Sites and thermodynamic quantities associated with proton and metal ion interaction with ribonucleic acid, deoxyribonucleic acid, and their constituent bases, nucleosides, and and nucleotides

Izatt, R.M.; Christensen, Jeppe; Rytting, J. Howard

doi:10.1021/cr60273a002

Cited by 756 publications

(451 citation statements)

References 32 publications

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“…Thymine is the less basic nucleoside in solution [44] and in the gas phase [22]. The theoretical calculations have shown that a couple of nucleosides interact through a strong OH™O hydrogen bond (d H™O ϭ 1.680 Å) and a weaker NH™O interaction (d H™O ϭ 1.986 Å); these data are in agreement with the mass spectrometric investigation.…”

Section: Discussionsupporting

confidence: 71%

Self-Assembling of cytosine nucleoside into triply-bound dimers in acid Media. A comprehensive evaluation of proton-bound pyrimidine nucleosides by electrospray tandem mass spectrometry, X-rays diffractometry, and theoretical calculations

Armentano

Munno

Donna

et al. 2004

J. Am. Soc. Mass Spectrom.

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Electrospray tandem mass spectrometry (ESI-MS/MS) is used to evaluate the assembling of cytosine and thymine nucleosides in the gas phase, through the formation of hydrogen bonded supermolecules. Mixtures of cytidine analogues and homologues deliver in the gas phase proton-bound heterodimers stabilized by multiple interactions, as proven by the kinetics of their dissociation into the corresponding protonated monomers. Theoretical calculations, performed on initial structures of methylcytosine homodimers available in the literature, converged to a minimized structure whereby the two pyrimidine rings interact through the formation of three hydrogen bonds of similar energy. The crystallographic data here reported show the equivalency of the two interacting pyrimidines which is attributable to the presence of an inversion center. Thymine and uracil pyrimidyl nucleosides form, by ESI, gaseous proton-bound dimers. The kinetic of their dissociation into the related protonated monomers shows that the nucleobases are weekly interacting through a single hydrogen bond. The minimized structure of the protonated heterodimer formed by thymine and N-1-methylthymine confirmed the existence of mainly one hydrogen bond which links the two nucleobases through the O4 oxygens. No crystallographic data exists on thymine proton-bound species, nor have we been able to obtain these aggregates in the solid phase. The gaseous phase, under high vacuum conditions, seems therefore a suitable environment where vanishing structures produced by ESI can be studied with a good degree of approximation. (J Am Soc Mass Spectrom 2004, 15, 268Ϫ279)

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Section: Discussionsupporting

confidence: 71%

Self-Assembling of cytosine nucleoside into triply-bound dimers in acid Media. A comprehensive evaluation of proton-bound pyrimidine nucleosides by electrospray tandem mass spectrometry, X-rays diffractometry, and theoretical calculations

Armentano

Munno

Donna

et al. 2004

J. Am. Soc. Mass Spectrom.

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“…t Similar information is give n in thi s pa pe r for urac il , a pyrimidine base of the nucle ic acid s. Th e structural formul a [4] is…”

Section: Introductionmentioning

confidence: 69%

“…Thi s would indicate that all occl uded H20 may not have been re moved during th e vacuum drying. In ge ne ral, th e re appears to be greater variation in the purity of these urac il samples than was found in the o th e r bases prev iously desc ribed in 4 Anal yses by J. A. Noms, Center for Anal yti cal C he mistry, Nati onal Measure me nt Laboratory, National Bureau of Standards.…”

Section: 12 Other Analysesmentioning

confidence: 86%

“…2 for Ura 1, 4.2 for Ura 2, and 4 .5 for Ura 3. Since the H + conce ntrati on of th e fin al solutions was 4 to 5 ord ers of magnitude smaller tha n the ionizati on consta nt , 3 X 10 9 [4], a nd th e correcti on to infinite dilution was negligibly s mall , our measured value for the e nthalpy of solution was conside red to be eq ual to that at infinite d ilution.…”

