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A polarized-light spectroscopy study of interactions of a hairpin polyamide with DNA

Caesar, Christina E. B. ; Johnsson, Richard LU ; Ellervik, Ulf LU ; Fox, Keith R. ; Lincoln, Per and Norden, Bengt (2006) In Biophysical Journal 91(3). p.904-911
Abstract
We here study the interactions of a polyamide with large DNA, and compare to those of minor groove binder distamycin (DST), including high ligand/DNA binding ratios. Specific as well as nonspecific binding is probed using polarized-light spectroscopy combined with singular value decomposition analysis. Circular and linear dichroism data confirm binding geometries consistent with minor groove binding for both of the ligands. Interestingly, at high and intermediate ligand/DNA ratios the polyamide exhibits no significant sequence discrimination between mixed-sequence (calf thymus) and AT DNA as compared to DST. Each ligand is concluded to exhibit two different binding modes depending upon ligand/DNA ratio and nucleo-base sequence. At high... (More)
We here study the interactions of a polyamide with large DNA, and compare to those of minor groove binder distamycin (DST), including high ligand/DNA binding ratios. Specific as well as nonspecific binding is probed using polarized-light spectroscopy combined with singular value decomposition analysis. Circular and linear dichroism data confirm binding geometries consistent with minor groove binding for both of the ligands. Interestingly, at high and intermediate ligand/DNA ratios the polyamide exhibits no significant sequence discrimination between mixed-sequence (calf thymus) and AT DNA as compared to DST. Each ligand is concluded to exhibit two different binding modes depending upon ligand/DNA ratio and nucleo-base sequence. At high binding ratios, distinct differences between the ligands are observed: circular dichroism spectra exciton effects provide evidence of bimolecular interactions of the polyamide when bound to AT-DNA, whereas no effects are seen with DST or mixed-sequence DNA. Also linear dichroism indicates that a change in binding geometry occurs at high polyamide/AT ratios, and that the effect occurs only with polyamide in contrast to DST. Since the effect is insignificant with DST, or with calf thymus DNA, it is concluded that it relates to the sizes of the ligands and the minor grooves, becoming critical in the limit of crowding. (Less)
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author
; ; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Biophysical Journal
volume
91
issue
3
pages
904 - 911
publisher
Cell Press
external identifiers
  • wos:000239086800016
  • scopus:33746698355
ISSN
1542-0086
DOI
10.1529/biophysj.105.080564
language
English
LU publication?
yes
additional info
The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Organic chemistry (S/LTH) (011001240)
id
b523e64b-64f0-4fa8-b1f2-2b79b21db05b (old id 402394)
date added to LUP
2016-04-01 12:22:05
date last changed
2021-09-22 04:24:55
@article{b523e64b-64f0-4fa8-b1f2-2b79b21db05b,
  abstract     = {We here study the interactions of a polyamide with large DNA, and compare to those of minor groove binder distamycin (DST), including high ligand/DNA binding ratios. Specific as well as nonspecific binding is probed using polarized-light spectroscopy combined with singular value decomposition analysis. Circular and linear dichroism data confirm binding geometries consistent with minor groove binding for both of the ligands. Interestingly, at high and intermediate ligand/DNA ratios the polyamide exhibits no significant sequence discrimination between mixed-sequence (calf thymus) and AT DNA as compared to DST. Each ligand is concluded to exhibit two different binding modes depending upon ligand/DNA ratio and nucleo-base sequence. At high binding ratios, distinct differences between the ligands are observed: circular dichroism spectra exciton effects provide evidence of bimolecular interactions of the polyamide when bound to AT-DNA, whereas no effects are seen with DST or mixed-sequence DNA. Also linear dichroism indicates that a change in binding geometry occurs at high polyamide/AT ratios, and that the effect occurs only with polyamide in contrast to DST. Since the effect is insignificant with DST, or with calf thymus DNA, it is concluded that it relates to the sizes of the ligands and the minor grooves, becoming critical in the limit of crowding.},
  author       = {Caesar, Christina E. B. and Johnsson, Richard and Ellervik, Ulf and Fox, Keith R. and Lincoln, Per and Norden, Bengt},
  issn         = {1542-0086},
  language     = {eng},
  number       = {3},
  pages        = {904--911},
  publisher    = {Cell Press},
  series       = {Biophysical Journal},
  title        = {A polarized-light spectroscopy study of interactions of a hairpin polyamide with DNA},
  url          = {http://dx.doi.org/10.1529/biophysj.105.080564},
  doi          = {10.1529/biophysj.105.080564},
  volume       = {91},
  year         = {2006},
}