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  • 1
    ISSN: 1573-5001
    Keywords: DNA ; Conformational analysis ; Mini-hairpin ; Two-base loop
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary The circular DNA decamer 5′-d〈pCGC-TT-GCG-TT〉-3′ was studied in solution by means of NMR spectroscopy and molecular dynamics in H2O. At a temperature of 269 K, a 50/50 mixture of two dumbbell structures (denoted L2L2 and L2L4) is present. The L2L2 form contains three Watson-Crick C-G base pairs and two two-residue loops in opposite parts of the molecule. On raising the temperature from 269 K to 314 K, the L2L4 conformer becomes increasingly dominant (95% at 314 K). This conformer has a partially disrupted G(anti)-C(syn) closing base pair in the 5′-GTTC-3′ loop with only one remaining (solvent-accessible) hydrogen bond between NHα of the cytosine dC(1) and O6 of the guanine dG(8). The opposite 5′-CTTG-3′ loop remains stable. The two conformers occur in slow equilibrium (rate constant 2–20 s−1). Structure determination of the L2L2 and L2L4 forms was performed with the aid of a full relaxation matrix approach (IRMA) in combination with restrained MD. Torsional information was obtained from coupling constants. Coupling constant analysis (3JHH, 3JHP, 3JCP) gave detailed information about the local geometry around backbone torsion angles β, γ, δ and ε, revealing a relatively high flexibility of the 5′-GTTC-3′ loop. The values of the coupling constants are virtually temperature-independent. ‘Weakly constrained’ molecular dynamics in solvent was used to sample the conformational space of the dumbbell. The relaxation matrices from the MD simulation were averaged over 〈r−3〉 to predict dynamic NOE volumes. In order to account for the 1:1 conformational mixture of L2L2 and L2L4 present at 271 K, we also included S2 factors and 〈r−6〉 averaging of the 〈r−3〉-averaged relaxation matrices. On matrix averaging, the agreement of NOE volumes with experiment improved significantly for protons located in the thermodynamically less stable 5′-GTTC-3′ loop. The difference in stability of the 5′-CTTG-3′ and 5′-GTTC-3′ loops is mainly caused by differences in the number of potential hydrogen bonds in the minor groove and differences in stacking overlap of the base pairs closing the minihairpin loops. The syn conformation for dC(1), favored at high temperature, is stabilized by solvation in the major groove. However, the conformational properties of the dC(1) base, as deduced from R-factor analysis and MD simulations, include a large flexibility about torsion angle χ.
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  • 2
    ISSN: 1573-5001
    Keywords: Isl-1 ; homeodomain ; protein ; DNA-binding ; NMR assignment
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational behavior of DNA minihairpin loops is sensitive to the directionality of the base pair that closes the loop. Especially tailored circular dumbbells, consisting of a stem of three Watson-Crick base pairs capped on each side with a minihairpin loop, serve as excellent model compounds by means of which deeper insight is gained into the relative stability and melting properties of hairpin loops that differ only in directionality of the closing pair: C-G vs G-C. For this reason the thermodynamic properties of the circular DNA decamers 5′-d〈pCGC-TT-GCG-TT〉-3′(I) and reference compounds 5′-d〈pGGC-TT-GCC-TT≤-3′(II) and 5′-d(GCG-TC-CGC)-3′(III) are studied by means of nmr spectroscopy. MoleculesIandIIadopt dumbbell structures closed on both sides by a two-membered hairpin hop. At low temperatureIconsists of a mixture of two slowly exchanging forms, denotedL2L2andL2L4. The low-temperatureL2L2form is the fully intact minihairpin structure with three Watson-Crick C-G base pairs. The high-temperature form,L2L4,contains a partially disrupted closing G-C base pair in the 5′-GTTC-3′ loop, with the cytosine base placed in a syn orientation. The opposite 5′-CTTG-3′ loop remains stable. A study of the noncircular hairpin structureIIIshows similar conformational