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E Sletten

Publications and source records attributed to E Sletten.

At least 19 recordsLinked to original sources
PubMed2003

Sequence-selective metalation of double-helical oligodeoxyribonucleotides with PtII, MnII, and ZnII ions.

Reactions of [PtCl(dien)](+) (dien=diethylenetriamine), Mn(2+) and Zn(2+) ions with three different double-helical oligodeoxyribonucleotides, which contain the central sequence GGXY (XY=AT, TA or CC) have been monitored by NMR spectroscopy. 2 D [(1)H, (15)N] HSQC/HMQC NMR spectroscopy using (15)N-labeled Pt(dien) shows that the rate of formation of 3'-G-N 7 and 5'-G-N 7 platinated adducts is highly sequence dependent. The relative rates of platination of 5'-G versus 3'-G are largest for the sequence -GGCC-, for which only a small fraction of the 3'-G adduct is formed; for -GGTA-, the rate of 5'-G platination is about eight times that of 3'-G, and for -GGAT- the ratio is 1.2. These values are in qualitative agreement with those obtained for G-N 7/Mn(2+) selectivity as determined by paramagnetic line broadening of the adjacent G-H 8, and also G-N 7/Zn(2+) selectivity as determined by G-H 8 chemical shift changes. Fluctuation in the nucleophilicity of G-N 7 may be explained by variation of the pi-stacking interaction between base residues along the double helix. The reaction mixtures containing platinated 3'-G and 5'-G fractions were separated by HPLC. Since the duplexes are self-complementary, the platinated single strands were readily annealed to duplexes with twofold symmetry and analyzed by 2 D [(1)H, (1)H] NOESY NMR spectroscopy. Unexpectedly, the 5'-G-H 8 resonance signals of both 5'-G and 3'-G platinated duplexes showed large downfield shifts in the range delta=0.3-0.6 ppm, while the 3'-G-H 8 resonance signals in both cases exhibited no, or only slight, upfield shifts. Resonance signals for several other protons in the central region undergo large chemical shift variations induced by platination, indicating that monofunctional binding to DNA leads to appreciable conformational changes.

Base Sequence↗
PubMed2000

Parallel-stranded DNA with Hoogsteen base pairing stabilized by a trans-[Pt(NH3)2]2+ cross-link: characterization and conversion into a homodimer and a triplex.

The oligonucleotides 5'-d(TTTTCTTTTG) and 5'-d(AAAAGAAAAG) were cross-linked with a trans-[Pt(NH3)2]2+ entity via the N7 positions of the 3'-end guanine bases to give parallel-stranded (ps) DNA. At pH 4.2, CD and NMR spectroscopy indicate the presence of Hoogsteen base pairing. In addition, temperature-dependent UV spectroscopy shows an increase in melting temperature for the platinated duplex (35 degrees C) as compared to the non-platinated, antiparallel-stranded duplex formed from the same oligonucleotides (21 degrees C). A monomer-dimer equilibrium for the platinated 20mer is revealed by gel electrophoresis. At pH 4.2, addition of a third strand of composition 5'-d(AGCTTTTCTTTTAG) to the ps duplex leads to the formation of a triple helix with two distinct melting points at 38 degrees C (platinum cross-linked Hoogsteen part) and 21 degrees C (Watson-Crick part), respectively.

Base Pairing↗
PubMed2000

NMR studies on metal complexes of DNA oligomers.

A short overview of NMR spectroscopic applications for the study of metal ion complexes of DNA oligomers is presented. One typical example is given to illustrate the scope of the methods: the NMR structure of a trans-DDP interstrand cross-linked duplex, d(CTCCTG*TGTCTC) x d(GAGATA*AGGAG). The solution structure of this double-stranded DNA oligonucleotide, containing a trans-diammineplatinum(II) interstrand cross-link, was determined using two-dimensional nuclear magnetic resonance (2D NMR) and NOE-restrained molecular dynamics and energy minimization refinement. The duplex is a non-palindromic 12/11-mer with a missing central residue in the lower strand and in addition it contains a GT mismatched base pair. The analysis indicated that an interstrand cross-link is established between G6-N7 of the upper strand and A18-N1 of the lower strand.

