The synthesis of 2-pyrimidinone nucleosides and their incorporation into oligodeoxynucleotides

Gildea, Brian; McLaughlin, Larry W.

doi:10.1093/nar/17.6.2261

Cited by 61 publications

(60 citation statements)

References 28 publications

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“…By modulating the DNA duplex stability through 'anomalous' base pairs and measuring their effect on the free energy of binding, we were able to correlate the stability of the duplex with the stability of the protein-DNA complex. Previously published reports showed that the DNA duplex stability can be altered by replacing the C paired with 2AP by the T base, resulting in a higher melting temperature for the DNA (31)(32)(33)38). The reason for the increased DNA stability is apparent from NMR studies which showed that the 2AP-C forms a partially charged species to accommodate the pairing.…”

Section: Discussionmentioning

confidence: 99%

“…These changes were at positions 9 and 11 on To further assess the role of duplex stability on the bimolecular process, we measured the affinity of the repressor protein for operator when the lac operator was substituted with 2-aminopurine-uracil base pairs (2AP.U) instead of the 2-aminopurine.cytosine. Thermal denaturation experiments have shown that duplexes containing 2AP paired with thymine are more stable than duplexes containing 2-aminopurine paired with cytosine (31)(32)(33). The use of the uracil analogue was dictated by the need to mimic the structure of cytosine which does not contain a 5-methyl group in the major groove.…”

Section: Competition Equilibrium Dissociation Assaysmentioning

confidence: 99%

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Modified nucleotides reveal the indirect role of the central base pairs in stabilizing thelacrepressor-operator complex

Zhang

Gottlieb

1995

Nucl Acids Res

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Guanine residues in the lac operator were replaced by 2-aminopurine or purine analogues, pairing the modified nucleotides with C. The observed equilibrium dissociation constants for lac repressor binding to substituted operators were measured in 10 mM Tris, 150 mM KCI, 0.1 mM EDTA, 0.1 mM DTE, pH 7.6 at 250C. These measurements revealed five positions that destabilized the complex when substituted with either analogue. Two positions, which are related by a 2-fold symmetry, are in the major groove of the operator thought to directly interact with the protein. Three sites were in the central region of the operator. A purine analogue at a sixth site perturbed the local DNA structure and destabilized the complex. Alkylation interference experiments of the 2-aminopurine substituted operators demonstrated that, of the five affected, two substitutions displayed altered phosphate interference patterns at the phosphate adjacent to the substituted base. For these operators, complex formation was measured in different concentrations of KCI to assess the contribution of counterion release to the bimolecular process. The results indicated that both complexes were similar to wild-type, although minor changes were observed. The Iobs of the complex was then measured when 2-aminopurine or purine analogues were paired with uracil nucleotide, a base pair that serves to stabilize the DNA. The introduction of the new base pairs revealed two effects on the bimolecular interaction. For those operator sites that are thought to perturb the interaction directly, the affinity of the complex was weakened to levels observed for the singly-substituted operators. In contrast, the nucleotides of 2-aminopurine paired with uracil positioned in the central region of the operator served to enhance the stability of the complex. The purine-uracil base pair substitution op the other hand had a significant destabilizing effect on the interaction. We propose that the central base pairs modulate binding of the complex by altering the intrinsic properties of the DNA. Two specific attributes are required to achieve the lowest free energy of interaction. The DNA must have two interstrand hydrogen bonds to stabilize the duplex and it must have properties associated with directional bending or unwinding. This analysis does not rule out contributions by direct interactions between the protein and the central region of the operator but underscores how indirect effects play a major role in complex formation in this system.

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Section: Discussionmentioning

confidence: 99%

Section: Competition Equilibrium Dissociation Assaysmentioning

confidence: 99%

Modified nucleotides reveal the indirect role of the central base pairs in stabilizing thelacrepressor-operator complex

Zhang

Gottlieb

1995

Nucl Acids Res

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“…Recently it has been shown that 2'-deoxyzebularine triphosphate (dZTP) is incorporated by DNA polymerases opposite to guanine (G) and when Z is at the template it directs dGTP incorporation [5]. In spite of the absence of the amino group, 2'-deoxyzebularine behaved similar to 2'-deoxycytidine pairing with guanine [5][6][7]. In this report we describe the melting behaviour of DNA duplexes carrying the 1, 2-dihydropyrimidin-2-one (Z) residue opposite to all four natural bases.…”

