Effective water resonance suppression in 1D‐ and 2D‐FT–<sup>1</sup>H‐nmr spectroscopy of biopolymers in aqueous solution

Haasnoot, C. A. G.; Hilbers, Cornelis W.

doi:10.1002/bip.360220502

Cited by 87 publications

(22 citation statements)

References 13 publications

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“…The DNA octamer was synthesized via an improved phosphotriester method (7,8) Imino-proton spectra were recorded with a time-shared pulse as described elsewhere (9). 1H-NMR spectra were recorded on a…”

Section: Methodsmentioning

confidence: 99%

Hairpin and duplex formation of the DNA octamer d(m⁵C-G-m⁵C-G-T-G-m5C-G) in solution. An NMR study

et al. 1986

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Section: Methodsmentioning

confidence: 99%

Hairpin and duplex formation of the DNA octamer d(m⁵C-G-m⁵C-G-T-G-m5C-G) in solution. An NMR study

et al. 1986

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“…In the case of the D20 samples the residual HDO peak was suppressed by irradiation at the HDO frequency. The intensity of the H20 signal in the imino-proton spectra was reduced by means of a time-shared long pulse in combination with a data-shift accumulation routine [9,10].…”

Section: Vd(a-g-c-c-g-t-a-c-t-g-c-a) 3'd(t-c-g-g-c-a)(t-g-a-c-g-t)5'mentioning

confidence: 99%

Conformational and thermodynamic consequences of the introduction of a nick in duplexed DNA fragments: an NMR study augmented by biochemical experiments

et al. 1989

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NMR studies were carried out on various equimolar mixtures consisting of a combination of oligomers: d(ACGGCT) (I), d(pACGGCT) (Ia), d(TGCAGT) (II), d(AGCCGTACTGCA) (III), d(TGCAGTACGGCT) (IV). It is shown that I + II + III (MI) INTRODUCTION [1,2]The role of DNA ligases is well established in DNA replication, in DNA repair and in genetic recombination in prokaryotic and in eukaryotic cells [3]. These enzymes catalyse the restoration of an interruption of a single strand in double-helical DNA. For the joining activity the enzyme requires juxtaposed 3'-hydroxyl and 5'-phosphoryl ends aligned in a duplex structure [4]. The enzymes obtained from unaffected and from T4-infected E. coli have been investigated most thoroughly [4]. However, until now little information is available concerning structural details of the nicked duplex structure.The present work describes an NMR study, augmented with biochemical experiments, of a synthetic nicked duplex structure. The compound consists of a 12 base-paired duplex that features an interruption in the centre of one strand of the double helix. The conformational properties of the nicked duplex are compared with those of the intact doublehelical fragment. Furthermore, the influence of removal of the phosphate at the interruption is demonstrated. Thermodynamic analysis of duplex formation of the nicked as well as of the intact duplex structure is used to study the amount of cooperativity of the two hexamer strands in the melting behaviour of the nicked duplex. Finally, the T4 polynucleotide ligase activity upon this synthetic nicked duplex fragment is reported.

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“…One-dimensional NMR spectroscopy Imino-proton spectra were recorded at 300 MHz on a Bruker WM-300 spectrometer using a time-shared long pulse in combination with the alternate-delay-accumulation (ADA) technique [26]. NMR spectra of the non-exchangeable resonances were recorded at 500 MHz and 300 MHz on a Bruker WM-500 and WM-300 spectrometer respectively.…”