Base Sequence↗
PubMed1999

Interaction of cis- and trans-RuCl2(DMSO)4 with the nucleotides GpA, d(GpA), ApG, d(ApG) and d(CCTGGTCC): high-field NMR characterization of the reaction products.

Both cis- and trans-RuCl2(DMSO)4 (cis-Ru and trans-Ru) react with ApG, GpA, d(ApG) and d(GpA) to yield products with bifunctional metal coordination of the bases. For each dinucleotide one major product and several minor species are formed. This is in contrast to previous results on analogous reactions between trans-Ru and d(GpG) where a substantial amount of an intermediate species was found. The rates of reaction between dinucleotides and cis-Ru are approximately 20-fold slower than for trans-Ru. The compounds formed with the two isomers exhibit identical proton NMR spectra, suggesting the same coordination mode for ruthenium in the final product. The two purine bases are coordinated to ruthenium through N7 in a head-to-head conformation with the glycosidic angles being in the anti range. Coupling constants indicate a relatively pure 3'-endo conformation for the 5'-sugar and mainly 2'-endo for the 3'-sugar. The similar bifunctional binding mode of cis- and trans-Ru(II) with dinucleotides as evident from the NMR spectra are in contrast to the different mode of interaction suggested earlier for cis- and trans-Ru complexes with DNA. trans-Ru interacts with the deoxyoctanucleotide d(CCTGGTCC), giving two main products during the first 2 h of incubation time. Four H8 guanine resonances are shifted downfield, characteristic of N7 metal coordination. The products are not analyzed in detail, but it is suggested that the structures may be described as two chiral G(N7/N7) chelates.

Chromatography, High Pressure Liquid↗
PubMed1998

Sequence-dependent binding of metal ion to DNA oligomeres. A comparison of molecular electrostatic potentials with NMR data.

Experimentally observed sequence-selective binding of metal ion to DNA oligonucleotides have been compared with variations of electrostatic potential (EP) along the helix. Calculations of EP have been performed for three atomic models of the oligonucleotide duplex [d(CGCGAATTCGCG)2] using several variants of EP calculations, including a solution of non-linear Poisson-Boltzmann equation (NPBE). N7 atom of guanine adjacent to adenine base was identified as a region with the most negative electrostatic potential in the major groove. The EP value for the Me ion binding site surpasses the value for N7 of other guanines by 10-26% depending on particular duplex conformation. Qualitatively, the sequence dependent variations of EP near guanine N7 atoms are in agreement with the sequence-selective behavior of Mn(II) and Zn(II) ions as revealed by NMR experiments. But the difference in EP between the two most negative regions near guanine N7 atoms does not exceed 1.25 kT/e. Simple model suggests that metal ions are capable to form ion-hydrate complexes with G-Pu steps of DNA duplex. These complexes are formed via one Me...G and five Me...water coordination bonds with water molecules hydrogen bonded to two adjacent purine bases in the same chain. We suppose that such a stereospecific structural possibility is the main factor which control the sequence-selectivity in the metal ion binding. A combination of both mechanisms allows to explain sequence specific Mn(II) and Zn(II) binding to a set of oligonucleotides.

Computer Simulation↗
PubMed1996

Proton nuclear magnetic resonance spectroscopy of serum from patients with colorectal neoplasia.

Proton nuclear magnetic resonance (NMR) spectra of serum have been recorded from patients with colorectal neoplastic polyps, before and after treatment of colorectal cancer, in patients with advanced lung cancer, and also from healthy controls. Digitally defined NMR profiles of the methyl and methylene peaks were used as input for supervised principal component modelling. An unknown sample was classified according to its residual, i.e. the difference between the spectral pattern of the unknown and control group. There was a statistically significant difference between the mean residual in the untreated colorectal cancer group and in controls (P = 0.003). The sensitivity of detecting untreated colorectal cancer was only 20%. There were no stage-dependent differences between the residuals within the untreated colorectal cancer group. After curative surgery, four patients had recurrence of malignant disease without an increase in residual prior to recurrence. Patients with advanced malignant disease (lung cancer WHO stage IIIB and IV) had a highly significant difference in mean residual from that of controls, with a sensitivity of detecting cancer of 87.5%. This increase in residual could not be explained by increase in the level of serum triglyceride. NMR spectroscopy was not a useful diagnostic tool in patients with colorectal neoplastic polyps and cancer.

