Spatial configuration of deoxyribotrinucleoside diphosphates in aqueous solution

Cheng, Doris M.; Dhingra, M. M.; Sarma, Ramaswamy H.

doi:10.1093/nar/5.11.4399

Cited by 30 publications

(17 citation statements)

References 15 publications

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“…2). The flaps were comprised of different lengths of oligodeoxythymidine in order to minimize secondary structure formation (11). We found that flap cleavage efficiency decreased markedly with increasing flap length, from 80% cleavage with a 20-bp flap to 28% with a 120-bp flap.…”

Section: Resultsmentioning

confidence: 99%

Novel Function of Rad27 (FEN-1) in Restricting Short-Sequence Recombination

Negritto¹,

Qiu

Ratay³

et al. 2001

Molecular and Cellular Biology

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Saccharomyces cerevisiae mutants lacking the structure-specific nuclease Rad27 display an enhancement in recombination that increases as sequence length decreases, suggesting that Rad27 preferentially restricts recombination between short sequences. Since wild-type alleles of both RAD27 and its human homologue FEN1 complement the elevated short-sequence recombination (SSR) phenotype of a rad27-null mutant, this function may be conserved from yeast to humans. Furthermore, mutant Rad27 and FEN-1 enzymes with partial flap endonuclease activity but without nick-specific exonuclease activity partially complement the SSR phenotype of the rad27-null mutant. This suggests that the endonuclease activity of Rad27 (FEN-1) plays a role in limiting recombination between short sequences in eukaryotic cells.

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Section: Resultsmentioning

confidence: 99%

Novel Function of Rad27 (FEN-1) in Restricting Short-Sequence Recombination

Negritto¹,

Qiu

Ratay³

et al. 2001

Molecular and Cellular Biology

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“…The H2' and H2" protons of a particular residue are distinguished on the basis of (a) the larger deshielding effect of 3'-phosphorylation at H2", (b) the deshielding effect of 04-alkylation at H2" (0.09 ppm) and comparable shielding effect at H2' (0.07 ppm) observed at the nucleoside level, and (c) coupling constant trends (26,27). The H5' and H5" protons were assigned according to the literature (28).…”

Section: Results and Discussion ' H Nuclear Magnetic Resonance Spectrmentioning

confidence: 99%

“…At 20°C the Np and pN fragments of the three dimers show preferences for gf in the narrow range 6 1 1+-5 and 79 + 2%, respectively. A preference for gf is generally observed in oligomers (27,29,30). Increasing the temperature to 70°C reduces this preference in Np to 52 & 2%, and in pN to 64 -+ 2%.…”

Section: Sugar Conformationmentioning

confidence: 94%

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An NMR study of dinucleoside monophosphates with an O4-ethylated thymine. d(e⁴TpT) and d(Tpe⁴T)

Buchko¹,

Hruska²,

Sadana³

1989

Can. J. Chem.

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. Can. J. Chem. 67, 109 (1989). Syntheses are described for d ( e q p~) (1) and d (~~e ? ) (2), the 04-ethylated analogues of d(TpT) (3), and mass spectrometric (FAB), 'H nuclear magnetic resonance (300 MHz), and circular dichroic data are provided for the three molecules. The [M -HI-ions as well as the aggregates [2M -HI-and, in the case of 1, [3M -HI-, are easily detected by FAB mass spectrometry operating in the negative ion mode. In contrast with the modified nucleoside, e 4 d~, the two methylene protons of the 04-ethyl groups of 1 and 2 are nonequivalent in the NMR spectra, and their chemical shift difference decreases with increasing temperature. This chemical shift difference can be related to intramolecular base stacking. The vicinal coupling constants of the sugar rings reveal an unusual shift at low temperature towards the 3'-endo conformation of the e v p unit of 1, but this shift is not noted for the pe? unit of 2.04-Alkylation of either unit of 3 effects a large reduction in the amplitude of the negative CD peak at 252 nm. The CD spectra of 1 and 2 are qualitatively similar to those of d(CpT) and d(TpC), respectively, and suggest that in some respects an 04-alkylated thymine base is "cytosine-like". The amplitudes of the positive CD peaks of 1 and 3 are reduced by 40% as the temperature is increased from 10 to 65"C, indicating the presence of some base stacking at low temperatures. However, the CD spectrum of 2 shows a much smaller reduction (

