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

Research output: Contribution to journalArticle

Standard

A polarized-light spectroscopy study of interactions of a hairpin polyamide with DNA. / Caesar, Christina E. B.; Johnsson, Richard; Ellervik, Ulf; Fox, Keith R.; Lincoln, Per; Norden, Bengt.

In: Biophysical Journal, Vol. 91, No. 3, 2006, p. 904-911.

Research output: Contribution to journalArticle

Harvard

APA

CBE

MLA

Vancouver

Author

Caesar, Christina E. B. ; Johnsson, Richard ; Ellervik, Ulf ; Fox, Keith R. ; Lincoln, Per ; Norden, Bengt. / A polarized-light spectroscopy study of interactions of a hairpin polyamide with DNA. In: Biophysical Journal. 2006 ; Vol. 91, No. 3. pp. 904-911.

RIS

TY - JOUR

T1 - A polarized-light spectroscopy study of interactions of a hairpin polyamide with DNA

AU - Caesar, Christina E. B.

AU - Johnsson, Richard

AU - Ellervik, Ulf

AU - Fox, Keith R.

AU - Lincoln, Per

AU - Norden, Bengt

N1 - 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)

PY - 2006

Y1 - 2006

N2 - 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.

AB - 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.

U2 - 10.1529/biophysj.105.080564

DO - 10.1529/biophysj.105.080564

M3 - Article

VL - 91

SP - 904

EP - 911

JO - Biophysical Journal

JF - Biophysical Journal

SN - 1542-0086

IS - 3

ER -