behavior for the 5′-GTTC-3′ loop as found inIa syn orientation for C(6) and two slowly exchanging imino proton signals for G(3). The melting point Tm of IIwas estimated to lie above 365 K. The Tm value of the duplex stem and the 5′-CTTG-3′ loop of theL2L4form ofIis 352 ± 2 K. The ΔH° is calculated as -89 ± 10 kJ/mol. The Tm value determined for the individual residues of the 5′-GTTC-3′ loop lies 4°-11° lower. The enthalpy ΔH° of melting the thymine residues in the 5′-GTTC-3′ loop is calculated to be -61± 7 kJ/mol. Thermodynamic data of the equilibrium between the slowly exchanging two- and four-membered loop conformers of I reveal an upper limit for ΔH° of +30 kJ/mol in going from a two-memberedto a four-membered loop, in agreement with the enthalpy difference of +28 k.j/mol between the two loops at the Tm midpoint. For hairpin III the upper limit for ΔH° going from a two-membered to a four-membered loop amounts to ±21 kJ/mol. The mutual exchange rate between the L2 and L4 form in III is estimated as 13.6 s-1. Our results clearly suggest that small four-way DNA junctions(model for immobilized Holliday junctions) can be designed that consist of a single DNA strandthat features -CTTG-caps on three of the four arms of the junction. © 1995 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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  • 4
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In recent years various examples of highly stable two-residue hairpin loops (miniloops) in DNA have been encountered. As the detailed structure and stability of miniloops appear to be determined not only by the nature and sequence of the two bases in the loop, but also by the closing base pair, it is desirable to carry out in-depth studies of especially designed small model DNA compounds. Therefore, a circular DNA dumbbell-like molecule is tailored to consist of a stem of three Watson-Crick base pairs, flanked on each side by a minihairpin loop. The resulting circular DNA decanter 5′-d〈pCGC- TT-GCG- TT〉 -3′ (I) is studied in solution by means of nmr spectroscope. At a temperature of 269 K the molecule occurs in a 50/50 mixture of two dumbbell structures (denoted L2L2 and L2L4). L2L2 contains three Watson-Crick C-G base pairs and two two-residue loops (H2-family type) in opposite parts of the molecule. On raising the temperature from 269 to 314 K. The L2L4 conformer becomes increasingly dominant (95% at 314 K). This conformer has a partially disrupted closing G-C base pair in the 5′-GTTC-3′ loop with only one remaining solvent-accessible hydrogen bond between NHα of the cytosine C(1) and O6 of the guanine G(8), whereas the opposite 5′-CTTG-3′ loop remains stable.The disruption of the C(1)-G(8) base pair in the L2L4 form is correlated with the presence of a syn orientation for the C(1) base at the 5′-3′ loop-stem junction in the 5′-GTTC-3′ loop. The two conformers. L2L2 and L2L4, occur in slow equilibrium (2-20 s-1). Moderate line broadening of specific 1H, 13C, and 31P resonances of residues C(1), G(8), T(9), and T(10) at low temperatures, due to chemical exchange between L2L2 and L2L4, show that the interconversion from an anti to syn conformer in residue C(1) has a small local effect on the structure of the dumbbell. T1 relaxation measurements, chemical-shift considerations, and complete hand-shape calculations of the exchange process of the G(8) imino proton reveal a possibility for the existence of multiconformational slates in the anti-syn equilibrium. © 1995 John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 0749-1581
