Influence of dA · dT and d(2aminoA) · dT base pairs on the B⇄Z transition of DNA fragments

Cavaillès, Jean-Aristide; Neumann, Jean‐Michel; Tran-Dinh, S.; Huynh‐Dinh, Tam; d’Estaintot, Béatrice Langlois; Igolen, J.

doi:10.1111/j.1432-1033.1985.tb08735.x

Cited by 15 publications

(10 citation statements)

References 14 publications

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“…Similar effects are seen for the base signals of core residues in d(G-A-G-A-T-C-T-C)2. Chemical shift changes for 'H and 31P resonances of nuclei located in the core of intact duplexes have been reported for other DNA oligonucleotides [26,36,41,43,46, 47, 51, 521. These findings suggest that small and local conformational changes occur in the core of the intact duplex before melting takes place.…”

Section: Temperature-dependent Conformational Behaviourmentioning

confidence: 99%

Influence of the base sequence on the conformational behaviour of DNA polynucleotides in solution

Rinkel¹,

Marel²,

Boom³

et al. 1987

Eur J Biochem

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. Assignments, based upon one-dimensional NOE and homonucleardecoupling and two-dimensional correlated and NOE spectroscopies are given of the resonances of most of the base and sugar protons. Chemical shift vs temperature profiles, constructed for all samples, yielded insight into the temperature-and concentration-dependent conformational behaviour of the compounds and were used to obtain thermodynamic parameters pertaining to the stacked-single-strand + random-coil and duplex randomcoil equilibria. Vicinal proton-proton couplings were analyzed in terms of the conformation of the deoxyribose rings in the single-stranded tetramers and duplexed octamers.The NOE patterns, chemical shift profiles, imino-proton resonances and coupling data revealed that the compounds adopt B-DNA-like structures. The ratio duplexed/stacked-single-strand/random coil depends upon external conditions as well as upon base sequence. The thermodynamic data indicate that: (a) in terms of singlehelical stacking, the R-R steps ( T , 321 -328 K) appear more stable than the Y-R or R-Y steps (T, 308 -316 K) and the Y-Y steps score least (T, 290-300 K), and (b) the duplexes consisting of alternating, d(Y-R),, strands are more stable, in terms of AH", compared to the d(R-R), . d(Y-Y)" duplexes. The analyses of the couplings demonstrated that the sugars of the single-stranded tetramers and duplexed octamers occur as a blend of N -and S-type conformers, with a preference for the S-type (C2'-endo) sugar conformation: upon duplex formation, no significant shift in the N-type/S-type ratio was observed. The fraction S-type sugar conformation of a given residue, % S , in the stacked-single strands was found to depend upon the nature of its own base and that of the adjacent residues: sugars in an R-R stretch display high values of % S (90-loo), whereas those in Y-Y stretches show relatively low values (z 65). It appears that a good stacking interaction between bases goes hand-in-hand with high values of % S.

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Section: Temperature-dependent Conformational Behaviourmentioning

confidence: 99%

Influence of the base sequence on the conformational behaviour of DNA polynucleotides in solution

Rinkel¹,

Marel²,

Boom³

et al. 1987

Eur J Biochem

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“…For the experiments, the peptides were synthesized by standard Fmoc chemistry. The experimental IR spectra were recorded using the Fourier transform ion cyclotron (FT-ICR) mass spectrometer [16] at the free-electron laser FELIX [17]. Ions were brought into the gas-phase by electrospray ionization (ESI) (∼ 1 mg of peptide in 900 µl TFA/100 µl H 2 O) and mass selected and trapped inside the ICR cell which is optically accessible.…”

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confidence: 99%

Secondary Structure of Ac-Ala_n-LysH⁺ Polyalanine Peptides (n = 5,10,15) in Vacuo: Helical or Not?

