Thermodynamic analysis of nylon nucleic acids

Yu Liu, Risheng Wang, Liang Ding, Ruojie Sha, Philip S. Lukeman, James W. Canary, Nadrian C. Seeman

Research output: Contribution to journalArticlepeer-review

Abstract

The stability and structure of nylon nucleic acid duplexes with complementary DNA and RNA strands was examined. Thermal denaturing studies of a series of oligonucleotides that contained nylon nucleic acids (1-5 amide linkages) revealed that the amide linkage significantly enhanced the binding affinity of nylon nucleic acids towards both complementary DNA (up to 26°C) increase in the thermal transition temperature (Tm) for five linkages) and RNA (around 15°C increase in Tm for five linkages) compared with nonamide linked precursor strands. For both DNA and RNA complements, increasing derivatization decreased the melting temperatures of uncoupled molecules relative to unmodified strands; by contrast, increasing lengths of coupled copolymer raised Tm from less to slightly greater than Tm of unmodified strands. Thermodynamic data extracted from melting curves and CD spectra of nylon nucleic acid duplexes were consistent with loss of stability due to incorporation of pendent groups on the 2′-position of ribose and recovery of stability upon linkage of the side chains.

Original languageEnglish (US)
Pages (from-to)1641-1648
Number of pages8
JournalChemBioChem
Volume9
Issue number10
DOIs
StatePublished - Jul 2 2008

Keywords

  • Circular dichroism
  • Conformational restriction
  • DNA analogues
  • Template synthesis
  • Thermodynamics

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Medicine
  • Molecular Biology
  • Organic Chemistry

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