Table of Contents
Retracted

This article has been retracted upon the authors’ request, as they have incorporated the studies of two oncogene promoter regions which form G-quadruplex complex (i.e., Bcl2 and KRAS), but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, Article ID 786596, 12 pages
http://dx.doi.org/10.5402/2012/786596
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.

Abstract

Oncogenes are rich in guanine and capable of forming quadruplex structure. Promoter regions oncogenes such as Bcl2 and KRAS NHPPE are rich in guanine content and they can form quadruplex structures. Alterations in the mode and nature of molecular binding to DNA, certainly has effect on the posttranscriptional activities. Recent experiments indicate that structure of quadruplex complex and ligand has predominant role on ligand-quadruplex DNA interaction. In order to understand the nature of each ligand interaction with quadruplex DNA, Bcl2, KRAS NHPPE quadruplex DNA interaction with three porphyrin was studied using spectroscopy, microcalorimetry and mass spectrometry. Our studies, indicate that mode of ligand interaction varies with structure, environment and concentration of ligand. Fluorescence quenching experiments show that TMPyP4 interaction is ligand concentration dependent. Job plots and ITC experiments demonstrate that four molecules of TMPyP4 and two molecules of TMPyP3, TMPyP2 interact with each quadruplex complex. Through ITC titrations, ligand binding constant are higher for TMPyP4 (≈107 M−1) compared to TMPyP3, TMPyP2 (≈105 M−1). ESI-MS experiments confirm the stoichiometry of TMPyP4 : 39Bcl2 is 4 : 1 at saturation and it is 2 : 1 in case of KRAS NHPPE quadruplex.