Fundamental aspects of the nucleic acid i-motif structures

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Abstract

The latest research on fundamental aspects of i-motif structures is reviewed with special attention to their hypothetical role in vivo.

Abstract

The i-motif structure is formed in cytosine-rich sequences, its building block being the cytosine·cytosine + base pair. This structure is particularly stable at pH values below physiological (∼7.4) and, because of that, it has not attracted as much biological interest as other non-canonical structures such as the G-quadruplex. Nowadays, the proposal of potential roles in vivo, as well as nanotechnological applications, has produced an increasing interest in its study. In this context, the present work provides an overall picture of the i-motif structure. Those aspects related to formation and stability, such as chemical modifications or the interaction with ligands, are discussed. Special attention has been made to the i-motif structures that could have a hypothetical role in vivo, such as those present near the promoter region of several oncogenes.

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Most cited references 182

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Using circular dichroism collected as a function of temperature to determine the thermodynamics of protein unfolding and binding interactions.

Norma J Greenfield (2006)

Circular dichroism (CD) is an excellent spectroscopic technique for following the unfolding and folding of proteins as a function of temperature. One of its principal applications is to determine the effects of mutations and ligands on protein and polypeptide stability. If the change in CD as a function of temperature is reversible, analysis of the data may be used to determined the van't Hoff enthalpy and entropy of unfolding, the midpoint of the unfolding transition and the free energy of unfolding. Binding constants of protein-protein and protein-ligand interactions may also be estimated from the unfolding curves. Analysis of CD spectra obtained as a function of temperature is also useful to determine whether a protein has unfolding intermediates. Measurement of the spectra of five folded proteins and their unfolding curves at a single wavelength requires approximately 8 h.

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Human telomeric DNA: G-quadruplex, i-motif and Watson-Crick double helix.

Anh Tuân Phan, Jean-Louis Mergny (2002)

Human telomeric DNA composed of (TTAGGG/CCCTAA)n repeats may form a classical Watson-Crick double helix. Each individual strand is also prone to quadruplex formation: the G-rich strand may adopt a G-quadruplex conformation involving G-quartets whereas the C-rich strand may fold into an i-motif based on intercalated C*C+ base pairs. Using an equimolar mixture of the telomeric oligonucleotides d[AGGG(TTAGGG)3] and d[(CCCTAA)3CCCT], we defined which structures existed and which would be the predominant species under a variety of experimental conditions. Under near-physiological conditions of pH, temperature and salt concentration, telomeric DNA was predominantly in a double-helix form. However, at lower pH values or higher temperatures, the G-quadruplex and/or the i-motif efficiently competed with the duplex. We also present kinetic and thermodynamic data for duplex association and for G-quadruplex/i-motif unfolding.

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The importance of negative superhelicity in inducing the formation of G-quadruplex and i-motif structures in the c-Myc promoter: implications for drug targeting and control of gene expression.

Daekyu Sun, Laurence H Hurley (2009)

The importance of DNA supercoiling in transcriptional regulation has been known for many years, and more recently, transcription itself has been shown to be a source of this superhelicity. To mimic the effect of transcriptionally induced negative superhelicity, the G-quadruplex/i-motif-forming region in the c-Myc promoter was incorporated into a supercoiled plasmid. We show, using enzymatic and chemical footprinting, that negative superhelicity facilitates the formation of secondary DNA structures under physiological conditions. Significantly, these structures are not the same as those formed in single-stranded DNA templates. Together with the recently demonstrated role of transcriptionally induced superhelicity in maintaining a mechanosensor mechanism for controlling the firing rate of the c-Myc promoter, we provide a more complete picture of how c-Myc transcription is likely controlled. Last, these physiologically relevant G-quadruplex and i-motif structures, along with the mechanosensor mechanism for control of gene expression, are proposed as novel mechanisms for small molecule targeting of transcriptional control of c-Myc.

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Author and article information

Journal

Journal ID (publisher-id): RSCACL

Title: RSC Adv.

Abbreviated Title: RSC Adv.

Publisher: Royal Society of Chemistry (RSC)

ISSN (Electronic): 2046-2069

Publication date Created: 2014

Publication date (Electronic): 2014

Volume: 4

Issue: 51

Pages: 26956-26980

Affiliations

[1 ]Department of Analytical Chemistry

[2 ]University of Barcelona

[3 ]E-08028 Barcelona, Spain

[4 ]Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)

[5 ]CIBER-BBN Networking Centre on Bioengineering

[6 ]Biomaterials and Nanomedicine

[7 ]E-08034 Barcelona, Spain

[8 ]Institute of Physical Chemistry “Rocasolano”

[9 ]CSIC

[10 ]E-28006 Madrid, Spain

Article

DOI: 10.1039/C4RA02129K

SO-VID: 43efc10b-679e-41ae-8e90-7491c5f32923

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