DNA complexes containing joined triplex and duplex motifs: Melting behavior of intramolecular and bimolecular complexes with similar sequences

Hui Ting Lee, Irine Khutsishvili, Luis A Marky

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

Our laboratory is interested in predicting the thermal stability and melting behavior of nucleic acids from knowledge of their sequence. One focus is to understand how sequence, duplex and triplex stabilities, and solution conditions affect the melting behavior of complex DNA structures, such as intramolecular DNA complexes containing triplex and duplex motifs. Nucleic acid oligonucleotides (ODNs), as drugs, present an exquisite selectivity and affinity that can be used in antigene and antisense strategies for the control of gene expression. In this work, we try to answer the following question: How does the molecularity of a DNA complex affect its overall stability and melting behavior? We used a combination of temperature-dependent UV spectroscopy and calorimetric (DSC) techniques to investigate the melting behavior of DNA complexes with a similar helical stem sequence, TC+TC+TC+T/AGAGAGACGCG/CGCGTCTCTCT, but formed with different strand molecularity. We determined standard thermodynamic profiles, and the differential binding of protons and counterions accompanying their unfolding. The formation of a DNA complex is accompanied by a favorable free energy term resulting from the typical compensation of favorable enthalpy-unfavorable entropy contributions. As expected, acidic pH stabilized each complex by allowing protonation of the cytosines in the third strand; however, the percentage of protonation increases as the molecularity decreases. The results help in the design of oligonucleotide sequences as targeting reagents that could effectively react with DNA or RNA sequences involved in human diseases, thereby increasing the feasibility of using the antigene and antisense strategies, respectively, for therapeutic purposes.

Original languageEnglish (US)
Pages (from-to)541-548
Number of pages8
JournalJournal of Physical Chemistry B
Volume114
Issue number1
DOIs
StatePublished - Jan 14 2010

Fingerprint

Melting
DNA
deoxyribonucleic acid
melting
oligonucleotides
Oligonucleotides
Protonation
Nucleic acids
nucleic acids
strands
Nucleic Acids
gene expression
Cytosine
Ultraviolet spectroscopy
RNA
stems
Gene expression
Free energy
reagents
affinity

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

Cite this

DNA complexes containing joined triplex and duplex motifs : Melting behavior of intramolecular and bimolecular complexes with similar sequences. / Lee, Hui Ting; Khutsishvili, Irine; Marky, Luis A.

In: Journal of Physical Chemistry B, Vol. 114, No. 1, 14.01.2010, p. 541-548.

Research output: Contribution to journalArticle

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