Post-synthetic and site-specific modification of endocyclic nitrogen atoms of purines in DNA and its potential for biological and structural studies

Narukulla, Raman; Shuker, David E. G.; Xu, Yao−Zhong

doi:10.1093/nar/gki315

Cited by 14 publications

(19 citation statements)

References 29 publications

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“…Its binary mixtures are employed in high-performance thin layer chromatography, for example, in the process of separation of biological compounds. [1][2][3][4] Chemically, p-anisaldehyde is produced through liquid-phase oxidation of p-methoxy-toluene. 5 p-Anisaldehyde has been reported to dimerize readily in solution due to hydrogen bond formation, [6][7][8] and it is suggested that a charge transfer from the methoxy group to the aldehyde group is responsible for this type of aggregation.…”

Section: -Methoxybenzaldehyde (Known Also As P-anisaldehyde)mentioning

confidence: 99%

Thermal and Photoinduced Control of Relative Populations of 4-Methoxybenzaldehyde (p-Anisaldehyde) Conformers

Kuş¹,

Sharma²,

Reva³

et al. 2010

J. Phys. Chem. A

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Two almost isoenergetic conformers of 4-methoxybenzaldehyde (p-anisaldehyde), O-trans and O-cis, are nearly equally populated in gas phase at room temperature. The existence of these two conformers of similar energy makes p-anisaldehyde an attractive molecule for conformational investigations, in which the relative populations of the two forms might be subjected to optical control. In the present study, monomers of the compound were trapped from the room-temperature gas phase into cryogenic argon and xenon matrices. The initial relative amount of the two conformers present in the freshly deposited matrices is shifted slightly in favor of the O-trans conformer. The ratio of the two forms could be reversibly varied by irradiating the sample with UV light in different wavelength ranges or by using the temperature variation. Increasing the temperature of the xenon matrix up to ca. 57 K led to conversion of the less stable O-cis form into the O-trans conformer, shifting the O-cis/O-trans ratio to ca. 1:7. A series of UV irradiations with different long-pass cutoff filters was carried out. UV excitation induced transformation of O-cis and O-trans conformers into each other. These transformations were leading to the UV-wavelength-specific photostationary equilibria characterized by the O-cis/O-trans ratios of about 1:2.2, 1:1.4, 1:1.1, and 1:0.89 for λ > 328, 295, 288, and 234 nm cutoff filters, respectively. The isomerization processes were probed by infrared spectroscopy and supported by quantum chemical calculations. The absorption bands observed in the infrared spectra of p-anisaldehyde isolated in argon and xenon matrices were assigned to the theoretically predicted normal modes.

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Section: -Methoxybenzaldehyde (Known Also As P-anisaldehyde)mentioning

confidence: 99%

Thermal and Photoinduced Control of Relative Populations of 4-Methoxybenzaldehyde (p-Anisaldehyde) Conformers

Kuş¹,

Sharma²,

Reva³

et al. 2010

J. Phys. Chem. A

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“…Structures and the conventional numberings of these three nucleosides are shown in Scheme 1. In our recent work, [12] we have developed a novel method to prepare oligodeoxyribonucleotides (oligomers) containing modified purines. One of the key compounds was N1-dinitrophenyldeoxyinosine 4 that was prepared from 3 and subsequently converted into various purine-modified nucleosides (5)(6)(7)(8) as shown in Scheme 2.…”

Section: Resultsmentioning

confidence: 99%

“…[31,32] Recently, we reported a simple protocol for site-specific 15 N-labelling of nucleosides and oligomers containing modified purine. [12] As an example, treatment of N1-dinitrophenyl-2 -deoxyinosine 4 with 15 N-labelled ammonia gave the desired product, N1-15 N-labelled deoxyinosine 5 (Scheme 2).…”

Section: Exploitation Of Site-specific Isotopic 15 N-labellingmentioning

confidence: 99%

“…[33] N1-methyl-2 -deoxyinosine (6), N1-(2-aminoethyl)-2 -deoxyinosine (7) and N1-hydroxy-2 -deoxyinosine (8) were prepared by treatment of 4, respectively with methylamine (40% aqueous solution), ethylenediamine or hydroxylamine (from hydroxylamine hydrochloride and KOH) using the procedures described in our previous paper. [12] 1-Deazapurine-2 -deoxyribonucleosides (10/11) were prepared based on a published protocol. [27] DAP ribonucleosides (12/13) were prepared based upon a published protocol.…”

Section: Preparation Of Purine-modified Nucleosidesmentioning

confidence: 99%

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Unambiguous structural elucidation of base‐modified purine nucleosides using NMR

Narukulla

Shuker

Ramesh

et al. 2007

Magnetic Reson in Chemistry

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A general and unambiguous approach has been developed for structural elucidation of modified purine nucleosides using NMR spectroscopy. Systematic assignment of proton and carbon signals of modified nucleosides was firmly established by COSY and the anomerism of the glycosidic linkage of synthetic nucleosides clearly elucidated by NOESY experiments. Characteristic properties of 15N-isotopic labelling at specific positions of nucleosides were also employed for structural studies. The reported approach is applicable to other modified nucleosides and nucleotides, as well as nucleobases.

