The applications of universal DNA base analogues

Nucleic Acids Research

Volumn 29, Issue 12, 2001, Pages 2437-2447

  Loakes, D ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

3 NITROPYRROLE; 5 NITROINDOLE; DNA BASE; DOUBLE STRANDED DNA; INDOLE DERIVATIVE; PYRROLE DERIVATIVE; RNA; UNCLASSIFIED DRUG; 3-NITROPYRROLE; DNA; HYPOXANTHINE; NUCLEOSIDE; NUCLEOTIDE; PRIMER DNA; TRIPLEX DNA;

ARTICLE; BASE PAIRING; BIOCHEMISTRY; CONTROLLED STUDY; HYDROGEN BOND; HYDROPHOBICITY; MEDICAL LITERATURE; MOLECULAR INTERACTION; MOLECULAR STABILITY; PRIORITY JOURNAL; CHEMISTRY; DNA DENATURATION; DNA PROBE; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; REVIEW; THERMODYNAMICS;

BASE PAIRING; BASE SEQUENCE; DNA; DNA PRIMERS; DNA PROBES; HYDROGEN BONDING; HYPOXANTHINE; NUCLEIC ACID DENATURATION; NUCLEOSIDES; NUCLEOTIDES; PYRROLES; THERMODYNAMICS;

EID: 0035875112     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (92)

