Search tips
Search criteria 


Logo of narLink to Publisher's site
Nucleic Acids Res. 1991 May 11; 19(9): 2463–2470.
PMCID: PMC329458

Hybridization and dissociation rates of phosphodiester or modified oligodeoxynucleotides with RNA at near-physiological conditions.


We have used RNase H to study both the rates of oligonucleotide hybridization and dissociation at near-physiological conditions. We have studied the Effects of oligonucleotide length, mismatch, and chemical modifications on oligonucleotide association and dissociation with RNA. Dissociation results were compared with standard thermal melting curves to compare relative stabilities evaluated by the two techniques. Although generally the two techniques correlate for the compounds evaluated, we found several instances where the thermal melting curves failed to reflect the relative stability of different oligonucleotides at 37 degrees C using near-physiological conditions. This study suggests that direct measurement of hybridization and dissociation of an oligomer with RNA more accurately assesses the complicated kinetic scheme at 37 degrees C using near-physiological conditions than thermal melting curves would predict.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1.5M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Click on the image to see a larger version.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • van der Krol AR, Mol JN, Stuitje AR. Modulation of eukaryotic gene expression by complementary RNA or DNA sequences. Biotechniques. 1988 Nov-Dec;6(10):958–976. [PubMed]
  • Zon G. Oligonucleotide analogues as potential chemotherapeutic agents. Pharm Res. 1988 Sep;5(9):539–549. [PubMed]
  • Weintraub HM. Antisense RNA and DNA. Sci Am. 1990 Jan;262(1):40–46. [PubMed]
  • Breslauer KJ, Frank R, Blöcker H, Marky LA. Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci U S A. 1986 Jun;83(11):3746–3750. [PubMed]
  • Puglisi JD, Tinoco I., Jr Absorbance melting curves of RNA. Methods Enzymol. 1989;180:304–325. [PubMed]
  • Asseline U, Delarue M, Lancelot G, Toulmé F, Thuong NT, Montenay-Garestier T, Hélène C. Nucleic acid-binding molecules with high affinity and base sequence specificity: intercalating agents covalently linked to oligodeoxynucleotides. Proc Natl Acad Sci U S A. 1984 Jun;81(11):3297–3301. [PubMed]
  • Mori K, Subasinghe C, Cohen JS. Oligodeoxynucleotide analogs with 5'-linked anthraquinone. FEBS Lett. 1989 Jun 5;249(2):213–218. [PubMed]
  • Bazile D, Gautier C, Rayner B, Imbach JL, Paoletti C, Paoletti J. alpha-DNA X: alpha and beta tetrathymidilates covalently linked to oxazolopyridocarbazolium (OPC): comparative stabilization of oligo beta-[dT]:oligo beta-[dA] and oligo alpha-[dT]:oligo beta-[dA] duplexes by the intercalating agent. Nucleic Acids Res. 1989 Oct 11;17(19):7749–7759. [PMC free article] [PubMed]
  • Lemaitre M, Bayard B, Lebleu B. Specific antiviral activity of a poly(L-lysine)-conjugated oligodeoxyribonucleotide sequence complementary to vesicular stomatitis virus N protein mRNA initiation site. Proc Natl Acad Sci U S A. 1987 Feb;84(3):648–652. [PubMed]
  • Shea RG, Marsters JC, Bischofberger N. Synthesis, hybridization properties and antiviral activity of lipid-oligodeoxynucleotide conjugates. Nucleic Acids Res. 1990 Jul 11;18(13):3777–3783. [PMC free article] [PubMed]
  • Boutorin AS, Gus'kova LV, Ivanova EM, Kobetz ND, Zarytova VF, Ryte AS, Yurchenko LV, Vlassov VV. Synthesis of alkylating oligonucleotide derivatives containing cholesterol or phenazinium residues at their 3'-terminus and their interaction with DNA within mammalian cells. FEBS Lett. 1989 Aug 28;254(1-2):129–132. [PubMed]
  • Letsinger RL, Zhang GR, Sun DK, Ikeuchi T, Sarin PS. Cholesteryl-conjugated oligonucleotides: synthesis, properties, and activity as inhibitors of replication of human immunodeficiency virus in cell culture. Proc Natl Acad Sci U S A. 1989 Sep;86(17):6553–6556. [PubMed]
  • Ts'o PO, Miller PS, Aurelian L, Murakami A, Agris C, Blake KR, Lin SB, Lee BL, Smith CC. An approach to chemotherapy based on base sequence information and nucleic acid chemistry. Matagen (masking tape for gene expression). Ann N Y Acad Sci. 1987;507:220–241. [PubMed]
  • Agrawal S, Goodchild J, Civeira MP, Thornton AH, Sarin PS, Zamecnik PC. Oligodeoxynucleoside phosphoramidates and phosphorothioates as inhibitors of human immunodeficiency virus. Proc Natl Acad Sci U S A. 1988 Oct;85(19):7079–7083. [PubMed]
