Next Article in Journal / Special Issue
Synthesis, Molecular Structure and Reactivity of 5-Methylidene-1,2,3,5-tetrahydroimidazo[2,1-b]quinazolines
Previous Article in Journal / Special Issue
New Synthetic Routes to Furocoumarins and Their Analogs: A Review
Article Menu

Export Article

Open AccessArticle
Molecules 2004, 9(3), 67-85;

Probing the Structure of DNA Aptamers with a Classic Heterocycle.

Department of Chemistry and Biochemistry, Mississippi College, 200 South Capitol St., Clinton, MS 39058. USA
Author to whom correspondence should be addressed.
Received: 5 February 2004 / Revised: 9 February 2004 / Accepted: 15 February 2004 / Published: 28 February 2004
(This article belongs to the Special Issue Biologically Relevant Heterocyclic Compounds)
Full-Text   |   PDF [309 KB, uploaded 18 June 2014]   |  


DNA aptamers are synthetic, single-stranded DNA oligonucleotides selectedby SELEX methods for their binding with specific ligands. Here we present ethidiumbinding results for three related DNA aptamers (PDB code: 1OLD, 1DB6, and 2ARG)that bind L-argininamide (L-Arm). The ligand bound form of each aptamer's structurehas been reported and each are found to be composed primarily of two domainsconsisting of a stem helical region and a loop domain that forms a binding pocket for thecognate ligand. Previous thermodynamic experiments demonstrated that the DNAaptamer 1OLD undergoes a large conformational ordering upon binding to L-Arm. Herewe extend those linkage binding studies by examining the binding of the heterocyclicintercalator ethidium to each of the three aptamers by fluorescence and absorptionspectrophotometric titrations. Our results reveal that ethidium binds to each aptamer with∆Go's in the range of -8.7 to -9.4 kcal/mol. The stoichiometry of binding is 2:1 for eachaptamer and is quantitatively diminished in the presence of L-Arm as is the overallfluorescence intensity of ethidium. Together, these results demonstrate that a portion ofthe bound ethidium is excluded from the aptamer in the presence of a saturating amountof L-Arm. These results demonstrate the utility of ethidium and related compounds forthe probing of non-conventional DNA structures and reveal an interesting fundamentalthermodynamic linkage in DNA aptamers. Results are discussed in the context of thethermodynamic stability and structure of each of the aptamers examined. View Full-Text
Keywords: Ethidium; intercalator; DNA; aptamer; thermodynamics; linkage; fluorescence; free energy; Job plot Ethidium; intercalator; DNA; aptamer; thermodynamics; linkage; fluorescence; free energy; Job plot

Figure 1

This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

Share & Cite This Article

MDPI and ACS Style

Wood IV, A.E.; Bishop, G.R. Probing the Structure of DNA Aptamers with a Classic Heterocycle.. Molecules 2004, 9, 67-85.

Show more citation formats Show less citations formats

Related Articles

Article Metrics

Article Access Statistics



[Return to top]
Molecules EISSN 1420-3049 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top