[14] 31P NMR of DNA

Gorenstein, David G.

doi:10.1016/0076-6879(92)11016-c

Cited by 92 publications

(109 citation statements)

References 72 publications

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“…The fast interconversion between BI/BII substates of DNA, which are assumed to interconvert at physiological temperatures on the subnanosecond time, [53][54][55][56] allows an exhaustive description of this conformational aspect by current force fields and computer simulation techniques. [57][58][59] For more clarity, we want to split our results into two sections.…”

Section: Resultsmentioning

confidence: 99%

M.TaqI facilitates the base flipping via an unusual DNA backbone conformation

et al. 2005

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MD simulations have been carried out to understand the dynamical behavior of the DNA substrate of the Thermus aquaticus DNA methyltransferase (M.TaqI) in the methylation process at N6 of adenine. As starting structures, an x-ray structure of M.TaqI in complex with DNA and cofactor analogue (PDB code: 1G 38) and free decamer d(GTTCGATGTC)(2) were taken. The x-ray structure shows two consecutive BII substates that are not observed in the free decamer. These consecutive BII substates are also observed during our simulation. Additionally, their facing backbones adopt the same conformations. These double facing BII substates are stable during the last 9 ns of the trajectories and result in a stretched DNA structure. On the other hand, protein-DNA contacts on 5' and 3' phosphodiester groups of the partner thymine of flipped adenine have changed. The sugar and phosphate parts of thymine have moved further into the empty space left by the flipping base without the influence of protein. Furthermore, readily high populated BII substates at the GpA step of palindromic tetrad TCGA rather than CpG step are observed in the free decamer. On the contrary, the BI substate at the GpA step is observed on the flipped adenine strand. A restrained MD simulation, reproducing the BI/BII pattern in the complex, demonstrated the influence of the unusual backbone conformation on the dynamical behavior of the target base. This finding along with the increased nearby interstrand phosphate distance is supportive to the N6-methylation mechanism.

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Section: Resultsmentioning

confidence: 99%

M.TaqI facilitates the base flipping via an unusual DNA backbone conformation

et al. 2005

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“…31 P NMR Spectroscopy 31 P NMR spectroscopic studies of oligonucleotide bound by intercalators provide direct information on any backbone distortion which accompanies any interaction. [30] Unlike 1 H nuclei, for which upfield movement of the ligand resonances is caused by increases in shielding due to penetration into the ring currents of the base stack, the move- 31 P nuclei in oligonucleotides is governed by changes in the torsion angles about the phosphate linkage. [31][32][33] As shown in Figure 7, the free oligonucleotide exhibits a sharp peak at 1.1 ppm, far away from the other resonances, which is typical for sheared G:A base pairs with a B II conformation.…”

Section: (Dpq)]mentioning

confidence: 98%

Study on the Binding of Base‐Mismatched Oligonucleotide d(GCGAGC)₂ by Cobalt(III) Complexes

2005

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The binding of [Co(phen)2(HPIP)]Cl3 and [Co(phen)2(DPQ)]Cl3 to the oligonucleotide d(GCGAGC)2 containing two sheared G:A mispairs has been studied by NMR spectroscopy for the first time. For both the complexes, a considerable number of intermolecular NOEs were observed in NOESY spectra of the cobalt‐complex‐bound hexanucleotide. The results suggest that [Co(phen)2(HPIP)]Cl3, with HPIP, intercalates between the G3:A4 base pairs from the minor groove and extends to the major groove, and [Co(phen)2 (DPQ)]3+ binds to the terminal G5:C6 region from two directions. 31P NMR spectroscopy indicates that [Co(phen)2(HPIP)]Cl3 binding induces a change in the phosphate backbone in the region of the mismatched base pairs, while [Co(phen)2 (DPQ)]3+ does not cause obvious changes in the backbone. Melting experiments indicate that [Co(phen)2(HPIP)]Cl3 stabilizes the double‐strand structure, while [Co(phen)2(DPQ)]Cl3 cause the duplex to untwist. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)

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“…1(a) and (b)). X-ray crystallography investigations have reported intercalation of daunomycin in d-(TGATCA) 2 sequence, [12] but there are no solution studies with this hexamer sequence reported in literature so far. Solution studies with 4 -epiadriamycin, a better tolerated drug, [13] are also not reported.…”

