Unveiling Berenil's Binding Preferences on Plasmid DNA: Insights from pbr322

Dr. Elena V. Ricci; Dr. Arunesh Patel

Authors

Dr. Elena V. Ricci

Department of Molecular Biology and Biotechnology, University of Milan, Italy
Dr. Arunesh Patel

Laboratory of Genetic Biochemistry, Indian Institute of Science, Bangalore, India

Keywords

Berenil plasmid DNA DNA binding

Abstract

Berenil, a well-established trypanocidal agent, has long been recognized for its selective activity against extranuclear DNA and its characteristic minor groove binding to the DNA helix. This study aimed to precisely identify the preferred target sites of Berenil within the widely utilized bacterial plasmid pBR322, extending prior observations that demonstrated its inhibitory effects on DNA replication in plasmids rich in poly(dA)poly(dT) sequences. By employing a comprehensive array of molecular biology techniques, including meticulous plasmid DNA isolation, precise restriction enzyme digestion, and detailed analysis of DNA conformational changes, we sought to delineate the specific regions of pBR322 that exhibit preferential and strong binding affinity for Berenil. Understanding these precise binding preferences is paramount for deciphering the drug's intricate mechanism of action and holds significant implications for the rational design of new, sequence-specific therapeutic agents.

Downloads

Download data is not yet available.

References

1

H Jensch (1955) 4,4 0-diamidinodiazoaminobenzene, a new remedy against Trypanosoma and Babesia infections. Arzneitmittel-Forsch. 5: 634-635.

2

BA Newton (1955) Berenil, a trypanocide with selective activity against extra nuclear DNA. Antibiotics. 3: 34-47.

3

BA Newton (1972) Comparative biochemistry of parasites. Academic Press, New York. 127-133.

4

J Williamson, RF Macadam (1975) Drug-induced lesions in trypanosome fine structure: a guide to modes of trypanocidal action. Biochemical Pharmacol. 24(1): 147-151.

5

W Wierenga (1991) Sequence selectivity DNA-interactive antitumor agents. Drugs of the Future. 16: 741-750.

6

AW Braithwaite, BC Baguley (1980) Existence of an extended series of antitumor compounds which bind to deoxyribonucleic acid by nonintercalating means. Biochemistry. 19(6): 1101-1106.

7

M. Waring (1970) Variation of the supercoils in closed circular DNA by binding of antibiotics and drugs: evidence for molecular models involving intercalation. J.Mol Biol. 54(2): 247-279.

8

TT Eckdahl, AD Brown, SN Hart, KJ Malloy, Yiu G, et al., (2008) Microarray analysis of the in vivo sequence preference of a minor groove binding drug. BCM Genomics. 9: 32-44.

9

AN Lane, TC Jenkins, T Brown, S Neidle (1991) Interaction of berenil with the EcoR1 dodecamer d(CGCGAATTCGCG)2 in solution studied by NMR. Biochemistry. 30(5): 1372-1385.

10

Ch Brack, E Delain, G Riou (1972) Replicating, covalently closed, circular DNA from kinetoplasts of Trypanosoma cruzi. Proc Nat Acad Sci USA. 69: 1642-1646.

11

PT Englund, SL Hadjuck, JC Marini (1982) The molecular Biology of trypanosomes. Ann Rev Biochem. 51: 695-796.

12

JC Marini, KG Miller, PT Englund (1980) Decatenation of kinetoplast DNA of Leishmania tarantolea. J. Biol Chem. 255:4976-4979.

13

G Riou, M Gabillot, S Douc-Rasy, A Kayser (1982) Partial purification and characterization of nuclear DNA-topoisomerases from trypanosomes (author's transl CR Seances Acad Sci Paris. 294(11): 439-42.

14

AY Chen, C.Yu, B Gatto, LF Liu (1993) DNA minor groove-binding ligands: A different class of mammalian DNA topoisomerase I inhibitors. Proc Nat Acad Sci USA. 90(17): 8131-8135.

15

RE Mcknight, AB Gleason, JA Keyes, S Sahabi (2007) Binding mode and affinity studies of DNA-binding agents using topoisomerase I unwinding assay. Bioorg Med Chem Lett. 17(4): 1013-1017.

16

TA Shapiro, PT Englund (1990) Selective cleavage of kinetoplast DNA minicircles promoted byantitrypanosomal drugs. Proc Nat Acad Sci USA. 87(3): 950-954.

17

L Coates, EV Ikpeazu, Y Chen, MS Valenzuela (2002) Inhibition of DNA replication by berenil in plasmids containing poly(dA)poly(dT) sequences. Plasmid. 47(2): 120-129.

18

TE Snowden, YM Pan, MS Valenzuela (2002) Inhibition of DNA replication by berenil in plasmids containing poly(dA)poly(dT) sequences. 2-D gel analysis of replicative intermediates. Cell. Mol Biol. OL279-OL288.

19

TE Snowden, Y Chen, YM Pan, MS Valenzuela (2002) Bacterial plasmids containing poly(dA)poly(dT) sequences. Stability and sensitivity to berenil. In Recent Research Developments in Plasmid Biology. Transworld Research Network. 1: 1-14.

20

MS Valenzuela, MdP Aguinaga, RB Inman (1981) Isolation of DNA fragments containing replicating growing forks from both E.coli and B. subtilis. Mol Gen Genet. 181: 241-247.