Adult↗
PubMed1996

Sequence-selective interaction between mercury(II) ions and the DNA dodecamer [d(GCCGATATCGGC)]2 studied by 1H NMR spectroscopy.

The palindromic dodecamer [d(GCCGATATCGGC)]2 has been titrated by Hg(ClO4)2 in order to study sequence dependent HgII ion interactions. The titration pattern as monitored by 1D and 2D 1H NMR is consistent with a transition to a new conformer of the dodecamer induced by HgII ions. At intermediate stages of the titration, the proton signals from the new conformer coexist with those of the original one, indicating slow exchange between the two forms on the NMR timescale. The data clearly show that there is no major alteration in the secondary structure, e.g. B-->Z-form or duplex-->hairpin transition. The intra- and inter-residue sequential walk is completed except for a break between T6 and A7. At a concentration level r = [HgII]/[nucleobase] < 0.20 all four central imino signals are present. This definitely excludes thymine N3 as a possible mercuration site. In the imino region of the spectra HgII ions induce a large upfield shift of the thymine imino resonance T8-N3H, while the other thymine resonance T6-N3H is unperturbed. The guanine imino signal G4-N1H shows a large downfield ring current shift caused by major conformational changes in the duplex. The complete titration experiment indicates that mercury, initially, binds selectively to the A5'-T8 base pair. A tentative model is proposed where mercury is cross-linking the two strands via thymine T8-O4 and the deprotonated amino group of the complementary adenine base A5'.

Cross-Linking Reagents↗
PubMed1995

Sequence-selective metal ion binding to DNA oligomers.

Sequence-selective interactions between DNA oligonucleotides and Pt(II) and Pd(II) complexes have been studied by 1D and 2D NMR spectroscopy. Titration of DNA oligomers with diamagnetic metal ion complexes induces chemical shifts of proton resonances close to the site of interaction. Conformational changes in the helical structure were monitored by measuring cross-peak intensities in 2D NOESY maps. Two duplex deoxynucleotides were studied, [d(CGCGCG)]2 and [d(CGCGAATTCGCG)]2, respectively. The hexamer was titrated in the duplex form with cis-[Pt(NH3)2Cl2]2+ (cis-DDP or cisplatin). The dodecamer was titrated with NO(3-)-salts of Pd(aq)2+, [Pd(en)(H2O)2]2+ and [Pd(dien)(H2O)]+, respectively. The reaction between cis-DDP and the hexamer at conditions where the duplex form is retained proceeded exceedingly slowly. In the initial phase of the titration the NOESY map indicates conformational changes induced by noncovalent adduct formation between the intact hexamer and cis-DDP. The more reactive Pd compounds show a tendency towards sequence-selective binding to the duplex dodecamer. The 'naked' Pd ion is very reactive and exhibits selectivity towards the thymine T8 imino proton and N7 on G4. At a Pd(II)/dodecamer ratio of 4:1 the metal ions induce helix-->coil transition. The mono- and bifunctional Pd complexes with 'bulky' ligands attack the dodecamer at the terminal GC base pairs, leaving the central Watson-Crick base pairs intact.

Base Sequence↗
PubMed1994

Sequence-selective metal ion binding to DNA hexamers.

Base-selective interaction between divalent metal ions and DNA oligomers has been studied by 1D and 2D NMR spectroscopy. Titration with paramagnetic metal ions induces selective line broadening of resonances from protons close to the binding site. Also the intensities of 2D NOESY cross-peaks involving paramagnetic affected protons will be quenched. Two hexamers, 5'-d(CGTACG)2 (I) and 5' (GCATGC)2 (II) have been titrated with Mn(II) ions. Manganese binds selectively to the terminal guanine, G1, in sequence II as manifested through pronounced paramagnetic line broadening and loss of intensities of NOESY cross-peaks involving G-H8 protons. The second guanine, G5, and the non-guanine residues are appreciably less affected. In sequence I both guanines, G2 and G6, are the targets for selective metal binding as judged from G-H8 line broadening. The extent of interaction is almost identical for the two G-residues and comparable to that observed for G1 in sequence II. The metal binding site in the duplexes is most likely nitrogen G-N7. Selective metal binding to oligonucleotides may be related to sequence-dependent variation in molecular electrostatic potentials (MEP) along the chain.

