Parameters for proton chemical shift calculation in oligoribonucleotides

Hader, P. A.; Alkema, Dirk; Bell, Russell A.; Neilson, Thomas

doi:10.1039/c39820000010

Cited by 18 publications

(12 citation statements)

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“…The NMR assignments of the tetramers (Table II) were based essentially on incremental analysis methods (Borer et al, 1975;Everett et al, 1980), and the assignments were confirmed with a computer program designed to predict RNA chemical shifts (Hader et al, 1982).…”

Section: Resultsmentioning

confidence: 99%

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Relative stability of guanosine-cytidine diribonucleotide cores: a proton NMR assessment

Sinclair¹,

Alkema²,

Ra³

et al. 1984

Biochemistry

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Proton NMR was used to study the secondary structure and melting behavior of six self-complementary oligoribonucleotide tetramers, each containing two guanosine and two cytidine residues (GGCC, CCGG, GCCG, CGGC, GCGC, and CGCG). GGCC and CCGG formed perfect duplexes containing four G.C base pairs with Tms of 54 and 47.8 degrees C, respectively; GCCG and CGGC formed staggered duplexes with two G.C base pairs and four 3' double-dangling bases, with Tms of 35.5 and 29.2 degrees C, respectively; GCGC formed a perfect duplex with a Tm of 49.9 degrees C, while CGCG formed a staggered duplex with a Tm of 36.9 degrees C. From these results, an order of stability of the cores containing two G.C base pairs was proposed: GC:GC is more stable than GG:CC which is more stable than CG:CG. The RY model for secondary structure stability prediction was applied to the above tetramers with reasonable success. Suggestions for refinements are discussed.

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Section: Resultsmentioning

confidence: 99%

“…cCalculated from UV spectrophotometric data by assuming a 90% hypochromicity factor. parameter set devised byHader et al (1982). The assignments were then further refined by application of the incremental analysis technique(Borer et al, 1975;Everett et al, 1980) by using the assigned shifts of the precursor dimers, trimers,…”

mentioning

confidence: 99%

Relative stability of guanosine-cytidine diribonucleotide cores: a proton NMR assessment

Sinclair¹,

Alkema²,

Ra³

et al. 1984

Biochemistry

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show abstract

“…These resonances are resolved by only 0.006 ppm and could not be distinguished in the NOE spectrum. The NOE approach takes less time than incremental analysis (Borer et al, 1975) and is more direct than empirical shift parameters (Hader et al, 1982). Thus it should be useful for oligomer studies.…”

Section: Discussionmentioning

confidence: 99%

Nuclear Overhauser studies of CCGGAp, ACCGGp, and ACCGGUp

Petersheim¹,

Turner²

1983

Biochemistry

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Nuclear Overhauser effect (NOE) measurements are reported for the nonexchangeable base and ribose 1' proton resonances of CCGGAp, ACCGGp, and ACCGGUp. The results permit assignment of these resonances to particular nucleotides in the sequences. The NOE data rule out conformations containing syn glycosidic linkages and conformations in which the purine 8 and pyrimidine 6 protons are closer to the 3' nearest-neighbor ribose 1' proton than to the 5' nearest-neighbor ribose 1' proton.

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“…Although convergence quickly sets in, the mean absolute error (MAE, relative to the results of the most elaborate model) only drops below 0.1 ppm once 7 nucleotide pairs are included. This corresponds to the methodology of the very first empirical 1 H chemical shift prediction methods 82,83 where also the three nearest nucleotide pairs on 39 and 59 side are taken into account.…”

Section: Resultsmentioning

confidence: 99%

Accurate prediction of 1H chemical shifts in interstrand cross-linked DNA

et al. 2013

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Structural analysis of modified DNA with NMR is becoming ever more difficult with increasingly complex\ud compounds under scrutiny for use in medical diagnosis, therapeutics, material science and chemical\ud synthesis. To facilitate this process, we developed a molecular modeling approach to predict proton\ud chemical shifts in sufficient agreement with experimental NMR measurements to guide structure\ud elucidation. It relies on a QM/MM partitioning scheme and first principle calculations to predict the spatial\ud structure and calculate corresponding proton chemical shifts. It is shown that molecular dynamics\ud simulations that take into account solvent and temperature effects properly are of utmost importance to\ud sample the conformational space sufficiently. The proposed computational procedure is applicable to\ud modified oligonucleotides and DNA, attaining a mean error for the proton chemical shifts of less than 0.2\ud ppm. Here, it is applied on the Drew–Dickerson d(CGCGAATTCGCG)2 dodecamer as a benchmark system\ud and the mispair-aligned N3T-ethyl-N3T cross-linked d(CGAAAT*TTTCG)2 undecamer, illustrating its use as\ud computational tool to assist in structure elucidation. For the proton chemical shifts in the cross-linked\ud system our methodology yields a strikingly superior description, surpassing the predictive power of (semi-)\ud empirical methods. In addition, our methodology is the only one available to make an accurate prediction\ud for the protons in the actual cross-link. To the best of our knowledge, this is the first computational study\ud that attempts to determine the chemical shifts of oligonucleotides of this size and at this level of\ud complexity

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Parameters for proton chemical shift calculation in oligoribonucleotides

Cited by 18 publications

References 1 publication

Relative stability of guanosine-cytidine diribonucleotide cores: a proton NMR assessment

Relative stability of guanosine-cytidine diribonucleotide cores: a proton NMR assessment

Nuclear Overhauser studies of CCGGAp, ACCGGp, and ACCGGUp

Accurate prediction of 1H chemical shifts in interstrand cross-linked DNA

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