TY - JOUR

T1 - Sequence-influenced interactions of oligoacridines with DNA detected by retarded gel electrophoretic migrations

AU - Nielsen, Peter E.

AU - Zhen, W P

AU - Henriksen, U

AU - Buchardt, O

PY - 1988/1/12

Y1 - 1988/1/12

N2 - We have found that di-, tri-, tetra-, and hexa-9-acridinylamines are so efficiently associated with DNA during electrophoresis in polyacrylamide or agarose gels that they retard its migration. The retardation is roughly proportional to the reagent to base pair ratio, and the magnitude of the retardation indicates that a combined charge neutralization/helix extension mechanism is mainly responsible for the effect. Furthermore, DNA sequence dependent differences are observed. Thus, the pUC 19 restriction fragments (HaeIII or AluI), which in the native state comigrate upon gel electrophoretic analysis, could be separated in the presence of a diacridine, and specific DNA fragments responded differently to different diacridines. These results suggest that the effect also is due to a contribution from the DNA conformation and that the DNA conformation dynamics are influenced differently upon binding of different diacridines. We foresee three applications of this observation: (1) in analytical gel electrophoretic separation of otherwise comigrating DNA molecules, (2) in studies of polyintercalator-DNA interaction, and (3) in measurements of polyintercalator-induced DNA unwinding.

AB - We have found that di-, tri-, tetra-, and hexa-9-acridinylamines are so efficiently associated with DNA during electrophoresis in polyacrylamide or agarose gels that they retard its migration. The retardation is roughly proportional to the reagent to base pair ratio, and the magnitude of the retardation indicates that a combined charge neutralization/helix extension mechanism is mainly responsible for the effect. Furthermore, DNA sequence dependent differences are observed. Thus, the pUC 19 restriction fragments (HaeIII or AluI), which in the native state comigrate upon gel electrophoretic analysis, could be separated in the presence of a diacridine, and specific DNA fragments responded differently to different diacridines. These results suggest that the effect also is due to a contribution from the DNA conformation and that the DNA conformation dynamics are influenced differently upon binding of different diacridines. We foresee three applications of this observation: (1) in analytical gel electrophoretic separation of otherwise comigrating DNA molecules, (2) in studies of polyintercalator-DNA interaction, and (3) in measurements of polyintercalator-induced DNA unwinding.

KW - Acridines

KW - Base Sequence

KW - DNA

KW - DNA Restriction Enzymes

KW - Deoxyribonuclease I

KW - Magnetic Resonance Spectroscopy

KW - Nucleic Acid Conformation

KW - Plasmids

KW - Structure-Activity Relationship

U2 - 10.1021/bi00401a012

DO - 10.1021/bi00401a012

M3 - Journal article

C2 - 2831963

VL - 27

SP - 67

EP - 73

JO - Biochemistry

JF - Biochemistry

SN - 0006-2960

IS - 1

ER -