1. An alternative approach to deoxynucleotides as hybridisation probes by insertion of deoxyinosine at ambiguous codon positions
2. Molecular-cloning of the human cholecystokinin gene by use of a synthetic probe containing deoxyinosine
3. PCR amplification using deoxyinosine to replace entire codon and at ambiguous positions
4. In vitro replication study of modified bases in RAS sequences
5. Base-pairing involving deoxyinosine-implications for probe design
6. Hybridisation probes with deoxyinosine, deoxyxanthosine or deoxynebularine at ambiguous codon positions
7. Oligonucleotides containing fluorescent 2′-deoxyisoinosine: Solid phase synthesis and duplex stability
8. 7-Deaza-2′-deoxyinosine: A stable nucleoside with the ambiguous base pairing properties of 2′-deoxyinosine
9. Synthesis and biophysical and biological properties of oligonucleotides containing 2-aza-2′-deoxyinosine
10. Studies on nucleic-acid interactions 1. Stabilities of mini-duplexes containing deoxyinosine and other mismatched bases
11. Design and synthesis of heterocyclic carboxamides as natural nucleic-acid base mimics
12. Exploratory studies on azole carboxamides as nucleobase analogs: Thermal denaturation studies on oligodeoxyribonucleotide duplexes containing pyrrole-3-carboxamide
13. Imidazole-4-carboxamide and 1,2,4-triazole-2-carboxamide deoxynucleotides as simplified DNA building blocks with ambiguous pairing capacity
14. Synthesis and biophysical studies of short oligodeoxynucleotides with novel modifications-a possible approach to the problem of mixed base oligodeoxynucleotide synthesis
15. Flexible aglycone residues in duplex DNA
16. Replication of non-hydrogen bonded bases by DNA polymerases: A mechanism for steric matching
17. Stability and structure of DNA oligonucleotides containing non-specific base analogues
18. Synthesis, structure and biochemical applications of a universal nucleic-acid spacer-1-(2′-deoxy-β-D-ribofuranosyl)-3-nitropyrrole
19. Synthesis, structure and biochemical applications of a nucleic-acid spacer-1-(2′-deoxy-β-D-ribofuranosyl)-3-nitropyrrole
20. Synthesis, structure and deoxyribonucleic acid sequencing with a universal base: 1-(2′-deoxy-β-D-ribofuranosyl)-3-nitropyrrole
21. 5-Nitroindole as an universal base analogue
22. Effect of the 1-(2′-deoxy-β-D-ribofuranosyl)-3-nitropyrrole residue on the stability of DNA duplexes and triplexes
23. Enhanced discrimination of single nucleotide polymorphisms by artificial mismatch hybridisation
24. Synthesis of novel polycyclic nucleoside analogues, incorporation into oligodeoxynucleotides and interaction with complementary sequences
25. NMR structure of a DNA duplex containing nucleoside analog 1-(2′-deoxy-β-D-ribofuranosyl)-3-nitropyrrole and the structure of the unmodified control
26. Comparison of the base pairing properties of a series of nitroazole nucleobase analogues in the oligodeoxyribonucleotide sequence 5′-d(CGCXAATTYGCG)-3′
27. Synthesis of 1-β-D-ribopyranosyl-6-nitroindole and ribofuranosyl-6-nitroindole and indoline for phosphotriester oligonucleotide synthesis
28. Synthesis of 4-substituted 1H benzimidazole 2′-deoxynucleosides and utility of the 4-nitro compound as universal base
29. In search of acyclic analogues as universal nucleosides in degenerate probes
30. An acyclic 5-nitroindazole nucleoside analogue as ambiguous nucleoside
31. Enzymatic recognition of acyclic universal base analogues in oligonucleotides
32. Oligodeoxyribonucleotides containing 4-aminobenzimidazole in place of adenine: Solid-phase synthesis and base pairing
33. Synthesis and structure of 1-deoxy-1-phenyl-β-D-ribofuranose and its incorporation into oligonucleotides
34. The use of tailed octamer primers for cycle sequencing
35. 5′-Tailed octanucleotide primers for cycle sequencing
36. Nitroazole universal bases in peptide nucleic acids
37. Modified oligonucleotides: Synthesis and strategy for users
38. 3-Nitropyrrole and 5-nitroindole as universal bases in primers for DNA sequencing and PCR
39. Amplification of human transferrin receptor gene using primers containing universal base nucleoside residues at ambiguous positions in degenerate amino-acid codons
40. Inosine containing primers for mRNA differential display
41. Cloning and developmental expression of a membrane-type matrix metaloproteinase from chicken
42. Nucleotide analogs facilitate base conversion with 3′ mismatch primers
43. Novel non-templates nucleotide addition-reactions catalysed by prokaryotic and eukaryotic DNA-polymerases
44. Template directed incorporation of nucleotide mixtures using azole-nucleobase analogs
45. Nitroindoles as universal bases
46. Melting behaviour of DNA hairpins containing the universal base 5-nitroindole
47. RNA template-directed RNA synthesis by T7 RNA polymerase
48. Non-hydrogen bonding terminator nucleosides increase the 3′-end homogeneity of enzymatic RNA and DNA synthesis
49. Quantification of Methanosaeta species in anaerobic bioreactors using genus- and species-specific hybridisation probes
50. Group-specific small-subunit rRNA hybridisation probes to characterise filamentous foaming in activated sludge systems
51. Quantification of syntrophic fatty acid-β-oxidising bacteria in a mesophilic biogas reactor by oligonucleotide probe hybridisation
52. Use of 5-nitroindole-2′-deoxyribose-5′-triphosphate for labelling and detection of oligonucleotides
53. Making the perfect mismatch
54. Modification of DNA duplexes to smooth their thermal stability independently of their base content for DNA sequencing by hybridisation
55. Improving the fidelity of Thermus thermophilus DNA-ligase
56. Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips
57. DNA-sequencing by hybridisation to microchip octanucleotide and decanucleotide extended by stacked pentanucleotides
58. Stabilisation effect of 5-nitroindole (universal base) on DNA duplexes immobilised on gel matrix
59. Optimal reconstruction of a sequence from its probes
60. Sequencing by hybridisation at the information-theory bound: An optimal algorithm
61. Test of the potential of a dATP surrogate for sequencing via MALDI-MS
62. Recognition of nonhybridising base pairs during nucleotide excision repair of DNA
63. Sequence determinants for the recognition of the fork junction DNA containing the -10 region of promoter DNA by E. coli RNA polymerase
64. Mutagenically separated PCR (MS-PCR): A highly specific one step procedure for easy mutation detection
65. Triple helices formed at oligopyrimidine-oligopurine sequences with base pair inversions: Effect of a triplex-specific ligand on stability and selectivity
66. Self-association and DNA-binding properties of 2 triple helix-specific ligands-comparison of a benzo[e]pyridoindole and a benzo[g]pyridoindole
67. Extension of the range of DNA sequences available for triple helix formation: Stabilisation of mismatched triplexes by acridine-containing oligonucleotides
68. Triple helix formation: Binding avidity of acridine-conjugated AG motif third strands containing natural, modified and surrogate bases opposed to pyrimidine interruptions in a polypurine target
69. Azole substituted oligonucleotides promote antiparallel triplex formation at non-homopurine duplex targets
70. DNA polymerase incorporation of universal base triphosphates
71. Efforts toward the expansion of the genetic alphabet: Information storage and replication with unnatural hydrophobic base pairs
72. Incorporation of unnatural nucleotides by DNA polymerases
73. Base-stacking and base-pairing contributions to helix stability: Thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp and ACCGGUp
74. Extra adenosine stacks into the self-complementary d(CGCAGAATTCGCG) duplex in solution
75. The three-dimensional structure of a DNA duplex containing looped-out bases
76. Experimental measurement of aromatic stacking affinities in the context of duplex DNA
77. Hydrophobic, non-hydrogen-bonding bases and base-pairs in DNA
78. Factors contributing to aromatic stacking in water: Evaluation in the context of DNA
79. Selective and stable DNA base pairing without hydrogen bonding
80. Aromatic nonpolar nucleosides as hydrophobic isosteres of pyrimidine and purine nucleosides
81. Mimicking the structure and function of DNA: Insights into DNA stability and replication
82. Adenylate oligomers in single- and double-stranded conformation
83. Melting studies of short DNA hairpins containing the universal base 5-nitroindole
84. Melting studies of short DNA hairpins: Influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability
85. Formation of stable DNA loops by incorporation of nonpolar, non-hydrogen-bonding nucleoside isosteres
86. Nucleosides and nucleotides. 25. Synthesis of a protected 1-(2′-deoxy-β-D-ribofuranosyl)-1H-benzimidazole 3′-phosphate
87. Synthesis of 2′-deoxyribofuranosyl indole nucleosides related to the antibiotics SF-2140 and Neosidomycin
88. Universal bases for hybridisation, replication and chain termination
89. Stable and selective hybridisation of oligonucleotides with unnatural hydrophobic bases
90. Efforts toward expansion of the genetic alphabet: DNA polymerase recognition of a highly stable, self-pairing hydrophobic base
91. 8-(2′-deoxyribofuranoside) of 8-aza-7-deazaadenine: A universal nucleoside forming specific hydrogen bonds with the four canonical constituents