Sequence‐specific assignment of the backbone <sup>1</sup>H‐ and <sup>31</sup>P‐nmr lines in a short DNA duplex with homo‐ and heteronuclear correlated spectroscopy

Mh, Frey; Leupin, Werner; Ow, Sørensen; Wa, Denny; Rr, Ernst

doi:10.1002/bip.360241214

Cited by 44 publications

(22 citation statements)

References 26 publications

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“…The twofold symmetry of d(GCATGC)2 and luzopeptin, which results in an equivalence of resonances from the two strands of the duplex and from the two halves of the depsipeptide of the antibiotic [7,15,16], is retained in the complex, as shown by the lack of doubling of resonances in both 'H-n.m.r. (Fig.…”

Section: Results and Discussion Symmetry Of The Complex And Evidence mentioning

confidence: 94%

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Interaction of the antitumour antibiotic luzopeptin with the hexanucleotide duplex d(5′-GCATGC)2. One-dimensional and two-dimensional n.m.r. studies

Searle

Hall

Denny

et al. 1989

Biochemical Journal

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1H- and 31P-n.m.r. spectroscopy were used to characterize the solution structure of the 1:1 complex formed between the antitumour antibiotic luzopeptin and the self-complementary hexanucleotide d(5'-GCATGC)2. Eighteen nuclear Overhauser effects between antibiotic and nucleotide protons, together with ring-current-induced perturbations to base-pair and quinoline 1H resonances, define the position and orientation of the bound drug molecule. Luzopeptin binds in the minor groove of the DNA with full retention of dyad symmetry, its quinoline chromophores intercalating at the 5'-CpA and 5'-TpG steps and its depsipeptide ring spanning the central two A.T base-pairs. The chromophores stack principally on the adenine base with their carbocyclic rings pointing towards the deoxyribose of the cytosine. There is no evidence for Hoogsteen base-pairing in the complex, all glycosidic bond angles and sugar puckers being typical of B-DNA as found for the free hexanucleotide. The 'breathing' motions of the A.T and internal G.C base-pairs are substantially slowed in the complex compared with the free DNA, and the observation that two phosphate resonances are shifted downfield by at least 0.5 p.p.m. in the 31P-n.m.r. spectrum of the complex suggests pronounced local helix unwinding at the intercalation sites. The data are consistent with a model of the complex in which luzopeptin bisintercalates with its depsipeptide essentially in the conformation found in the crystal of the free antibiotic [Arnold & Clardy (1981) J. Am. Chem. Soc. 103, 1243-1244]. We postulate only one conformational change within the peptide ring, which involves rotation of the pyridazine-glycine amide group linkage by 90 degrees towards the DNA surface. This manoeuvre breaks the glycine-to-glycine transannular hydrogen bonds and enables the glycine NH groups to bond to the thymine O-2 atoms of the sandwiched A.T base-pairs. It also shortens the major axis of the depsipeptide so that the interchromophore distance is more suitable for spanning two base-pairs. The model further implies that the carboxy and hydroxy groups of the L-beta-hydroxyvaline residue are appropriately positioned for hydrogen-bonding to the 2-amino group of guanine and the O-2 atom of cytosine of the adjacent G.C base-pair.

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Section: Results and Discussion Symmetry Of The Complex And Evidence mentioning

confidence: 94%

“…chemical shifts are referenced to the resonance from the phosphate buffer at pH 7.0. 'H and 31P resonance assignments for d(GCATGC)2, as well as 'H assignments for luzopeptin, have been reported previously [7,15,16].…”

Section: Introductionmentioning

confidence: 86%

Interaction of the antitumour antibiotic luzopeptin with the hexanucleotide duplex d(5′-GCATGC)2. One-dimensional and two-dimensional n.m.r. studies

Searle

Hall

Denny

et al. 1989

Biochemical Journal

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“…Apart from X-ray diffraction [3,4] and multidimensional nuclear magnetic resonance [5,6], vibrational spectroscopy has been applied to identify particular functional groups along with their local interactions and to characterize different helix structures of DNA oligomers in their native aqueous environment [7,8]. The infrared spectra of DNA are highly congested with numerous overlapping absorption bands in the fingerprint range and broad, essentially structureless spectral envelopes in the range between 3100 and 4000 cm À1 .…”