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“…There have already been shown that N 1 -(2,4-dinitrophenyl (or 4-nitrophenyl))inosines with primary alkylamines afford N 1 -alkyl inosines via an ANRORC mechanism. [5][6][7][8][9] Here we have described the reaction of 3 with primary alkylamines in detail.…”

mentioning

confidence: 99%

Polycyclic N-Heterocyclic Compounds. Part 60: Reactions of 3-(2-Cyanophenyl)quinazolin-4(3H)-ones with Primary Amines

Okuda

Tagata

Kashino

et al. 2009

CHEMICAL & PHARMACEUTICAL BULLETIN

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3-Substituted-quinazolin-4(3H)-ones are prominent structures in the fields of medicinal and natural product chemistry. 2)Their related analogues are, therefore, attractive for potential pharmaceutical applications.In our previous paper, 1,3) we described that fused 3-(2-bromoethyl)pyrimidin-4(3H)-ones (1) can react with primary alkylamines to afford abnormal rearranged products (fused 3-alkyl-4-alkyliminopyrimidines (2)) in addition to substituted 3-(2-alkylaminoethyl) derivatives (Fig. 1). The abnormal rearranged products seemed to be as a result of a new type of Dimroth rearrangement. We also showed that one of the rearranged products had considerable antidepressant activity, comparable to that of imipramine.In 2000, W. Szczepankiewicz and J. Suwinski reported the one-pot reaction of 2-aminobenzonitrile and formic acid to form 3-(2-cyanophenyl)quinazolin-4(3H)-one (3), instead of quinazolin-4(3H)-one, which was the anticipated product. 4)We, therefore, wondered if a Dimroth-type rearrangement with primary alkylamines could be applied to substrate 3 to afford 3-alkyl-4-alkyliminoquinazolines. Another possibility was that an addition of the nucleophile, ring opening, and ring closure (ANRORC) reaction could occur to give 3-alkylquinazolin-4(3H)-ones (4). There have already been shown that N 1 -(2,4-dinitrophenyl (or 4-nitrophenyl))inosines with primary alkylamines afford N 1 -alkyl inosines via an ANRORC mechanism.5-9) Here we have described the reaction of 3 with primary alkylamines in detail.First, we tested the reaction of 3 with methylamine in N,N-dimethylformamide (DMF) at room temperature. The product 4a in 56% yield was obtained with 2-aminobenzonitrile as a side product, as confirmed by TLC (Chart 1). In the 1 H-NMR spectrum of 4a, one methyl group appeared at 3.61 ppm, one proton singlet of the pyrimidine ring appeared at 8.06 ppm, and four aromatic region signals of the 2-cyanophenyl moiety of 3 disappeared. In the IR spectrum of 4a, the appearance of a lactam carbonyl band at 1670 cm Ϫ1 and disappearance of the nitrile band were observed. These results suggested that an ANRORC reaction had occurred in the reaction of 3 with methylamine. Similar results were seen when ethylamine was used to give the product 4b in 52% yield.In addition, a reaction between 3 and n-propylamine did not proceed at room temperature, as shown by TLC analysis. Contrary to the reactions with methylamine or ethylamine, which were added as methanol or aqueous solutions, respectively, n-propylamine was used as a neat in DMF solution; we therefore assumed that a protic solvent was necessary to allow this ANRORC reaction. Addition of methanol as a cosolvent with DMF was tested to give the desired product 4c in 51% yield. We also tested combining 3 with tert-butylamine in the presence of methanol in DMF; however, no reaction occurred. Perhaps, steric hindrance of the tert-butyl group prohibited nucleophilic attack of amino functionality to 3. Furthermore, the reaction of 3 with dimethylamine did not proceed at all. We theorized that ...

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Post-synthetic and site-specific modification of endocyclic nitrogen atoms of purines in DNA and its potential for biological and structural studies

Cited by 14 publications

References 29 publications

Thermal and Photoinduced Control of Relative Populations of 4-Methoxybenzaldehyde (p-Anisaldehyde) Conformers

Thermal and Photoinduced Control of Relative Populations of 4-Methoxybenzaldehyde (p-Anisaldehyde) Conformers

Unambiguous structural elucidation of base‐modified purine nucleosides using NMR

Polycyclic N-Heterocyclic Compounds. Part 60: Reactions of 3-(2-Cyanophenyl)quinazolin-4(3H)-ones with Primary Amines

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