Stereoelectronic effects in biomolecules

Gorenstein, David G.

doi:10.1021/cr00081a009

Cited by 182 publications

(127 citation statements)

References 90 publications

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“…The enzyme's binding properties, coupled with catalytic functionalities strategically placed with the active site, decrease the activation energy for the reaction. 3,4 To be an efficient enzyme mimic, the designed molecule therefore needs to possess a binding cavity or site that is able to selectively recognize and bind a desired substrate, which in the next step has to be converted at a catalytic center in its direct proximity. Finally, and in the design of many artificial enzymes this has proven to be a major bottleneck, the catalyst should be able to release the converted substrate and have the ability to be regenerated; that is, turnover has to occur.…”

Section: Covalent Systemsmentioning

confidence: 99%

“…In another biomimetic approach, CaCO 3 was synthesized exclusively inside micrometer-sized polyelectrolyte capsules. 280 Urea hydrolysis, catalyzed by urease, led to the fermentative formation of CO 3 2-ions and the precipitation of CaCO 3 , which completely filled the capsule interior. The LbL approach was also adopted by Ghan et al to polymerize phenols within polyelectrolyte micro- capsules.…”

Section: Other Polymeric Systems As Nanoreactorsmentioning

confidence: 99%

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Self‐Assembled Nanoreactors

et al. 2005

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Section: Covalent Systemsmentioning

confidence: 99%

Section: Other Polymeric Systems As Nanoreactorsmentioning

confidence: 99%

Self‐Assembled Nanoreactors

et al. 2005

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“…As discussed in more detail below, two of the most important parameters controlling 31 P chemical shifts in phosphate esters are the P-O torsional angles (in nucleic acids the P-O5′ (α) and P-O3′ (ζ) torsional angles (65,66) and the C-O5′ (β) and C-O3′ (ε) torsional angles) ( 67,68), although the P-O torsional angle may be more important. Using the selective 2D-J resolved long-range correlation experiment, we can measure the three-bond H3′-C3′-O-P coupling constant (listed in table I) for each of the phosphates in the decamer (48,63).…”

Section: Positional and Sequence-specific Variation Of 31 P Chemical mentioning

confidence: 99%

Two-Dimensional¹H and³¹P NMR Spectra of a Decamer Oligodeoxyribonucleotide Duplex and a Quinoxaline ([MeCys³, MeCys⁷]TANDEM) Drug Duplex Complex

Powers

Olsen

Gorenstein

1989

Journal of Biomolecular Structure and Dynamics

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Assignment of the 1 H and 31 P NMR spectra of a decamer oligodeoxyribonucleotide duplex, d(CCCGATCGGG), and its quinoxaline ([MeCys 3 , MeCys 7 ]TANDEM) drug duplex complex has been made by two-dimensional 1 H-1 H and heteronuclear 31 P-1 H correlated spectroscopy. The 31 P chemical shifts of this 10 base pair oligonucleotide follow the general observation that the more internal the phosphate is located within the oligonucleotide sequence, the more upfield the 31 P resonance occurs. While the 31 P chemical shifts show sequence-specific variations, they also do not generally follow the Calladine "rules" previously demonstrated. 31 P NMR also provides a convenient monitor of the phosphate ester backbone conformational changes upon binding of the drug to the duplex. Although the quinoxaline drug, [MeCys 3 , MeCys 7 ]TANDEM, is generally expected to bind to duplex DNA by bis-intercalation, only small 31 P chemical shift changes are observed upon binding the drug to duplex d(CCCGATCGGG). Additionally, only small perturbations in the 1 H NMR and UV spectra are observed upon binding the drug to the decamer, although association of the drug stabilizes the duplex form relative to the other states. These results are consistent with a nonintercalative mode of association of the drug. Modeling and molecular mechanics energy minimization demonstrate that a novel structure in which the two quinoxaline rings of the drug binds in the minor groove of the duplex is possible.

