7-Deaza-2′-deoxyinosine: A Stable Nucleoside with the Ambiguous Base Pairing Properties of 2′-Deoxyinosine

Seela, Frank; Mittelbach, Cathrin

doi:10.1080/15257779908043087

Cited by 19 publications

(18 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The spectrum showed a pH dependence, and a pK a value of 8.7 was obtained from the analysis of the optical density versus pH curves. A similar experiment performed for 2'-deoxyinosine and inosine gave pK a values of 9.2 [13] and 8.8, respectively. [14] For comparison, a pK a of 8.4 has been reported for 8-bromoguanosine, [4] whereas pK a values for the related debrominated derivatives have been found to be substantially higher, for example, 9.40 for 2'-deoxyguanosine [15a] and 9.25 for guanosine.…”

Section: Resultsmentioning

confidence: 88%

Chemical Radiation Studies of 8‐Bromo‐2′‐deoxyinosine and 8‐Bromoinosine in Aqueous Solutions

Russo

Jiménez

Mulazzani

et al. 2006

Chemistry A European J

View full text Add to dashboard Cite

The reactions of hydrated electrons (e(aq) (-)) with 8-bromo-2'-deoxyinosine (8) and 8-bromoinosine (12) have been investigated by radiolytic methods coupled with product studies and have been addressed computationally by means of BB1K-HMDFT calculations. Pulse radiolysis revealed that one-electron reductive cleavage of the C--Br bond gives the C8 radical 9 or 13 followed by a fast radical translocation to the sugar moiety. Selective generation of a C5' radical occurs in the 2'-deoxyribo derivative, whereas in the ribo analogue the reaction is partitioned between the C5' and C2' positions with similar rates. Both C5' radicals undergo cyclizations, 10-->11 and 14-->15, with rate constants of 1.4 x 10(5) and of 1.3 x 10(4) s(-1), respectively. The redox properties of radicals 10 and 11 have also been investigated. A synthetically useful photoreaction has also been developed as a one-pot procedure that allows the conversion of 8 to 5',8-cyclo-2'-deoxyinosine in a high yield and a diastereoisomeric ratio (5'R)/(5'S) of 4:1. The present results are compared with data previously obtained for 8-bromoadenine and 8-bromoguanine nucleosides. Theory suggests that the behavior of 8-bromopurine derivatives with respect to solvated electrons can be attributed to differences in the energy gap between the pi*- and sigma*-radical anions.

show abstract

Section: Resultsmentioning

confidence: 88%

Chemical Radiation Studies of 8‐Bromo‐2′‐deoxyinosine and 8‐Bromoinosine in Aqueous Solutions

Russo

Jiménez

Mulazzani

et al. 2006

Chemistry A European J

View full text Add to dashboard Cite

show abstract

“…The naturally occurring hypoxanthine as its ribo-or 2'-deoxyribonucleoside form such base pairs with the other natural DNA/RNA bases [4]. Similar behavior exhibit 2'-deoxyinosine analogues: 7-deaza-2'-deoxyinosine [5] and 2-aza-2'-deoxyinosine [6]. Melting studies of oligonucleotides containing the deoxyribonucleotides of 3-nitro-1H-pyrrole [7 ± 9], 4-, 5-, or 6-nitro-1H-indole [10,11] or 4-nitro-1H-imidazole [12] have demonstrated that the nitroazoles show less discrimination in their base pairs with the four natural bases than other types of analogues investigated as universal base candidates.…”

mentioning

confidence: 94%

Synthesis of Acyclic Nitroazole Nucleosides and Their Incorporation into Oligonucleotides, and Their Duplex and Triplex Formation

Walczak

Wamberg

Pedersen

2004

Helvetica Chimica Acta

View full text Add to dashboard Cite

Acyclic nucleosides of 4-nitro-1H-imidazole and 4-nitropyrazole have been synthesized by nucleophilic addition of the appropriate 4-nitroazole to (À)-(S)-(hydroxymethyl)oxirane in the presence of a catalytic amount of potassium carbonate. ()-(R)-3-(4-nitro-1H-imidazol-1-yl)propane-1,2-diol and ()-(R)-3-(2-methyl-4-nitro-1H-imidazol-1-yl)propane-1,2-diol were also obtained in an independent reaction starting from appropriate 1,4-dinitro-1H-imidazole and ()-(R)-3-aminopropane-1,2-diol. ()-(R)-3-(4-Nitropyrazol-1-yl)-propane-1,2-diol was also obtained by direct noncatalyzed addition of 4-nitropyrazole to (À)-(S)-(hydroxymethyl)oxirane, whereas the (S)-enantiomer was obtained by reaction of 4-nitropyrazole with ()-(S)-1,2-Oisopropylideneglycerol under Mitsunobu reaction conditions, followed by a cleavage of the isopropylidene group with 80% AcOH. Racemization during any of these syntheses has not been observed. 3-(4-Nitroazol-1-yl)propane-1,2-diols were incorporated into a 26-mer oligonucleotide. UV Thermal melting studies of duplexes of the oligonucleotides with 4-nitropyrazole or 4-nitro-1H-imidazole paired with four natural bases showed moderately decreased stabilities of the duplexes. A narrow range of melting temperatures, typically being within 28 for each acyclic nucleoside, fulfill one of the requirements of using acyclic 4-nitroazoles as general bases. Single incorporation of 4-nitroazoles into a 14-mer triplex forming oligonucleotide resulted in considerably decreased triplex stabilities.