Base Sequence↗
PubMed1993

Investigation of solution structure of d(GAATTTAAATTC)2 by 1H NMR, molecular dynamics, mechanics, refinement by back-calculation of the NOESY spectrum and analysis of this structure using X-ray data.

1H NMR spectroscopy, restrained molecular mechanics and dynamics and refinements after back-calculation of the NOESY spectrum have been performed to study the structure of the d(GAATTTAAATTC)2 duplex and to determine whether it is bent or not. It is found that the duplex adopts a B-type conformation; all sugar conformations belong to the C2' endo region and purines have a larger pseudorotation angle as compared to pyrimidines. The cross-strand AH2(n)-AH1' (m + 1) distance (where (n) and (m) are complementary residues), crucial for an anomalous A/T tract structure, is large on the TA step and gradually decreases at the 3' and 5' ends of the TTTAAA tract and follows the rules proposed previously [Chuprina, V.P., Lipanov, A.A., Fedoroff, O.Yu, Kim, S.G., Kintanar, A., and Reid, B.R., Proc. Natl. Acad. Sci. U.S.A. 88, 9087 (1991)]. The changes in this distance correlate with those in the T1 value for AH2 protons which we measured for several oligonucleotide sequences. A total number of about 250 interproton distance constraints were determined from NOESY spectra and were used for structure determination by molecular mechanics, dynamics and refinement by back-calculations. It is shown that these data are not enough to determine whether the duplex is bent or not. The whole family of B-type conformations including bent and straight structures fit well with the available NMR data. In principle, additional non-NMR data could be used in order to reduce the number of the allowable structures. The refinement of the structures with additional different non-NMR constraints (used as a driving force) on P-P or H1'-H1' minor groove width distances in the TA region shows a very good correlation between these distances and the angle of bending of the dodecamer. The more the minor groove width increases in the TA region the more the duplex is bent at the major groove of this region. On the other hand, there is also a very good correlation between P-P, H1'-H1' and AH2-H1' cross-strand distances as follows from analysis of X-ray B-type structures. These two correlations, together with the increased AH2-H1' cross-strand NMR distance in the TA region of the dodecamer indicate that the duplex should be characterized by a wider minor groove in the TA region and be bent in the major groove in this region.

Base Sequence↗
PubMed1993

Base dependence of B-DNA sugar conformation in solution and in the solid state.

Analysis of 1H-NOESY solution data for eight short DNA duplexes has revealed pronounced differences between the sugar conformations of purine and pyrimidine nucleotides. It was found that the H1'-H4' interproton distance is less than ca. 3.0 A in pyrimidine sugars, while in purine sugars it is more than ca. 3.0A. This difference has been analyzed by comparison with the sugar conformations of highly resolved B-DNA crystal structures and model sugar conformations. The conclusion can be drawn that the deoxyribose conformation is of the general C2'-endo type but pyrimidine sugars are characterized by smaller phase angles of pseudorotation P (90 degrees < P < 150 degrees), while purine sugars have larger P values that are greater than ca. 140 degrees (140 degrees < P < 180 degrees). There is no such clear base dependence of sugar conformation in highly resolved B-DNA crystal structures; however the similar trend can be seen as in the solution studies. Based on B-type DNA crystal structures, J-coupling constants have been calculated, and the applicability of experimental coupling measurements to the determination of sugar conformation is discussed.

Base Sequence↗
PubMed1993

Sequence-selective metal ion binding to DNA oligonucleotides.

Metal ion titrations of several DNA oligonucleotides, 10 dodecamers and one decamer have been monitored by 1H NMR spectroscopy in order to elucidate metal ion binding patterns. Also, the effects of paramagnetic impurities on resonance linewidths and NOESY cross-peak intensities have been reversed by EDTA back-titration experiments. 1H 1D NMR spectra were recorded after successive additions of aliquots of different metal salts to oligonucleotide samples. Paramagnetic manganese(II) salts were used in most cases, but a few samples were also titrated with diamagnetic zinc(II). From this study, we conclude that there exists a sequence-selective metal ion binding pattern. The metal ions bind predominantly to 5'-G in the contexts 5'-GC and 5'-GA. The order of preference seems to be GG > or = GA > GT > > GC. No evidence of metal ion binding to 5'-G in 5'-GC steps or to non-G residues was found. The H6 or H8 resonances on preceding (5'-) bases were affected by the adjacent bound paramagnetic metal ion, but no effect was observed on the protons of the succeeding (3'-) base. The metal binding site in the duplexes is most likely at G-N7, as manifested by the pronounced paramagnetic line broadening or diamagnetic shift of the G-H8 signal. This sequence selectivity may be qualitatively explained by a sequence-dependent variation in the molecular electrostatic potentials of guanine residues (MEPs) along the oligonucleotide chain.

