Literature DB >> 7355127

Loopstructures in synthetic oligodeoxynucleotides.

C A Haasnoot, J H den Hartog, J F de Rooij, J H van Boom, C Altona.   

Abstract

A comparative nuclear magnetic resonance study of the hydrogen-bonded imino protons in a series of synthetic DNA fragments is presented. The fragments ATCCTA(Tn)TAGGAT are in principle capable of forming either a self-complementary hairpin loop structure (monomer form) or an interior loop structure (dimeric form). It has been shown, that for n = 1 only the dimer structure is present in aqueous solution, whereas the exclusive existence of the hairpin loop structure is indicated for n = 3, 4 & 5. Surprisingly, for n = 2 two different structures appear to be present in solution. Concentration studies show that both monomers and dimers exist side by side in this case. Hairpins as well as interior loops form extra "melting sites" in addition to the wellknown fraying phenomenon at the terminus of the double helix.

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Year:  1980        PMID： 7355127      PMCID： PMC327250          DOI： 10.1093/nar/8.1.169

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


  10 in total

1.  On the atomic or "local" contributions to proton chemical shifts due to the anisotropy of the diamagnetic susceptibility of the nucleic acid base.

Authors:  C Giessner-Prettre; B Pullman
Journal:  Biochem Biophys Res Commun       Date:  1976-05-17       Impact factor: 3.575

2.  Ring current shielding effects in nucleic acid double helices.

Authors:  D B Arter; P G Schmidt
Journal:  Nucleic Acids Res       Date:  1976-06       Impact factor: 16.971

3.  Improved estimation of secondary structure in ribonucleic acids.

Authors:  I Tinoco; P N Borer; B Dengler; M D Levin; O C Uhlenbeck; D M Crothers; J Bralla
Journal:  Nat New Biol       Date:  1973-11-14

4.  Free energy of imperfect nucleic acid helices. 3. Small internal loops resulting from mismatches.

Authors:  J Gralla; D M Crothers
Journal:  J Mol Biol       Date:  1973-08-05       Impact factor: 5.469

5.  Estimation of secondary structure in ribonucleic acids.

Authors:  I Tinoco; O C Uhlenbeck; M D Levine
Journal:  Nature       Date:  1971-04-09       Impact factor: 49.962

6.  Conformational analysis of the sugar ring in nucleosides and nucleotides. Improved method for the interpretation of proton magnetic resonance coupling constants.

Authors:  C Altona; M Sundaralingam
Journal:  J Am Chem Soc       Date:  1973-04-04       Impact factor: 15.419

7.  Proton nuclear magnetic resonance investigations of fraying in double-stranded d-ApTpGpCpApT in H2O solution.

Authors:  D J Patel; C W Hilbers
Journal:  Biochemistry       Date:  1975-06-17       Impact factor: 3.162

8.  Conformational analysis of a DNA triplet in aqueous solution. Thymidylyl-(3'-5')-thymidylyl-(3'-5')-2'-deoxyadenosine, d(T-T-A), studied by 1H nuclear magnetic resonance at 360 MHz.

Authors:  C Altona; J H Van Boom; C A Haasnoot
Journal:  Eur J Biochem       Date:  1976-12-11

9.  Local destabilisation of a DNA double helix by a T--T wobble pair.

Authors:  A G Cornelis; J H Haasnoot; J F den Hartog; M de Rooij; J H van Boom; A Cornelis
Journal:  Nature       Date:  1979-09-20       Impact factor: 49.962

10.  Conformation and interaction of short nucleic acid double-stranded helices. I. Proton magnetic resonance studies on the nonexchangeable protons of ribosyl ApApGpCpUpU.

Authors:  P N Borer; L S Kan; P O Ts'o
Journal:  Biochemistry       Date:  1975-11-04       Impact factor: 3.162
  10 in total
  18 in total

1.  Circular dichroism studies of an oligodeoxyribonucleotide containing a hairpin loop made of a hexaethylene glycol chain: conformation and stability.

Authors:  M Durand; K Chevrie; M Chassignol; N T Thuong; J C Maurizot
Journal:  Nucleic Acids Res       Date:  1990-11-11       Impact factor: 16.971

2.  Template-primer analogs as substrates for DNA polymerase.

Authors:  T R Webb; P Jhurani; P G Ng
Journal:  Nucleic Acids Res       Date:  1987-05-26       Impact factor: 16.971

3.  Amplification of chirality based upon the association of nucleic acid strands of opposite handedness.

Authors:  C A van Boeckel; G M Visser; R A Hegstrom; J H van Boom
Journal:  J Mol Evol       Date:  1987       Impact factor: 2.395

4.  Hairpin and duplex formation of the DNA octamer d(m5C-G-m5C-G-T-G-m5C-G) in solution. An NMR study.

Authors:  L P Orbons; G A van der Marel; J H van Boom; C Altona
Journal:  Nucleic Acids Res       Date:  1986-05-27       Impact factor: 16.971

Review 5.  Heteroduplex deoxyribonucleic acid base mismatch repair in bacteria.

Authors:  J P Claverys; S A Lacks
Journal:  Microbiol Rev       Date:  1986-06

6.  Nuclear magnetic resonance studies on yeast tRNAPhe. II. Assignment of the iminoproton resonances of the anticodon and T stem by means of nuclear Overhauser effect experiments at 500 MHz.

Authors:  A Heerschap; C A Haasnoot; C W Hilbers
Journal:  Nucleic Acids Res       Date:  1983-07-11       Impact factor: 16.971

7.  Primary and secondary structure specificity of the cleavage of 'single-stranded' DNA by endonuclease Hinf I.

Authors:  B Hofer; G Ruhe; A Koch; H Köster
Journal:  Nucleic Acids Res       Date:  1982-05-11       Impact factor: 16.971

8.  Nuclear magnetic resonance studies on yeast tRNAPhe I. Assignment of the iminoproton resonances of the acceptor and D stem by means of Nuclear Overhauser Effect experiments at 500 MHz.

Authors:  A Heerschap; C A Haasnoot; C W Hilbers
Journal:  Nucleic Acids Res       Date:  1982-11-11       Impact factor: 16.971

9.  The importance of a single G in the hairpin loop of the iron responsive element (IRE) in ferritin mRNA for structure: an NMR spectroscopy study.

Authors:  H Sierzputowska-Gracz; R A McKenzie; E C Theil
Journal:  Nucleic Acids Res       Date:  1995-01-11       Impact factor: 16.971

10.  Nuclear magnetic resonance and circular dichroism studies of a duplex--single-stranded hairpin loop equilibrium for the oligodeoxyribonucleotide sequence d(CGCGATTCGCG).

Authors:  M F Summers; R A Byrd; K A Gallo; C J Samson; G Zon; W Egan
Journal:  Nucleic Acids Res       Date:  1985-09-11       Impact factor: 16.971
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