show abstract

“…Other universal nucleosides, namely 2'-deoxyinosine as well as 7-deaza-2'-deoxyinosine [33] which are related to compounds 1 and 3 show a similar behavior. However, the base pairs of the 2'-deoxyinosines with dC are always stronger than those with the other canonical residues [33]. The T m decrease of duplexes within universal base pairs formed by 2'-deoxyxanthosine (1) and 7-deaza-2'-deoxyxanthosine (3) compared to 2'-deoxyinosine [33] can be explained by the spatial demand of the 2-oxo group.…”

mentioning

confidence: 51%

“…The T m values of duplexes containing a classical universal nucleoside, namely 5-nitro-1H-indole 2'-deoxy-b-D-ribofuranoside (N) which solely contributes base stacking to duplex stability are shown for comparison [31] [32]. Other universal nucleosides, namely 2'-deoxyinosine as well as 7-deaza-2'-deoxyinosine [33] which are related to compounds 1 and 3 show a similar behavior. However, the base pairs of the 2'-deoxyinosines with dC are always stronger than those with the other canonical residues [33].…”

mentioning

confidence: 51%

Oligonucleotides Containing 7-Deaza-2′-deoxyxanthosine: Synthesis, Base Protection, and Base-Pair Stability

Seela

Shaikh

2006

HCA

Self Cite

View full text Add to dashboard Cite

Oligonucleotides incorporating 7-deaza-2'-deoxyxanthosine (3) and 2'-deoxyxanthosine (1) were prepared by solid-phase synthesis using the phosphoramidites 6 -9 and 16 which were protected with allyl, diphenylcarbamoyl, or 2-(4-nitrophenyl)ethyl groups. Among the various groups, only the 2-(4-nitrophenyl)ethyl group was applicable to 7-deazaxanthine protection being removed with 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) by b-elimination, while the deprotection of the allyl residue with Pd 0 catalyst or the diphenylcarbamoyl group with ammonia failed. Contrarily, the allyl group was found to be an excellent protecting group for 2'-deoxyxanthosine (1). The base pairing of nucleoside 3 with the four canonical DNA constituents as well as with 3-bromo-1-(2-deoxy-b-D-erythro-pentofuranosyl)-1H-pyrazolo[3,4-d]pyrimidine-4,6-diamine (4) within the 12-mer duplexes was studied, showing that 7-deaza-2'-deoxyxanthosine (3) has the same universal base-pairing properties as 2'-deoxyxanthosine (1). Contrary to the latter, it is extremely stable at the N-glycosylic bond, while compound 1 is easily hydrolyzed under slightly acidic conditions. Due to the pK a values 5.7 (1) and 6.7 (3), both compounds form monoanions under neutral conditions (95% for 1; 65% for 3). Although both compounds form monoA C H T U N G T R E N N U N G anions at pH 7.0, pH-dependent T m measurements showed that the base-pair stability of 7-deaza-2'-deoxyxanthosine (3) with dT is pH-independent. This indicates that the 2-oxo group is not involved in base-pair formation.

show abstract

7-Deaza-2′-deoxyinosine: A Stable Nucleoside with the Ambiguous Base Pairing Properties of 2′-Deoxyinosine

Cited by 19 publications

References 34 publications

Chemical Radiation Studies of 8‐Bromo‐2′‐deoxyinosine and 8‐Bromoinosine in Aqueous Solutions

Chemical Radiation Studies of 8‐Bromo‐2′‐deoxyinosine and 8‐Bromoinosine in Aqueous Solutions

Synthesis of Acyclic Nitroazole Nucleosides and Their Incorporation into Oligonucleotides, and Their Duplex and Triplex Formation

Oligonucleotides Containing 7-Deaza-2′-deoxyxanthosine: Synthesis, Base Protection, and Base-Pair Stability

Contact Info

Product

Resources

About