Rossi

Blüm

Kupser

et al. 2010

J. Phys. Chem. Lett.

146

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The polyalanine-based peptide series Ac-Alan-LysH + (n=5-20) is a prime example that a secondary structure motif which is well-known from the solution phase (here: helices) can be formed in vacuo. We here revisit this conclusion for n=5,10,15, using density-functional theory (van der Waals corrected generalized gradient approximation), and gas-phase infrared vibrational spectroscopy. For the longer molecules (n=10,15) α-helical models provide good qualitative agreement (theory vs. experiment) already in the harmonic approximation. For n=5, the lowest energy conformer is not a simple helix, but competes closely with α-helical motifs at 300 K. Close agreement between infrared spectra from experiment and ab initio molecular dynamics (including anharmonic effects) supports our findings.

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“…Ions were injected into a home-built FT-ICR mass spectrometer described in detail elsewhere. 22 Instrument operating parameters, such as desolvation temperature, cone voltage, and ion accumulation and transfer optics voltages, were optimized to maximize formation of TEPþK þ and transfer of the species to the ICR cell. Dry nitrogen ($328C) was used to assist in the desolvation process.…”

Section: Experimental Esi Fourier Transform Ion Cyclotron Resonance (mentioning

confidence: 99%

“…IR spectra of gaseous coordination complexes can be generated using tandem mass spectrometry and (wavelength-selective) infrared multiple photon dissociation (IRMPD) spectroscopy. 15,16 In the IRMPD experiment, coordination complexes are transferred from the solution phase to the solvent-controlled environment of a trapped ion mass spectrometer using electrospray ionization (ESI). After isolation, complexes are irradiated at mid-IR wavelengths using a free electron laser (FEL).…”

mentioning

confidence: 99%

Infrared spectrum of potassium‐cationized triethylphosphate generated using tandem mass spectrometry and infrared multiple photon dissociation

Groenewold

Leavitt

Dain

et al. 2009

Rapid Comm Mass Spectrometry

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Tandem mass spectrometry and wavelength-selective infrared photodissociation were used to generate an infrared spectrum of gas-phase triethylphosphate cationized by attachment of K(+). Prominent absorptions were observed in the region of 900 to 1300 cm(-1) that are characteristic of phosphate P=O and P-O-R stretches. The relative positions and intensities of the IR absorptions were reproduced well by density functional theory (DFT) calculations performed using the B3LYP functional and the 6-31+G(d), 6-311+G(d,p) and 6-311++G(3df,2pd) basis sets. Because of good correspondence between experiment and theory for the cation, DFT was then used to generate a theoretical spectrum for neutral triethylphosphate, which in turn accurately reproduces the IR spectrum of the neat liquid when solvent effects are included in the calculations.

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Influence of dA · dT and d(2aminoA) · dT base pairs on the B⇄Z transition of DNA fragments

Cited by 15 publications

References 14 publications

Influence of the base sequence on the conformational behaviour of DNA polynucleotides in solution

Influence of the base sequence on the conformational behaviour of DNA polynucleotides in solution

Secondary Structure of Ac-Ala_n-LysH⁺ Polyalanine Peptides (n = 5,10,15) in Vacuo: Helical or Not?

Infrared spectrum of potassium‐cationized triethylphosphate generated using tandem mass spectrometry and infrared multiple photon dissociation

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Influence of dA · dT and d(2aminoA) · dT base pairs on the B⇄Z transition of DNA fragments

Cited by 15 publications

References 14 publications

Influence of the base sequence on the conformational behaviour of DNA polynucleotides in solution

Influence of the base sequence on the conformational behaviour of DNA polynucleotides in solution

Secondary Structure of Ac-Alan-LysH+ Polyalanine Peptides (n = 5,10,15) in Vacuo: Helical or Not?

Infrared spectrum of potassium‐cationized triethylphosphate generated using tandem mass spectrometry and infrared multiple photon dissociation

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Product

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Secondary Structure of Ac-Ala_n-LysH⁺ Polyalanine Peptides (n = 5,10,15) in Vacuo: Helical or Not?