.scopus.com/inward/record.url?scp=84884970433&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84884970433&partnerID=8YFLogxK
U2 - 10.1002/bip.22265
DO - 10.1002/bip.22265
M3 - Review article
C2 - 23606337
AN - SCOPUS:84884970433
SN - 0006-3525
VL - 99
SP - 1032
EP - 1045
JO - Biopolymers
JF - Biopolymers
IS - 12
ER -