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Literature DB >> 3671080

The stability of oligodeoxyribonucleotide duplexes containing degenerate bases.

Abstract

Oligodeoxyribonucleotides containing N4-methoxycytosine (mo4C), N4-methoxy-5-methylcytosine (mo4m5C) and other base-analogues were synthesised and used to compare the stabilities of duplexes containing mo4C.A and mo4C.G base pairs with those containing normal and mismatch pairs. The Tm values and other thermodynamic parameters are recorded. The otherwise identical duplexes containing a mo4C.A and a mo4C.G base pair have closely similar stabilities to each other and to the corresponding duplexes containing normal base pairs, considerably greater than the stabilities of those containing mismatch pairs. Corresponding observations are recorded in dot-blot experiments using M13 cloned DNA carrying an insert complementary to the oligonucleotides; approximate Td values are given.

Entities: Chemical

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Year: 1987 PMID： 3671080 PMCID： PMC306351 DOI： 10.1093/nar/15.20.8167

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

20 in total

1. Stacking self-association of pyrimidine nucleosides and of cytosines: effects of methylation and thiolation.

Authors: E Plesiewicz; E Stepień; K Bolewska; K L Wierzchowski
Journal: Nucleic Acids Res Date: 1976-05 Impact factor: 16.971

2. Studies on nucleic acid interactions. I. Stabilities of mini-duplexes (dG2A4XA4G2-dC2T4YT4C2) and self-complementary d(GGGAAXYTTCCC) containing deoxyinosine and other mismatched bases.

Authors: Y Kawase; S Iwai; H Inoue; K Miura; E Ohtsuka
Journal: Nucleic Acids Res Date: 1986-10-10 Impact factor: 16.971

3. 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

4. The tautomeric state of N(4)-hydroxy- and of N(4)-amino-cytosine derivatives.

Authors: D M Brown; M J Hewlins; P Schell
Journal: J Chem Soc Perkin 1 Date: 1968

5. Nucleosides. XLVII. Synthesis of some N4-substituted derivarives of 1-beta-D-arabinofuranosylcytosine and -5-fluorocytosine.

Authors: I Wempen; N Miller; E A Falco; J J Fox
Journal: J Med Chem Date: 1968-01 Impact factor: 7.446

6. Isolation of a human anti-haemophilic factor IX cDNA clone using a unique 52-base synthetic oligonucleotide probe deduced from the amino acid sequence of bovine factor IX.

Authors: M Jaye; H de la Salle; F Schamber; A Balland; V Kohli; A Findeli; P Tolstoshev; J P Lecocq
Journal: Nucleic Acids Res Date: 1983-04-25 Impact factor: 16.971

3. Modified base compositions at degenerate positions of a mutagenic oligonucleotide enhance randomness in site-saturation mutagenesis.

Authors: A Airaksinen; T Hovi
Journal: Nucleic Acids Res Date: 1998-01-15 Impact factor: 16.971

4. The synthesis and properties of oligodeoxyribonucleotides containing N6-methoxyadenine.

Authors: H Nishio; A Ono; A Matsuda; T Ueda
Journal: Nucleic Acids Res Date: 1992-02-25 Impact factor: 16.971

4 in total

The stability of oligodeoxyribonucleotide duplexes containing degenerate bases.

1. Stacking self-association of pyrimidine nucleosides and of cytosines: effects of methylation and thiolation.

2. Studies on nucleic acid interactions. I. Stabilities of mini-duplexes (dG2A4XA4G2-dC2T4YT4C2) and self-complementary d(GGGAAXYTTCCC) containing deoxyinosine and other mismatched bases.

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

4. The tautomeric state of N(4)-hydroxy- and of N(4)-amino-cytosine derivatives.

5. Nucleosides. XLVII. Synthesis of some N4-substituted derivarives of 1-beta-D-arabinofuranosylcytosine and -5-fluorocytosine.

6. Isolation of a human anti-haemophilic factor IX cDNA clone using a unique 52-base synthetic oligonucleotide probe deduced from the amino acid sequence of bovine factor IX.

7. Nucleosides. XXIX. 1-beta-D-arabinofuranosyl-5-fluorocytosine and related arabino nucleosides.

8. Mechanism of hydroxylamine mutagenesis. Crystal structure and conformation of 1,5-dimethyl-N4-hydroxycytosine.

9. Isolation of a genomic clone for bovine pancreatic trypsin inhibitor by using a unique-sequence synthetic DNA probe.

10. Hybridization of synthetic oligodeoxyribonucleotides to phi chi 174 DNA: the effect of single base pair mismatch.

1. Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases.

2. Synthesis and duplex stability of oligonucleotides containing cytosine-thymine analogues.

3. Modified base compositions at degenerate positions of a mutagenic oligonucleotide enhance randomness in site-saturation mutagenesis.

4. The synthesis and properties of oligodeoxyribonucleotides containing N6-methoxyadenine.