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Literature DB >> 8628662

An oligodeoxyribonucleotide N3'--> P5' phosphoramidate duplex forms an A-type helix in solution.

D Ding¹, S M Grayaznov, D H Lloyd, S Chandrasekaran, S Yao, L Ratmeyer, Y Pan, W D Wilson.

Abstract

The solution conformations of the dinucleotide d(TT) and the modified duplex d(CGCGAATTCGCG)2 with N3'--> P5' phosphoramidate internucleoside linkages have been studied using circular dichroism (CD) and NMR spectroscopy. The CD spectra indicate that the duplex conformation is similar to that of isosequential phosphodiester RNA, a A-type helix, and is different from that of DNA, a B-type helix, NMR studies of model dimers d(TpT) and N3'--> P5' phosphoramidate d(TnpT) show that the sugar ring conformation changes from predominantly C2'-endo to C3'-endo when the 3'-phosphoester is replaced by a phosphoramidate group. Two-dimensional NMR (NOESY, DQF-COSY and TOCSY spectra) studies of the duplex provide additional details about the A-type duplex conformation of the oligonucleotide phosphoramidate and confirm that all furanose rings of 3'-aminonucleotides adopt predominantly N-type sugar puckering.

Entities: Chemical

Mesh：

Substances：

Year: 1996 PMID： 8628662 PMCID： PMC145634 DOI： 10.1093/nar/24.2.354

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

12 in total

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Journal: Nucleic Acids Res Date: 1985-07-11 Impact factor: 16.971

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Journal: Eur J Biochem Date: 1983-07-01

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Journal: Science Date: 1982-04-30 Impact factor: 47.728

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Authors: S H Chou; P Flynn; B Reid
Journal: Biochemistry Date: 1989-03-21 Impact factor: 3.162

6. Duplex stabilities of phosphorothioate, methylphosphonate, and RNA analogs of two DNA 14-mers.

Authors: L Kibler-Herzog; G Zon; B Uznanski; G Whittier; W D Wilson
Journal: Nucleic Acids Res Date: 1991-06-11 Impact factor: 16.971

7. Systemic administration of a phosphorothioate oligonucleotide with a sequence complementary to p53 for acute myelogenous leukemia and myelodysplastic syndrome: initial results of a phase I trial.

Authors: E Bayever; P L Iversen; M R Bishop; J G Sharp; H K Tewary; M A Arneson; S J Pirruccello; R W Ruddon; A Kessinger; G Zon
Journal: Antisense Res Dev Date: 1993

8. Thermodynamics of DNA duplexes with adjacent G.A mismatches.

Authors: Y Li; G Zon; W D Wilson
Journal: Biochemistry Date: 1991-07-30 Impact factor: 3.162

9. Conformational analysis of the deoxyribofuranose ring in DNA by means of sums of proton-proton coupling constants: a graphical method.

Authors: L J Rinkel; C Altona
Journal: J Biomol Struct Dyn Date: 1987-02

9. The ups and downs of nucleic acid duplex stability: structure-stability studies on chemically-modified DNA:RNA duplexes.

Authors: S M Freier; K H Altmann
Journal: Nucleic Acids Res Date: 1997-11-15 Impact factor: 16.971

10. RNA mimetics: oligoribonucleotide N3'-->P5' phosphoramidates.

Authors: S M Gryaznov; H Winter
Journal: Nucleic Acids Res Date: 1998-09-15 Impact factor: 16.971

An oligodeoxyribonucleotide N3'--> P5' phosphoramidate duplex forms an A-type helix in solution.

1. Evidence for Z-form RNA by vacuum UV circular dichroism.

Review 2. The interaction of intercalators and groove-binding agents with DNA triple-helical structures: the influence of ligand structure, DNA backbone modifications and sequence.

3. DNA fragment conformations. 1H-NMR comparative studies of helix-coil transition and conformation of d(C-A-C-G-T-G) and d(G-T-G-C-A-C). Influence of helix formation on proton chemical shifts.

4. The anatomy of A-, B-, and Z-DNA.

5. Solid-phase synthesis and high-resolution NMR studies of two synthetic double-helical RNA dodecamers: r(CGCGAAUUCGCG) and r(CGCGUAUACGCG).

6. Duplex stabilities of phosphorothioate, methylphosphonate, and RNA analogs of two DNA 14-mers.

7. Systemic administration of a phosphorothioate oligonucleotide with a sequence complementary to p53 for acute myelogenous leukemia and myelodysplastic syndrome: initial results of a phase I trial.

8. Thermodynamics of DNA duplexes with adjacent G.A mismatches.

9. Conformational analysis of the deoxyribofuranose ring in DNA by means of sums of proton-proton coupling constants: a graphical method.

10. Interaction of berenil with the EcoRI dodecamer d(CGCGAATTCGCG)2 in solution studied by NMR.

1. Solution structure of a DNA duplex with a chiral alkyl phosphonate moiety.

2. NMR structure of an alpha-L-LNA:RNA hybrid: structural implications for RNase H recognition.

3. DNA polymerase activity on synthetic N3'→P5' phosphoramidate DNA templates.

4. Oligo-2'-fluoro-2'-deoxynucleotide N3'-->P5' phosphoramidates: synthesis and properties.

5. RNase H-independent antisense activity of oligonucleotide N3 '--> P5 ' phosphoramidates.

6. alpha-Oligodeoxyribonucleotide N3'-->P5' phosphoramidates: synthesis and duplex formation.

7. Re-examination of the intrinsic, dynamic and hydration properties of phosphoramidate DNA.

8. Oligonucleotide N3'-->P5' phosphoramidates as antisense agents.

9. The ups and downs of nucleic acid duplex stability: structure-stability studies on chemically-modified DNA:RNA duplexes.

10. RNA mimetics: oligoribonucleotide N3'-->P5' phosphoramidates.