    Keywords: Electronegativity ; Proton NMR spectroscopy ; NMR couplings ; Monosbustituted ethanes ; 1,1-Di-substituted ethanes ; Substituent constants ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electronegativity dependence of the torsion angle-independent term in the Karplus equation, i.e. of the ‘constant’ A in the Fourier expansion A + B cos φ + C cos 2φ +…, was investigated. Experimental proton-proton coupling constants of substituted ethanes and isopropanes appeared to be suitable for this purpose. A data set was constructed which contained 70 couplings, newly measured or remeasured at 300 MHz, and 25 couplings taken from the literature. The accuracy of each data point is estimated as ≤0.02 Hz, with a few exceptions. The actual analysis was carried out on 93 data points, i.e. on J values of 55 mono- and of 38 1,1-di-substituted ethanes, including 22 isopropyl derivatives. A total of 55 chemical groups is represented in the set; some of these were taken together, leaving 50 distinct groups. Regression analysis of the present data versus standard electronegativities did not yield acceptable results. Instead, substituent parameters λe, valid for 3J(HH) in saturated H—C—C—H fragments, were derived in a least-squares procedure from the data set. The couplings from mono- and 1,1-di-substituted ethanes could be accounted for in a simple expression that contains an interaction term C012(λ1λ2). The best equation obtained is \documentclass{article}\pagestyle{empty}\begin{document}$$ {}^3J{\rm (HH) = 7}{\rm .84 - 0}{\rm .59(}\lambda _{\rm 1} + \lambda _{\rm 2}) - 0.42(\lambda _{\rm 1} \lambda _{\rm 2}) $$\end{document} The parameters are valid for λe values scaled according to the Huggins electronegativities: λH = 0, λOR = 1.40. The equation fits 84 experimental couplings with a root-mean-square deviation of 0.018 Hz and a maximum deviation of 0.06 Hz. Some exceptions occur. (i) CH3CH3, CH3CHCl2 and CH3CHF2 appear to follow a different, but correlated, regression; (ii) C(=O)H, C(=O)R, SO2Cl and POCl2 groups require different λe values according to the substitution pattern, i.e. mono- or 1,1-di-substitution. The striking difference between the new λe substituent-effect scale and other empirical electronegativity scales lies in the inverse correlation of λe with increasing electronegativity of β-substituents. The inverse relationship is not only found for α-carbon atoms, but appears to represent a general phenomenon, also seen for substituted α-hetero atoms (O, N, S).
    Additional Material: 8 Tab.
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  • 6
    ISSN: 0749-1581
    Keywords: NMR ; 1HNMR ; Coupling constants ; Substituted ethanes ; Substituent electronegativity parameters ; Solvent effects ; Haasnoot equation ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Empirical group electronegativities (substituent parameters λi), valid for 3J(HH) in saturated H—C—C—H fragments, were derived from the coupling to methyl in substituted ethanes and isopropyl derivatives according to the equation \documentclass{article}\pagestyle{empty}\begin{document}$$ \langle {}^3J({\rm{HH)}}\rangle = 7.660 - 0.596(\lambda _1 + \lambda _2) - 0.419(\lambda _1 \lambda _2) $$\end{document} In contrast to earlier work, it was found advantageous to differentiate between the λi values of hydrogen acting as substituent in CH3 as compared with H in CH2. Special attention was paid to solvent effects, in particular the influence of D2O, on the vicinal couplings and thus on λi. The previously derived λi values remain valid in all common organic solvents but a special effect of D2O on λ is manifest in cases where the α-substituent carries one or two non-conjugated lone pairs of electrons that readily act as hydrogen bond acceptors: Δλ= -0.11 ± 0.03 for NH2, NHR, NR2, OH, OR, R = alkyl. Protonation of NH2 to give NH3+ lowers λi by 0.28 units. The λi values for the nucleic acid bases (Ade, Gua, Ura, Thy, Cyt), as determined from the N-isopropyl derivatives, are 0.56 ± 0.01 irrespective of the solvent. Secondary amides display similar values. The parameters of the Haasnoot equation, originally derived with the aid of a Pauling-type electronegativity scale, were reoptimized on the basis of the present λi scale; the previous overall r.m.s. error of 0.48 Hz now drops to 0.36 Hz and separate parameterization of H—C—C—H fragments with different substitution patterns appears to be no longer necessary.
    Additional Material: 3 Ill.
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