Base Sequence↗
PubMed1993

NMR studies of a plant flavonoid--DNA oligonucleotide complex.

A structural model of the solution complex between a flavonoid and a DNA dodecamer containing the E. coli wild-type lac promoter sequence (TATGTT) was obtained using simulated annealing for refinement. The distance constraints were derived from NOESY NMR spectra. The minor groove binding of this flavonoid displays possible hydrogen bonds to the DNA, and these can take part in complex formation. This work is the first description of how a molecule of this class of natural compounds may interact with DNA.

Base Sequence↗
PubMed1991

The binding of manganese(II) and zinc(II) to the synthetic oligonucleotide d(C-G-C-G-A-A-T-T-C-G-C-G)2. A 1H NMR study.

The interaction of the synthetic oligonucleotide d(C-G-C-G-A-A-T-T-C-G-C-G)2 with two different transition-metal ions has been investigated in aqueous solution by means of 1H NMR spectroscopy. The effects on the DNA due to the presence of manganese(II) or zinc(II) have been monitored by observing the paramagnetic broadening and diamagnetic shifts of the non-exchangeable proton resonance lines, respectively. The 1H NMR spectra acquired during the course of the manganese(II) titration show very distinct broadening effects on certain DNA resonance lines. Primarily, the H8 resonance of G4 is affected, but also the H5 and H6 resonances of C3 are clearly affected by the metal. The results imply that the binding of manganese(II) to DNA is sequence specific. The 1H spectra obtained during the zinc(II) titration reveal diamagnetic shift effects which largely conform with the paramagnetic broadening effects due to the presence of manganese(II), although this picture is somewhat more complex. The H8 resonance of G4 displays a clearly visible high-field shift, while for the other guanosine H8 protons this effect is absent. The H1' and H2' protons of C3 show an effect of similar strength, although in the opposite direction, while H5 and H6 of C3 are only slightly affected. Local differences in the structure of the DNA and the basicities of potential binding sites on different base steps in the sequence might account for the observed sequence selectivity.

Base Sequence↗
PubMed1990

Proton nuclear magnetic resonance spectroscopy of serum lipoproteins in rabbits with implanted VX-2 carcinoma.

Serum from two groups of rabbits, all offspring from the same parents, was subjected to NMR spectroscopy in order to monitor the progress of malignant disease. One group had VX-2 carcinoma implanted in the kidney while the control group were sham-operated with injection of physiological saline. Later, the control group was subjected to dietary restrictions to produce a weight loss equivalent to that of the rabbits with tumor. Progressive cancerous growth with cachexia produced characteristic changes in the lipoprotein spectra distinctly different from those induced by weight loss induced by food intake restrictions. A shoulder on the high-field side of the methylene resonance observed in the control spectra disappeared during the progress of cancerous growth. These spectral changes, however, are not adequately described by line width measurements at half-height as suggested for the original Fossel test.

Animals↗
PubMed1990

Detection of malignant tumours by multivariate analysis of proton magnetic resonance spectra of serum.

Proton magnetic resonance spectra of blood serum have been subjected to multivariate data analysis to discriminate between samples from cancer patients and from controls. The main feature was the use of digitally defined resonance profiles. The methyl and methylene lipoprotein signals centred at 1.3 and 0.9 parts per million are non-lorentzian composite peaks that cannot be described properly by the line width at half-height. Instead 71 and 76 data points were used to describe the methylene and methyl peak profiles, respectively. These data points were used as input to a principal component analysis to distinguish between malignant (n = 29) and control samples (n = 55). At a probability level of 0.01 (F-test) modelling classified all patients except 2 correctly, while 1 control was slightly above the predictive level for malignancy.

Female↗