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“…No such effects are observed for the pNp fragment of the all-pyrimidine trimers 7 (Table 1) and 21 (33). However, it is surprising that As(H2') for the trimers at 10°C is only 60% of that for the dimers 1 and 4.…”

Section: Chemical Shift Temperature Projiles: Pyrimidine Unitsmentioning

confidence: 92%

Synthesis and properties of DNA oligomers containing an O4-ethylated thymine. d(e⁴TpA), d(Ape⁴T), d(Ape⁴TpA), and d(Tpe⁴TpT)

Buchko¹,

Hruska²,

Sadana³

1990

Can. J. Chem.

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. Can. J. Chem. 68, 201 1 (1990). Syntheses via the phosphotriester method are described for DNA oligonucleotides containing 04-ethylated thymine (e4Thy) and adenine (Ade) bases, d ( e V p~) , d (~~e~~) , and ~( A~~V~A ) , for their unmodified analogs, d(TpA), d(ApT), and d(ApTpA), and for d(TpeVpT). 'H NMR chemical shift data obtained from 10 to 70°C at 300 and 500 MHz show that these molecules form right-handed minihelices at low temperature in aqueous solution; the presence of the 04-ethyl group does not seem to have a drastic effect on the stacking geometry of the thymine base. The presence of right-handed stacking is confirmed by circular dichroic data obtained over a similar temperature range. Coupling constants for the sugar ring indicate that the e V P unit of d ( e 4 T p~) does not show the shift towards the 3'-endo ( N ) pucker noted for the corresponding unit of d(e4TpT). A prominent quasimolecular ion peak [M -HI-is observed for the modified and unmodified molecules in the spectra obtained by Fast Atom Bombardment mass spectrometry (FAB-MS) operating in the negative ion mode, indicating that the labile 04-ethyl group is sufficiently stable to withstand the ionization process used in this method. In addition, a number of fragment ion peaks such as [04-ethylthymine -HI-are observed that reveal the potential of FAB-MS for characterizing DNA oligomers modified by alkylating agents.Key words: oligonucleotides, 0-alkylation, stereochemistry, NMR, mass spectrometry.

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Spatial configuration of deoxyribotrinucleoside diphosphates in aqueous solution

Cited by 30 publications

References 15 publications

Novel Function of Rad27 (FEN-1) in Restricting Short-Sequence Recombination

Novel Function of Rad27 (FEN-1) in Restricting Short-Sequence Recombination

An NMR study of dinucleoside monophosphates with an O4-ethylated thymine. d(e⁴TpT) and d(Tpe⁴T)

Synthesis and properties of DNA oligomers containing an O4-ethylated thymine. d(e⁴TpA), d(Ape⁴T), d(Ape⁴TpA), and d(Tpe⁴TpT)

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Spatial configuration of deoxyribotrinucleoside diphosphates in aqueous solution

Cited by 30 publications

References 15 publications

Novel Function of Rad27 (FEN-1) in Restricting Short-Sequence Recombination

Novel Function of Rad27 (FEN-1) in Restricting Short-Sequence Recombination

An NMR study of dinucleoside monophosphates with an O4-ethylated thymine. d(e4TpT) and d(Tpe4T)

Synthesis and properties of DNA oligomers containing an O4-ethylated thymine. d(e4TpA), d(Ape4T), d(Ape4TpA), and d(Tpe4TpT)

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An NMR study of dinucleoside monophosphates with an O4-ethylated thymine. d(e⁴TpT) and d(Tpe⁴T)

Synthesis and properties of DNA oligomers containing an O4-ethylated thymine. d(e⁴TpA), d(Ape⁴T), d(Ape⁴TpA), and d(Tpe⁴TpT)