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This article has been retracted upon the authors’ request, as they have incorporated the studies of two oncogene promoter regions which form G-quadruplex complex (i.e., Bcl2 and KRAS), but the DNA considered for the studies was not from these regions. The DNA samples got mixed up, and they are from other regions of oncogene promoter. The complete ESI-MS (mass data) and the ITC (microcalorimetry data) were wrong. Since the mistake occurred at the fundamental level (i.e., at the DNA itself), the whole experiment gave wrong data. Additionally, the article was submitted for publication by the author Narayana Nagesh without the knowledge and approval of the other author Arumugam Ganesh Kumar.

ISRN Biophysics
Volume 2012 (2012), Article ID 786596, 12 pages
Research Article

Interaction of TMPyP4, TMPyP3, and TMPyP2 with Intramolecular G-Quadruplex Formed by Promoter Region of Bcl2 and KRAS NHPPE

1Department of Medicinal Chemistry, Centre for Cellular and Molecular Biology, Hyderabad 500007, India
2Marine Biotechnology, National Institute of Ocean Technology, Chennai 600100, India

Received 5 September 2011; Accepted 2 October 2011

Academic Editors: M. P. Evstigneev and M. P. Ponomarenko

Copyright © 2012 Narayana Nagesh and Arumugam Ganesh Kumar. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

TInteraction of various ligands with quadruplex DNA and their capability in imparting stability to quadruplex structure has gained interest in the recent years. Ligands capable of interacting with quadruplex DNA and stabilize were reported to function as cancer drugs. There are many experimental methods to understand the mode and nature of quadruplex DNA-ligand interaction, like spectroscopy, microcalorimetry, mass spectroscopy etc., But among them, spectroscopy and microcalorimetric experiments require relatively higher concentration of ligand/DNA for studying the interaction, which is far from the in vivo situation. In order to study the interaction at low ligand-DNA concentrations (relatively close to the in vivo condition), ESI-MS studies emerge as one of the promising technology. In the present study interaction of TMPyP4, with Bcl2 and KRAS NHPPE promoter region quadruplex DNA complex, was considered to understand the stoichiometry, number of cations stabilizing the complex and interaction efficiency with different quadruplex forms.

Results from the mass spectral studies, indicate that TMPyP4 has better interacting capability with Bcl2 quadruplex compared to quadruplex formed by KRAS NHPPE element. Stoichiometry of TMPyP4 binding to Bcl2 quadruplex was 1 : 1 (m/z 1396), 1 : 2 (m/z 1533), 1 : 3 (m/z 1668) and 1 : 4 (m/z 1805) (Figure S1). Whereas with KRAS NHPPE element, the stoichiometry was 1 : 1 ((m/z 928) and 1 : 2 (m/z 1136) (Figure S2). Higher stoichiometry, like 1 : 3 and 1 : 4, was not observed with KRAS NHPPE quadruplex. ESI-MS results indicate that TMPyP4 interact with 39Bcl2 quadruplex by both end loop binding as well as intercalation. Whereas with KRAS NHPPE quadruplex, will bind to the end loop region more than intercalation. The difference in the nature of ligand interaction with each of the quadruplex complex formed by the promoter region of two oncogenes, may be due to the variation in folding pattern and sequence of quadruplex forming DNA.

  1. Supplementary Material