Section: Introductionmentioning

confidence: 97%

“…[8 -11] The temperature dependence of 31 P chemical shift monitors melting or structural transitions in the phosphate ester backbone. [5] We have set out to examine the structure of DNA hexamer sequences complexed with anthracycline drugs, that is, adriamycin-d-(TGATCA) 2 and 4 -epiadriamycin-d-(CGATCG) 2 ( Fig. 1(a) and (b)).…”

Section: Introductionmentioning

confidence: 99%

“…[1 -4] The 31 P chemical shifts have been correlated to the conformation of two of the six torsional angles [5 -9] (α: O3 -P-O5 -C5 and ζ : C3 -O3 -P-O5 ) in phosphodiester backbone and uncoiling of duplex DNA on binding of drug. [2] Besides exchange of a phosphate between several different sites can lead to exchange broadened lines or even to separately resolved signals for the different sites that can be detected by 2D 31 P NMR. [8 -11] The temperature dependence of 31 P chemical shift monitors melting or structural transitions in the phosphate ester backbone.…”

Section: Introductionmentioning

confidence: 99%

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Studies on drug–DNA complexes, adriamycin–d‐(TGATCA)₂ and 4′‐epiadriamycin–d‐(CGATCG)₂, by phosphorus‐31 nuclear magnetic resonance spectroscopy

Agrawal¹,

Govil²,

Barthwal³

2009

Magnetic Reson in Chemistry

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The complexes of adriamycin-d-(TGATCA)(2) and 4'-epiadriamycin-d-(CGATCG)(2) are studied by one- and two-dimensional (31)P nuclear magnetic resonance spectroscopy (NMR) at 500 MHz in the temperature range 275-328 K and as a function of drug to DNA ratio (0.0-2.0). The binding of drug to DNA is clearly evident in (31)P-(31)P exchange NOESY spectra that shows two sets of resonances in slow chemical exchange. The phosphate resonances at the intercalating steps, T1pG2/C1pG2 and C5pA6/C5pG6, shift downfield up to 1.7 ppm and that at the adjacent step shift downfield up to 0.7 ppm, whereas the central phosphate A3pT4 is relatively unaffected. The variations of chemical shift with drug to DNA ratio and temperature as well as linewidths are different in each of the two complexes. These observations reflect change in population of B(I)/B(II) conformation, stretching of backbone torsional angle zeta, and distortions in O-P-O bond angles that occur on binding of drug to DNA. To the best of our knowledge, there are no solution studies on 4'-epiadriamycin, a better tolerated drug, and binding of daunomycin or its analogue to d-(TGATCA)(2) hexamer sequence. The studies report the use of (31)P NMR as a tool to differentiate various complexes. The specific differences may well be the reasons that are responsible for different antitumor action of these drugs due to different binding ability and distortions in DNA.

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[14] 31P NMR of DNA

Cited by 92 publications

References 72 publications

M.TaqI facilitates the base flipping via an unusual DNA backbone conformation

M.TaqI facilitates the base flipping via an unusual DNA backbone conformation

Study on the Binding of Base‐Mismatched Oligonucleotide d(GCGAGC)₂ by Cobalt(III) Complexes

Studies on drug–DNA complexes, adriamycin–d‐(TGATCA)₂ and 4′‐epiadriamycin–d‐(CGATCG)₂, by phosphorus‐31 nuclear magnetic resonance spectroscopy

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[14] 31P NMR of DNA

Cited by 92 publications

References 72 publications

M.TaqI facilitates the base flipping via an unusual DNA backbone conformation

M.TaqI facilitates the base flipping via an unusual DNA backbone conformation

Study on the Binding of Base‐Mismatched Oligonucleotide d(GCGAGC)2 by Cobalt(III) Complexes

Studies on drug–DNA complexes, adriamycin–d‐(TGATCA)2 and 4′‐epiadriamycin–d‐(CGATCG)2, by phosphorus‐31 nuclear magnetic resonance spectroscopy

Contact Info

Product

Resources

About

Study on the Binding of Base‐Mismatched Oligonucleotide d(GCGAGC)₂ by Cobalt(III) Complexes

Studies on drug–DNA complexes, adriamycin–d‐(TGATCA)₂ and 4′‐epiadriamycin–d‐(CGATCG)₂, by phosphorus‐31 nuclear magnetic resonance spectroscopy