Nejvíce citovaný článek - PubMed ID 12810024
Internal consistency of NMR data obtained in partially aligned biomacromolecules
S3EPY is a Python extension to the program Sparky written to facilitate the assessment of coupling constants from in-phase/antiphase and spin-state-selective excitation (S(3)E) experiments. It enables the routine use of small scalar couplings by automating the coupling evaluation procedure. S3EPY provides an integrated graphical user interface to programs which outputs graphs and the table of determined couplings.
We describe a novel, fundamental property of nucleobase structure, namely, pyramidilization at the N1/9 sites of purine and pyrimidine bases. Through a combined analyses of ultra-high-resolution X-ray structures of both oligonucleotides extracted from the Nucleic Acid Database and isolated nucleotides and nucleosides from the Cambridge Structural Database, together with a series of quantum chemical calculations, molecular dynamics (MD) simulations, and published solution nuclear magnetic resonance (NMR) data, we show that pyramidilization at the glycosidic nitrogen is an intrinsic property. This property is common to isolated nucleosides and nucleotides as well as oligonucleotides-it is also common to both RNA and DNA. Our analysis suggests that pyramidilization at N1/9 sites depends in a systematic way on the local structure of the nucleoside. Of note, the pyramidilization undergoes stereo-inversion upon reorientation of the glycosidic bond. The extent of the pyramidilization is further modulated by the conformation of the sugar ring. The observed pyramidilization is more pronounced for purine bases, while for pyrimidines it is negligible. We discuss how the assumption of nucleic acid base planarity can lead to systematic errors in determining the conformation of nucleotides from experimental data and from unconstrained MD simulations.
- MeSH
- deoxyadenosiny chemie MeSH
- deoxycytidin chemie MeSH
- dusík chemie MeSH
- krystalografie rentgenová MeSH
- nukleární magnetická rezonance biomolekulární MeSH
- oligonukleotidy chemie MeSH
- počítačová simulace MeSH
- purinové nukleosidy chemie MeSH
- purinové nukleotidy chemie MeSH
- puriny chemie MeSH
- pyrimidinové nukleosidy chemie MeSH
- pyrimidinové nukleotidy chemie MeSH
- pyrimidiny chemie MeSH
- sacharidy chemie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- 2'-deoxyadenosine MeSH Prohlížeč
- deoxyadenosiny MeSH
- deoxycytidin MeSH
- dusík MeSH
- oligonukleotidy MeSH
- purinové nukleosidy MeSH
- purinové nukleotidy MeSH
- puriny MeSH
- pyrimidinové nukleosidy MeSH
- pyrimidinové nukleotidy MeSH
- pyrimidiny MeSH
- sacharidy MeSH
The paper presents a set of two-dimensional experiments that utilize direct (13)C detection to provide proton-carbon, carbon-carbon and carbon-nitrogen correlations in the bases of nucleic acids. The set includes a (13)C-detected proton-carbon correlation experiment for the measurement of (13)C-(13)C couplings, the CaCb experiment for correlating two quaternary carbons, the HCaCb experiment for the (13)C-(13)C correlations in cases where one of the carbons has a proton attached, the HCC-TOCSY experiment for correlating a proton with a network of coupled carbons, and a (13)C-detected (13)C-(15)N correlation experiment for detecting the nitrogen nuclei that cannot be detected via protons. The IPAP procedure is used for extracting the carbon-carbon couplings and/or carbon decoupling in the direct dimension, while the S(3)E procedure is preferred in the indirect dimension of the carbon-nitrogen experiment to obtain the value of the coupling constant. The experiments supply accurate values of (13)C and (15)N chemical shifts and carbon-carbon and carbon-nitrogen coupling constants. These values can help to reveal structural features of nucleic acids either directly or via induced changes when the sample is dissolved in oriented media.
- MeSH
- izotopy dusíku MeSH
- izotopy uhlíku MeSH
- nukleární magnetická rezonance biomolekulární metody MeSH
- nukleové kyseliny chemie MeSH
- protony MeSH
- puriny chemie MeSH
- pyrimidiny chemie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- izotopy dusíku MeSH
- izotopy uhlíku MeSH
- nukleové kyseliny MeSH
- protony MeSH
- puriny MeSH
- pyrimidiny MeSH