  • Milligan JF, Groebe DR, Witherell GW, Uhlenbeck OC. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 1987 Nov 11;15(21):8783–8798. [PMC free article] [PubMed]
  • Gubbins EJ, Maurer RA, Lagrimini M, Erwin CR, Donelson JE. Structure of the rat prolactin gene. J Biol Chem. 1980 Sep 25;255(18):8655–8662. [PubMed]
  • Melton DA, Krieg PA, Rebagliati MR, Maniatis T, Zinn K, Green MR. Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucleic Acids Res. 1984 Sep 25;12(18):7035–7056. [PMC free article] [PubMed]
  • Wagner RW, Nishikura K. Cell cycle expression of RNA duplex unwindase activity in mammalian cells. Mol Cell Biol. 1988 Feb;8(2):770–777. [PMC free article] [PubMed]
  • Wallace RB, Johnson MJ, Hirose T, Miyake T, Kawashima EH, Itakura K. The use of synthetic oligonucleotides as hybridization probes. II. Hybridization of oligonucleotides of mixed sequence to rabbit beta-globin DNA. Nucleic Acids Res. 1981 Feb 25;9(4):879–894. [PMC free article] [PubMed]
  • Nelson JW, Tinoco I., Jr Comparison of the kinetics of ribooligonucleotide, deoxyribooligonucleotide, and hybrid oligonucleotide double-strand formation by temperature-jump kinetics. Biochemistry. 1982 Oct 12;21(21):5289–5295. [PubMed]
  • Krämer A, Keller W, Appel B, Lührmann R. The 5' terminus of the RNA moiety of U1 small nuclear ribonucleoprotein particles is required for the splicing of messenger RNA precursors. Cell. 1984 Aug;38(1):299–307. [PubMed]
  • Walder RY, Walder JA. Role of RNase H in hybrid-arrested translation by antisense oligonucleotides. Proc Natl Acad Sci U S A. 1988 Jul;85(14):5011–5015. [PubMed]
  • Wyatt JR, Walker GT. Deoxynucleotide-containing oligoribonucleotide duplexes: stability and susceptibility to RNase V1 and RNase H. Nucleic Acids Res. 1989 Oct 11;17(19):7833–7842. [PMC free article] [PubMed]
  • Furdon PJ, Dominski Z, Kole R. RNase H cleavage of RNA hybridized to oligonucleotides containing methylphosphonate, phosphorothioate and phosphodiester bonds. Nucleic Acids Res. 1989 Nov 25;17(22):9193–9204. [PMC free article] [PubMed]
  • Agrawal S, Mayrand SH, Zamecnik PC, Pederson T. Site-specific excision from RNA by RNase H and mixed-phosphate-backbone oligodeoxynucleotides. Proc Natl Acad Sci U S A. 1990 Feb;87(4):1401–1405. [PubMed]
  • Martin FH, Castro MM, Aboul-ela F, Tinoco I., Jr Base pairing involving deoxyinosine: implications for probe design. Nucleic Acids Res. 1985 Dec 20;13(24):8927–8938. [PMC free article] [PubMed]
  • Kawase Y, Iwai S, Inoue H, Miura K, Ohtsuka E. Studies on nucleic acid interactions. I. Stabilities of mini-duplexes (dG2A4XA4G2-dC2T4YT4C2) and self-complementary d(GGGAAXYTTCCC) containing deoxyinosine and other mismatched bases. Nucleic Acids Res. 1986 Oct 10;14(19):7727–7736. [PMC free article] [PubMed]
  • Marcus-Sekura CJ, Woerner AM, Shinozuka K, Zon G, Quinnan GV., Jr Comparative inhibition of chloramphenicol acetyltransferase gene expression by antisense oligonucleotide analogues having alkyl phosphotriester, methylphosphonate and phosphorothioate linkages. Nucleic Acids Res. 1987 Jul 24;15(14):5749–5763. [PMC free article] [PubMed]
  • Asseline U, Toulme F, Thuong NT, Delarue M, Montenay-Garestier T, Hélène C. Oligodeoxynucleotides covalently linked to intercalating dyes as base sequence-specific ligands. Influence of dye attachment site. EMBO J. 1984 Apr;3(4):795–800. [PubMed]
  • Verspieren P, Cornelissen AW, Thuong NT, Hélène C, Toulmé JJ. An acridine-linked oligodeoxynucleotide targeted to the common 5' end of trypanosome mRNAs kills cultured parasites. Gene. 1987;61(3):307–315. [PubMed]
  • Craig ME, Crothers DM, Doty P. Relaxation kinetics of dimer formation by self complementary oligonucleotides. J Mol Biol. 1971 Dec 14;62(2):383–401. [PubMed]
  • Pörschke D, Eigen M. Co-operative non-enzymic base recognition. 3. Kinetics of the helix-coil transition of the oligoribouridylic--oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH. J Mol Biol. 1971 Dec 14;62(2):361–381. [PubMed]
  • Persson C, Wagner EG, Nordström K. Control of replication of plasmid R1: formation of an initial transient complex is rate-limiting for antisense RNA--target RNA pairing. EMBO J. 1990 Nov;9(11):3777–3785. [PubMed]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press