Section: Synthesis and Hybridization Properties Of Modified Oligodeoxmentioning

confidence: 99%

Synthesis and Hybridization Properties of Modified Oligodeoxynucleotides Carrying Non‐Natural Bases

Aviñó

Pérez-Rentero

Garibotti

et al. 2009

Chemistry & Biodiversity

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The impact of the presence of non-natural bases on the properties of oligodeoxynucleotides has been studied. First, oligodeoxynucleotides carrying 2'-deoxyzebularine were prepared and the stability of duplexes carrying this analogue was determined by DNA melting experiments. Melting temperatures and thermodynamic data showed the preference of 2'-deoxyzebularine for 2'-deoxyguanosine, which behaves as a 2'-deoxycytidine analogue forming a less stable base pair due to the absence of the amino group at position 4. Moreover, the duplex-hairpin equilibrium of a self-complementary oligodeoxynucleotide carrying several natural and non-natural bases including 2'-deoxyzebularine as a central mispair, was studied. Depending of the base present in the middle of the sequence it is possible to affect the stability of the bimolecular duplex modulating the duplex-hairpin equilibrium. Magnesium ions were shown to stabilize preferentially the bimolecular duplex form. The results indicate the importance of the modifications and the role of cations in shifting the structural equilibrium.--

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“…Pyrimidine nucleoside analogues of 2'-deoxycytidine (98) and thymidine (100) each lacking the functional group para to the glycosidic linkage (99 and 101, respectively) [242] were synthesized in order to quantify the contribution of these functional groups to duplex stability. Additional modified pyrimidine nucleosides incorporated into oligonucleotides are 04-methyl-or 04-ethylthymidine (m4T or et4T, 102),[2431 2'-deoxyuridine (dU, 103),[2271 5-methylcytidine (m5dC, 104),1227, 2441 the pyridopyrimidine nucleoside mentioned already (10512311) and a similar compound which is able to pair with several nucleobases (106[2451), 5-putrescinylthymidine (107) as well as some other 5-substituted thymi dine^,^'^^] which occur in bacteriophages and inhibit nuclease digestion, and an oligonucleotide with 5-azacytidine (z5dC, 108) (or 5,6-dihydr0-5-azacytidine~'~~'); thus, the pyrimidine field, too, presents compounds modified in the aromatic nucleus of the nucleobases.…”

Section: Modified Oligonucleotides As Substrates For Nucleases and Pomentioning

confidence: 99%

Chemically Modified Oligonucleotides as Probes and Inhibitors

Englisch

Gauss

1991

Angew. Chem. Int. Ed. Engl.

158

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Oligonucleotides bind specifically to single‐stranded nucleic acids to form a double helix if there is a complementary antiparallel nucleotide sequence. In addition, certain oligonucleotides bind specifically to a variety of proteins. Therefore, biological processes involving these nucleic acids or proteins can be modulated (normally inhibited) by addition of the respective oligonucleotides. The effects of these oligonucleotides and the fields of potential application can be broadened by the introduction of chemically modified nucleotides. For instance, replacing oligonucleotide phosphate groups by methylphosphonates results in the loss of one negative charge per nucleotide and the oligonucleotide becomes more lipophilic. An oligonucleotide carrying a reactive group can modify its binding partner. An oligonucleotide covalently linked to a dye can be localized in a biological specimen. Oligonucleotides attached to an enzyme can be detected in very small amounts since the enzyme can catalyze the formation of large amounts of the substance assayed (e.g., a fluorescent product). An important biochemical application is the detection and localization of a messenger RNA or its gene. Medical applications include the detection of bacterial or viral sequences. There is also great interest in inhibiting the translation of messenger RNA and the transcription and replication of DNA. So‐called antisense oligonucleotides are currently being used for the inhibition of protein biosynthesis and of reverse transcription of retroviruses.

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The synthesis of 2-pyrimidinone nucleosides and their incorporation into oligodeoxynucleotides

Cited by 61 publications

References 28 publications

Modified nucleotides reveal the indirect role of the central base pairs in stabilizing thelacrepressor-operator complex

Modified nucleotides reveal the indirect role of the central base pairs in stabilizing thelacrepressor-operator complex

Synthesis and Hybridization Properties of Modified Oligodeoxynucleotides Carrying Non‐Natural Bases

Chemically Modified Oligonucleotides as Probes and Inhibitors

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