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confidence: 99%

Conformational analysis of the octamer d(G‐G‐C‐C‐G‐G‐C‐C) in aqueous solution

Rinkel

Sanderson

Marel

et al. 1986

European Journal of Biochemistry

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Proton NMR studies in H 2 0 and 'HzO were carried out on the self-complementary DNA octamer d(G-G-C-C-G-G-C-C) and compared with similar studies on the dimethylated analogue d(G-G-m5C-m5C-G-G-C-C) [Sanderson, M. R., Mellema, J.-R., van der Marel, G. A., Wille, G., van Boom, J. H. & Altona, C. (1983) Nucleic Acids Res. 11, 3333-33461. Base, Hl', H2' and H2" resonances were assigned by means of two-dimensional nuclear Overhauser spectroscopy (NOESY) and correlated spectroscopy (COSY) experiments. Chemical shift vs temperature profiles were used to analyze the temperature-dependent conformational behaviour and to extract thermodynamic parameters for the duplex-to-coil transition. Analysis of proton-proton couplings were used to discriminate between J1.2, and J1,2,, and between the H2' and H2" resonances as well as to obtain conformational parameters of the sugar rings. From the NOESY and COSY experiments, the temperature profiles and the analysis of the coupling data it is concluded that: (a) the compound adopts a B-DNA-type helix in solution; (b) the sugar rings in the intact duplex display limited conformational freedom; (c) methylation of the cytosine bases at the C5 position has no measurable effect on the conformational behaviour of the octamer, nor on the conformation of the sugar rings; however, methylation does increase the stability of the duplex in aqueous solution under conditions of low salt concentration.Recent advances in DNA synthesis have opened the possibility of studying oligonucleotides of known specific sequence. So far, X-ray crystallography and high-field NMR spectroscopy have proved powerful tools in the study of the crystalline and solution structure of oligonucleotides, respectively. 2D NMR techniques have opened the way to the study of long DNA fragments. 2D correlation (COSY) experiments have been found useful to establish scalar connectivities between protons. In this way sets of proton resonances can be distinguished, each set belonging to a different sugar residue. In addition, 2D NOE (NOESY) experiments allow one to find intra-and inter-residual connectivities between base and sugar protons and thus to assign many of the resonances in the proton spectra [l -171. NOESY signal intensities serve to determine the helical type [3, 151 and local structural features of oligonucleotide fragments [5, 7, 18, 191 and, finally, to find answers to questions concerning possible differences between Correspondence to C . Altona, Gorlaeus Laboratoria der Rijksuniversiteit te Leiden,

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Effective water resonance suppression in 1D‐ and 2D‐FT–¹H‐nmr spectroscopy of biopolymers in aqueous solution

Cited by 87 publications

References 13 publications

Hairpin and duplex formation of the DNA octamer d(m⁵C-G-m⁵C-G-T-G-m5C-G) in solution. An NMR study

Hairpin and duplex formation of the DNA octamer d(m⁵C-G-m⁵C-G-T-G-m5C-G) in solution. An NMR study

Conformational and thermodynamic consequences of the introduction of a nick in duplexed DNA fragments: an NMR study augmented by biochemical experiments

Conformational analysis of the octamer d(G‐G‐C‐C‐G‐G‐C‐C) in aqueous solution

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Effective water resonance suppression in 1D‐ and 2D‐FT–1H‐nmr spectroscopy of biopolymers in aqueous solution

Cited by 87 publications

References 13 publications

Hairpin and duplex formation of the DNA octamer d(m5C-G-m5C-G-T-G-m5C-G) in solution. An NMR study

Hairpin and duplex formation of the DNA octamer d(m5C-G-m5C-G-T-G-m5C-G) in solution. An NMR study

Conformational and thermodynamic consequences of the introduction of a nick in duplexed DNA fragments: an NMR study augmented by biochemical experiments

Conformational analysis of the octamer d(G‐G‐C‐C‐G‐G‐C‐C) in aqueous solution

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Effective water resonance suppression in 1D‐ and 2D‐FT–¹H‐nmr spectroscopy of biopolymers in aqueous solution

Hairpin and duplex formation of the DNA octamer d(m⁵C-G-m⁵C-G-T-G-m5C-G) in solution. An NMR study

Hairpin and duplex formation of the DNA octamer d(m⁵C-G-m⁵C-G-T-G-m5C-G) in solution. An NMR study