2D-NMR Studies of the Unnatural Duplex Alpha-d(TCTAAAC)-beta-d(AGATTTG)

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1987 Sep 25

PMID 3658702

Citations 9

Authors

G Lancelot

J L Guesnet

V Roig

N T Thuong

Affiliations

Soon will be listed here.

Abstract

The unnatural oligonucleotide alpha-d(TCTAAAC) was synthesized and was found more resistant towards endonucleases than its beta-analog. 2D-NMR experiments allowed the assignment of all non-exchangeable aromatic and sugar protons except for the overlapping 5' -5" resonances, as well as the exchangeable imino protons of the parallel hybrid duplex alpha-d (TCTAAAC)-beta-d(AGATTTG). NMR studies show that the strength of the association between the alpha-strand and the beta parallel strand is equivalent to that between their anti-parallel complementary beta-analogs beta-d(CAAATCT) and beta-d(AGATTTG). NOE data provide evidence that both duplexes form stable right-helical duplexes with an anti-conformation on the glycosyl linkages and a Watson-Crick pairing. NOESY and COSY spectra allowed us to determine that alpha and beta deoxyriboses adopt a 3' -exo conformation.

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References

Stawinski J, Hozumi T, Narang S, Bahl C, Wu R . Arylsulfonyltetrazoles, new coupling reagents and further improvements in the triester method for the synthesis of deoxyribooligonucleotides. Nucleic Acids Res. 1977; 4(2):353-71. PMC: 342437. DOI: 10.1093/nar/4.2.353. View

Kan L, Borer P, Tso P . Conformation and interaction of short nucleic acid double-stranded helices. II. Proton magnetic resonance studies on the hydrogen-bonded NH-N protons of ribosyl ApApGpCpUpU helix. Biochemistry. 1975; 14(22):4864-9. DOI: 10.1021/bi00693a013. View

Thuong N, Chassignol M, Lancelot G, Mayer R, Hartmann B, Leng M . Synthesis and structural studies of a self-complementary decadeoxynucleotide d(AATTGCAATT). I.-Synthesis and chemical characterization of the decanucleotide. Biochimie. 1981; 63(10):775-84. DOI: 10.1016/s0300-9084(81)80037-5. View

Tomizawa J, Itoh T . Plasmid ColE1 incompatibility determined by interaction of RNA I with primer transcript. Proc Natl Acad Sci U S A. 1981; 78(10):6096-100. PMC: 348984. DOI: 10.1073/pnas.78.10.6096. View

Helene C, Lancelot G . Interactions between functional groups in protein-nucleic acid associations. Prog Biophys Mol Biol. 1982; 39(1):1-68. DOI: 10.1016/0079-6107(83)90013-5. View

Marion D, Wuthrich K . Application of phase sensitive two-dimensional correlated spectroscopy (COSY) for measurements of 1H-1H spin-spin coupling constants in proteins. Biochem Biophys Res Commun. 1983; 113(3):967-74. DOI: 10.1016/0006-291x(83)91093-8. View

Hare D, Wemmer D, Chou S, Drobny G, Reid B . Assignment of the non-exchangeable proton resonances of d(C-G-C-G-A-A-T-T-C-G-C-G) using two-dimensional nuclear magnetic resonance methods. J Mol Biol. 1983; 171(3):319-36. DOI: 10.1016/0022-2836(83)90096-7. View

Feigon J, Leupin W, Denny W, Kearns D . Two-dimensional proton nuclear magnetic resonance investigation of the synthetic deoxyribonucleic acid decamer d(ATATCGATAT)2. Biochemistry. 1983; 22(25):5943-51. DOI: 10.1021/bi00294a038. View

Feigon J, Wang A, van der Marel G, VAN Boom J, Rich A . A one- and two-dimensional NMR study of the B to Z transition of (m5dC-dG)3 in methanolic solution. Nucleic Acids Res. 1984; 12(2):1243-63. PMC: 318570. DOI: 10.1093/nar/12.2.1243. View

10.

Weiss M, Patel D, Sauer R, Karplus M . Two-dimensional 1H NMR study of the lambda operator site OL1: a sequential assignment strategy and its application. Proc Natl Acad Sci U S A. 1984; 81(1):130-4. PMC: 344624. DOI: 10.1073/pnas.81.1.130. View

11.

Broido M, Zon G, James T . Complete assignment of the non-exchangeable proton nmr resonances of [d-(GGAATTCC)]2 using two-dimensional nuclear overhauser effect spectra. Biochem Biophys Res Commun. 1984; 119(2):663-70. DOI: 10.1016/s0006-291x(84)80301-0. View

12.

Scheek R, Boelens R, Russo N, VAN Boom J, Kaptein R . Sequential resonance assignments in 1H NMR spectra of oligonucleotides by two-dimensional NMR spectroscopy. Biochemistry. 1984; 23(7):1371-6. DOI: 10.1021/bi00302a006. View

13.

Asseline U, Delarue M, Lancelot G, Toulme F, Thuong N, Helene 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; 81(11):3297-301. PMC: 345494. DOI: 10.1073/pnas.81.11.3297. View

14.

Wemmer D, Chou S, Hare D, Reid B . Sequence-specific recognition of DNA: assignment of nonexchangeable proton resonances in the consensus Pribnow promoter DNA sequence by two-dimensional NMR. Biochemistry. 1984; 23(10):2262-8. DOI: 10.1021/bi00305a027. View

15.

Guittet E, Piveteau D, Lallemand J, IGOLEN J . Nuclear magnetic resonance study of d-TGGCCA in solution. Nucleic Acids Res. 1984; 12(14):5927-41. PMC: 320041. DOI: 10.1093/nar/12.14.5927. View

16.

Yamaguchi T, Saneyoshi M . Synthetic nucleosides and nucleotides. XXI. On the synthesis and biological evaluations of 2'-deoxy-alpha-D-ribofuranosyl nucleosides and nucleotides. Chem Pharm Bull (Tokyo). 1984; 32(4):1441-50. DOI: 10.1248/cpb.32.1441. View

17.

Marion D, Lancelot G . Sequential assignment of the 1H and 31P resonances of the double stranded deoxynucleotide d (ATGCAT)2 by 2D-NMR correlation spectroscopy. Biochem Biophys Res Commun. 1984; 124(3):774-83. DOI: 10.1016/0006-291x(84)91025-8. View

18.

Wemmer D, Chou S, Hare D, Reid B . Duplex-hairpin transitions in DNA: NMR studies on CGCGTATACGCG. Nucleic Acids Res. 1985; 13(10):3755-72. PMC: 341271. DOI: 10.1093/nar/13.10.3755. View

19.

Helene C, Saison T, Takasugi M, Toulme J, Asseline U, Lancelot G . Oligodeoxynucleotides covalently linked to intercalating agents: a new class of gene regulatory substances. Biochimie. 1985; 67(7-8):777-83. DOI: 10.1016/s0300-9084(85)80167-x. View

20.

Morvan F, Rayner B, Imbach J, Chang D, Lown J . alpha-DNA. I. Synthesis, characterization by high field 1H-NMR, and base-pairing properties of the unnatural hexadeoxyribonucleotide alpha-[d(CpCpTpTpCpC)] with its complement beta-[d(GpGpApApGpG)]. Nucleic Acids Res. 1986; 14(12):5019-35. PMC: 311508. DOI: 10.1093/nar/14.12.5019. View