Photochemistry of N6-methoxyadenosine and of N4-hydroxycytidine and its methyl derivatives I: spectroscopic and quantum chemical investigation of ionic and tautomeric forms: syn-anti isomerization

Morozov, Yu. V.; Savin, F. A.; Chekhov, V. O.; Budowsky, E.I.; Yakovlev, D. Yu.

doi:10.1016/0047-2670(82)85038-7

Cited by 34 publications

(14 citation statements)

References 16 publications

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“…It showed that this correlated well with the effect of the electronegative oxygen atom in altering the tautomeric constant K T of cytosine from about 10 5 to 0.1-0.03, favoring the imino form (8,9). Thus the small free energy difference between the tautomers permitted stable hydrogen bonding with both A and G. The preferred syn orientation of the methoxyl group (10,11) with respect to N 3 in mo 4 C (Fig. 1, compound 1b) gave some destabilization in base pairing.…”

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confidence: 53%

Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases

Hill

Loakes

Brown

1998

Proc. Natl. Acad. Sci. U.S.A.

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A universal base that is capable of substituting for any of the four natural bases in DNA would be of great utility in both mutagenesis and recombinant DNA experiments. This paper describes the properties of oligonucleotides incorporating two degenerate bases, the pyrimidine base 6H,8H-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one and the purine base N 6 -methoxy-2,6-diaminopurine, designated P and K, respectively. An equimolar mixture of the analogues P and K (called M) acts, in primers, as a universal base. The thermal stability of oligonucleotide duplexes were only slightly reduced when natural bases were replaced by P or K. Templates containing the modified bases were copied by Taq polymerase; P behaved as thymine in 60% of copying events and as cytosine in 40%, whereas K behaved as if it were guanine (13%) or adenine (87%). The dUTPase gene of Caenorhabditis elegans, which we have found to contain three nonidentical homologous repeats, was used as a model system to test the use of these bases in primers for DNA synthesis. A pair of oligodeoxyribonucleotides, each 20 residues long and containing an equimolar mixture of P and K at six positions, primed with high specificity both T7 DNA polymerase in sequencing reactions and Taq polymerase in PCRs; no nonspecific amplification was obtained on genomic DNA of C. elegans. Use of P and K can significantly reduce the complexity of degenerate oligonucleotide mixtures, and when used together, P and K can act as a universal base.

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confidence: 53%

Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases

Hill

Loakes

Brown

1998

Proc. Natl. Acad. Sci. U.S.A.

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“…Final atomic parameters. (9) 1557 (11) 1572 (15) 120 (8) 523(6) -37(10) 280 (10) 95(9) 678(5) 653 (9) 623 (9) 854 (10) 132 (6) 505 (9) 613 (8) 455 (16) 246 (20) 536 (17) 30882 (17) 25966 (22) 31311 (17) 43110 (20) 49174 (20) 42909 (20) 47853 (18) 39189 (17) 45205 (33) 60954 (17) 61700 (21) 51148 (16) 48554 (22) 59072 (16) 39900 2133099 (16) 22558 (27) 48229 (22) 44042 (18) 35267 (29) 58836 (24) 70086 (28) 79189 (25) 89827 (37) 263 ( strong, low-order reflections suffered from extinction effects and were given zero weights. The final conventional residual index R is 0.038 and the weighted index R is 0.047 for 1757 observed and 32 unobserved jfjI < |tc.…”

Section: Methodsmentioning

confidence: 99%

Tautomerism and conformation of the promutagenic analogueN⁶-methoxy-2′,3′,5′-tri-O- methyladenosine⁺

1984

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N6-Methoxy-2',3',5'-tri-O-methyladenosine crystallizes in space group P2(1)2(1)2(1) with cell dimensions a = 4.693, b = 11.412, c = 31.741 A. Least-squares refinement of diffractometer data converged at R = 0.038. The location of a hydrogen atom at N1 and the observed bond lengths and bond angles indicate unequivocally the imino tautomer of the adenine moiety. The N6-methoxy group is oriented syn to N1 and the glycosidic torsion angle XCN is -3.6 degrees, i.e. in the anti range. The furanose ring has a C2'-exo/C3'- endo pucker (P = 0.9 degrees) and is unusually flattened (tau m = 30.0 degrees). The conformations of the O-methyl groups of the ribose ring are compared with those of monomethylated nucleosides, including the biologically important 2'-O-methyl nucleosides. Evidence is presented for the existence of C-H ... N intermolecular hydrogen bonds between adenine moieties. Bearing in mind that N6-methoxyadenosine is a promutagenic analogue, the results are compared with those for the corresponding promutagenic N4-methoxycytidine. They are also discussed in relation to the tautomerism, the conformation of the N6-methoxy group, and the associated base-pairing abilities in the absence and presence of polymerases.

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“…In the case of a methoxycytosine analogue, similar incorporation occurred during in vitro polymerization (Singer et al, 1984;Reeves & Beattie, 1985). N 4 -methoxycytidine also prefers an imino form in solution (Brown et al, 1968;Morozov et al, 1982). A DNA fragment containing this residue was examined by X-ray analysis (Meervelt et al, 1990).…”

Section: Introductionmentioning

confidence: 99%

Crystallization and preliminary analysis of a DNA dodecamer of d(CGCGmo⁶AATCCGCG) containing 2′-deoxy-N ⁶-methoxyadenosine: change in crystal packing with different humidity

Chatake

Sunami

Ono

et al. 1999

Acta Crystallogr D Biol Cryst

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The DNA dodecamer of (CGCGmo 6 AATCCGCG) containing 2 Hdeoxy-N 6 -methoxyadenosine has been crystallized for X-ray analysis in order to investigate the effects of the modi®ed adenosine on base pairing. It has been found that the crystal changes from one form to another during data collection in a manner similar to a phase transition. The two crystal structures show that this phenomenon, ascribed to differences in humidity, is correlated with a change in the contact angle between the two duplexes.

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Photochemistry of N6-methoxyadenosine and of N4-hydroxycytidine and its methyl derivatives I: spectroscopic and quantum chemical investigation of ionic and tautomeric forms: syn-anti isomerization

Cited by 34 publications

References 16 publications

Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases

Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases

Tautomerism and conformation of the promutagenic analogueN⁶-methoxy-2′,3′,5′-tri-O- methyladenosine⁺

Crystallization and preliminary analysis of a DNA dodecamer of d(CGCGmo⁶AATCCGCG) containing 2′-deoxy-N ⁶-methoxyadenosine: change in crystal packing with different humidity

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Photochemistry of N6-methoxyadenosine and of N4-hydroxycytidine and its methyl derivatives I: spectroscopic and quantum chemical investigation of ionic and tautomeric forms: syn-anti isomerization

Cited by 34 publications

References 16 publications

Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases

Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases

Tautomerism and conformation of the promutagenic analogueN6-methoxy-2′,3′,5′-tri-O- methyladenosine+

Crystallization and preliminary analysis of a DNA dodecamer of d(CGCGmo6AATCCGCG) containing 2′-deoxy-N 6-methoxyadenosine: change in crystal packing with different humidity

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Tautomerism and conformation of the promutagenic analogueN⁶-methoxy-2′,3′,5′-tri-O- methyladenosine⁺

Crystallization and preliminary analysis of a DNA dodecamer of d(CGCGmo⁶AATCCGCG) containing 2′-deoxy-N ⁶-methoxyadenosine: change in crystal packing with different humidity