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“…(29,(33)(34)(35). Theoretical studies have shown that of the six torsional angles that define the sugar phosphate backbone, the conformation of the α: O3′-P-O5′-C5′ and ζ: C3′-O3′-P-O5′ torsional angles appear to be most important in determining the 31 P chemical shifts (29,35,36).…”

Section: Introductionmentioning

confidence: 99%

“…Initial studies on duplex oligonucleotides have shown that 31 P chemical shifts are dependent upon position of the phosphate residue as well as sequence (33,35,37,40). That is, the more centralized the phosphate is within the oligonucleotide duplex the more upfield is its associated 31 P chemical shift; this is referred to as the "positional relationship."…”

Section: Introductionmentioning

confidence: 99%

TWo-Dimensional¹H and³¹P NMR Spectra and Restrained Molecular Dynamics Structure of an Oligodeoxyribonucleotide Duplex Refined via a Hybrid Relaxation Matrix Procedure

Powers

Jones

Gorenstein

1990

Journal of Biomolecular Structure and Dynamics

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Assignment of the 1 H and 31 P resonances of a decamer DNA duplex, d(CGCTTAAGCG)2 was determined by two-dimensional COSY, NOESY, and 1 H-31 P Pure Absorption phase Constant time (PAC) heteronuclear correlation spectroscopy. The solution structure of the decamer was calculated by an iterative hybrid relaxation matrix method combined with NOESY-distance restrained molecular dynamics. The distances from the 2D NOESY spectra were calculated from the relaxation rate matrix which were evaluated from a hybrid NOESY volume matrix comprising elements from the experiment and those calculated from an initial structure. The hybrid matrix-derived distances were then used in a restrained molecular dynamics procedure to obtain a new structure that better approximates the NOESY spectra. The resulting partially refined structure was then used to calculate an improved theoretical NOESY volume matrix which is once again merged with the experimental matrix until refinement is complete. JH3′-P coupling constants for each of the phosphates of the decamer were obtained from 1 H-31 P J-resolved selective proton flip 2D spectra. By using a modified Karplus relationship the C4′-C3′-O3′-P torsional angles (ε) were obtained. Comparison of the 31 P chemical shifts and JH3′-P coupling constants of this sequence has allowed a greater insight into the various factors responsible for 31 P chemical shift variations in oligonucleotides. It also provides an important probe of the sequence-dependent structural variation of the deoxyribose phosphate backbone of DNA in solution. These correlations are consistent with the hypothesis that changes in local helical structure perturb the deoxyribose phosphate backbone. The variation of the 31 P chemical shift, and the degree of this variation from one base step to the next is proposed as a potential probe of local helical conformation within the DNA double helix. The pattern of calculated ε and ζ torsional angles ( 1 9 9 0 ) 2 from the restrained molecular dynamics refinement agrees quite well with the measured JH3′-P coupling constants. Thus, the local helical parameters determine the length of the phosphodiester backbone which in turn constrains the phosphate in various allowed conformations.

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Stereoelectronic effects in biomolecules

Cited by 182 publications

References 90 publications

Self‐Assembled Nanoreactors

Self‐Assembled Nanoreactors

Two-Dimensional¹H and³¹P NMR Spectra of a Decamer Oligodeoxyribonucleotide Duplex and a Quinoxaline ([MeCys³, MeCys⁷]TANDEM) Drug Duplex Complex

TWo-Dimensional¹H and³¹P NMR Spectra and Restrained Molecular Dynamics Structure of an Oligodeoxyribonucleotide Duplex Refined via a Hybrid Relaxation Matrix Procedure

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Stereoelectronic effects in biomolecules

Cited by 182 publications

References 90 publications

Self‐Assembled Nanoreactors

Self‐Assembled Nanoreactors

Two-Dimensional1H and31P NMR Spectra of a Decamer Oligodeoxyribonucleotide Duplex and a Quinoxaline ([MeCys3, MeCys7]TANDEM) Drug Duplex Complex

TWo-Dimensional1H and31P NMR Spectra and Restrained Molecular Dynamics Structure of an Oligodeoxyribonucleotide Duplex Refined via a Hybrid Relaxation Matrix Procedure

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Two-Dimensional¹H and³¹P NMR Spectra of a Decamer Oligodeoxyribonucleotide Duplex and a Quinoxaline ([MeCys³, MeCys⁷]TANDEM) Drug Duplex Complex

TWo-Dimensional¹H and³¹P NMR Spectra and Restrained Molecular Dynamics Structure of an Oligodeoxyribonucleotide Duplex Refined via a Hybrid Relaxation Matrix Procedure