Full Paper

Thermodynamic Analysis of Nylon Nucleic Acids

  1. Yu Liu1,
  2. Risheng Wang1,
  3. Liang Ding Dr.1,2,
  4. Ruojie Sha Dr.1,
  5. Philip S. Lukeman Dr.1,3,
  6. James W. Canary Prof. Dr.1,
  7. Nadrian C. Seeman Prof. Dr.1

Article first published online: 9 JUN 2008

DOI: 10.1002/cbic.200800032

Issue

ChemBioChem

ChemBioChem

Volume 9, Issue 10, pages 1641–1648, July 2, 2008

Additional Information

How to Cite

Liu, Y., Wang, R., Ding, L., Sha, R., Lukeman, P. S., Canary, J. W. and Seeman, N. C. (2008), Thermodynamic Analysis of Nylon Nucleic Acids. ChemBioChem, 9: 1641–1648. doi: 10.1002/cbic.200800032

Author Information

  1. 1

    Department of Chemistry, New York University, 100 Washington Square E., New York, NY 10003 (USA), Fax: (+1) 212-260-7905

  2. 2

    Current address: Department of Biological and Environmental Engineering, Cornell University, 325 Riley-Robb Hall, Ithaca, NY 14853 (USA)

  3. 3

    Current address: Department of Chemistry, California State Polytechnic University, 3801 West Temple Avenue, Pomona CA 91768 (USA)

Publication History

  1. Issue published online: 23 JUN 2008
  2. Article first published online: 9 JUN 2008
  3. Manuscript Received: 18 JAN 2008

Funded by

  • NSF. Grant Numbers: CTS-0548774, CTS-0608889, CHE-0316589
  • NIGMS. Grant Numbers: GM-076202, GM-29554
  • NSF. Grant Number: DMI-0210844, EIA-0086015, CCF-0432009, CTS-0548774, CTS-0608889, CCF-0726378, and CCF-0523290
  • ARO. Grant Numbers: 48681-EL, MURI W911NF-07-1-0439
  • DOE. Grant Number: DE-FG02-06ER64281
  • W. M. Keck Foundation
  • Research Facilities Improvement. Grant Number: C06 RR-16572-01
  • National Center for Research Resources, National Institutes of Health
  • NSF. Grant Numbers: CHE-0234863, MRI-0116222

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Keywords:

  • circular dichroism;
  • conformational restriction;
  • DNA analogues;
  • template synthesis;
  • thermodynamics

Graphical Abstract

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Out of the closet: Oligonucleotides containing nylon nucleic acids were studied and were found to form stable complexes with complementary DNA and RNA. They showed significantly enhanced binding affinity when compared with nonamide-linked precursor strands (see figure). CD spectroscopy studies suggest that stabilization of the duplexes in this system originates from conformational restriction enforced by the amide links.

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.

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