Section: Introductionmentioning

confidence: 99%

Ultrafast dynamics of N–H and O–H stretching excitations in hydrated DNA oligomers

et al. 2009

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“…Even though such possibilities have been suggested earlier [29,30], their application to large DNA molecules has remained limited due to inadequate sensitivity in the previously used 3~p-1H J correlation schemes. The procedure utilises the fact that each phosphorous spin P(i) is coupled to the H3' proton of the preceding nucleotide unit (i-1) and the H4' proton belonging to the same nucleotide (i).…”

Section: Assignment Of Non-exchangeable 1h and 31p Spinsmentioning

confidence: 99%

Inosine — Adenosine base pairing in d-GGTACIAGTACC: Duplex and hairpin with a two-base loop

et al. 1994

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Adstract. An oligonucleotide dodecamer d-GGTAClAGTACC containing two inosine-adenosine mismatched base-pairs has been studied by ~H and 3~p NMR spectroscopy. Unique assignments of ~H and ~rp spins have been achieved by using a recently proposed two-dimensional heteronuclear long range correlation (2D-HELCO) teehnique. The 2D nuclear Overhauser enhancement speclroscopy (NOESY) speclrum recorded in a mixed solvent of 90 % 1-I20 + 10 % 2H20 has been used to assign all the exchangeable imino and amino proton resonanees. NMR results indieate that at concentmtions above 5 mM, the molecule adopts a duplex structure where the inosine imino protons are hydrogen bonded. Crossstrand NOEs between the imino proton of 16 and H2 proton of A7 and that between I4_2 of 16 and H2 of A7 provide evidence for inosine-adenosine base-pairing, with both bases 16 and A7 in anti conformation. The observed NOE eonnectivifles dl, a'2 and d3 from almost the middle of the molecule to the two ends are consistent with a ¡ handed B-DNA conformation. However, the molecule adopts a more extended conformation in the mismatch regiun to aceomodate the bulky purine-purine (lA) base pairs. NMR experiments at lower concentrations indicate the coexistente of a monomeric hairpin with a two base loop, eonsisting of 16 and A7 units, in equilibrium with the duplex. 2D-ROESY expe¡ at such a concenlration shows that the conformation of the stem of the hairpin does not deviate much fi'om the corresponding region of the duplex and four nucleotides C5, I6, A7 and G8 undergo significant structural changes during the formation of hairpin loop.

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Sequence‐specific assignment of the backbone ¹H‐ and ³¹P‐nmr lines in a short DNA duplex with homo‐ and heteronuclear correlated spectroscopy

Cited by 44 publications

References 26 publications

Interaction of the antitumour antibiotic luzopeptin with the hexanucleotide duplex d(5′-GCATGC)2. One-dimensional and two-dimensional n.m.r. studies

Interaction of the antitumour antibiotic luzopeptin with the hexanucleotide duplex d(5′-GCATGC)2. One-dimensional and two-dimensional n.m.r. studies

Ultrafast dynamics of N–H and O–H stretching excitations in hydrated DNA oligomers

Inosine — Adenosine base pairing in d-GGTACIAGTACC: Duplex and hairpin with a two-base loop

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Sequence‐specific assignment of the backbone 1H‐ and 31P‐nmr lines in a short DNA duplex with homo‐ and heteronuclear correlated spectroscopy

Cited by 44 publications

References 26 publications

Interaction of the antitumour antibiotic luzopeptin with the hexanucleotide duplex d(5′-GCATGC)2. One-dimensional and two-dimensional n.m.r. studies

Interaction of the antitumour antibiotic luzopeptin with the hexanucleotide duplex d(5′-GCATGC)2. One-dimensional and two-dimensional n.m.r. studies

Ultrafast dynamics of N–H and O–H stretching excitations in hydrated DNA oligomers

Inosine — Adenosine base pairing in d-GGTACIAGTACC: Duplex and hairpin with a two-base loop

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Sequence‐specific assignment of the backbone ¹H‐ and ³¹P‐nmr lines in a short DNA duplex with homo‐ and heteronuclear correlated spectroscopy