Section: Enthalpy Of Solutionmentioning

confidence: 92%

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Enthalpies of solution of the nucleic acid bases. 4. Uracil in water

Kilday

1978

J. RES. NATL. BUR. STAN.

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An adiabatic soluti on calorimete r wa s used to measure e nthalpies of solulion in wate r uf 7 urac il sa mpl es in a co nce nt rati on ra nge of 3 to 4 5 I11mol· kg-I and over a tempera ture ra nge of 298 K to :325 K. Ana lytica l d ata fo r the sa mpl es are give n.Our best va lue fo r the e nthalpy of soluti on is Mr (co, 298.1 5 K) = (29. 3 ± 1.2) kJ· mo l-I a nd for the c ha nge in heat ca pac ity for the re ac ti on with tempera ture ,No c hange in the e ntha lpy of soluti on with conce ntrati on was found in thi s range . Va lues we re ca lcul ated for the e ntropy of solution , LlS 0 = (68. J ± 4.2) J. 11101-1 • K-I, a nd for the a ppa re nt mo lal heat ca pac it y at infinit e d ilution, Cp~ = (178 ± I S) J . mol-I. K-I.Ke ywords: Calorime try; 2,4-dioxopyrimidine; nuc le ic acid base s; 2,4(l H , 3 H)-pyril11idinerli one ; the rm uc he mi stry; u rac il: de ns it y, e nthalpy of solution, entropy of soluti on.

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“…A further chemical shift change is observed at about pH* 8.5-9.0; due to deprotonation of guanine N1. The pKa of this deprotonation is substantially less than in unmodified guanines [22]. For those two compounds containing a terminal 5'-phosphate group an additional chemical shift change is found at about pH * 6.5, due to phosphate protonation.…”

Section: Cm-is Found For All Tetranucleotides and Anmentioning

confidence: 85%

Interaction of platinum compounds with short oligodeoxynucleotides containing guanine and cytosine

Marcelis¹,

Hartog²,

Marel³

et al. 1983

Eur J Biochem

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The products resulting from reaction of cis-Pt(NH,),Cl, with d(CpCpGpG), d(GpCpG), d(pCpGpCpG), d(pGpCpGpC) and d (CpGpCpG) and from reaction of [Pt(dien)Cl]Cl with d(CpCpGpG) and d(GpCpG) have been characterized with the aid of proton NMR spectroscopy, circular dichroic spectroscopy and Pt analysis. The binding sites of the Pt compounds were determined by pH-dependent NMR spectroscopy. Binding of the two Pt compounds invariably occurs at the guanine N7 atoms. In all compounds containing [C~S-P~(NH,),]~+ chelates are formed by coordination of platinum to two guanines of the same oligonucleotide. The resulting intrastrand-cross-linked oligonucleotides contain either d(GpG) . cisPt units, or d(GpCpG) . cisPt units. In the latter case the middle cytosine is not coordinated to platinum. As a result the conformational changes originating from these two chelates are different from each other.In the case of [Pt(dien)Cl]Cl as a starting product, two types of oligonucleotide adducts are formed, i.e. those with one Pt atom/molecule and those with two Pt atoms/molecule. The NMR spectra of the adducts containing only one Pt(dien),+ show that only one adduct is formed, although two guanine bases are present. This indicates a preference for one of the N7 atoms in the molecule.The mechanism of action of the antitumor drug cisdiamminedichloroplatinum(I1) has been the subject of many investigations. Most of the present evidence suggests that DNA is the primary target of the platinum drug [l]. One of the hypotheses that have been put forward to explain the antineoplastic activity of cis-Pt(NH,),Cl, (cisPt) as compared with the inactivity of trans-Pt(NH,),Cl, and [Pt(dien)Cl]Cl, involves a cross-link of two bases in one DNA strand by a bifunctional coordination of cisPt [2] (and previous work cited therein). Because the N7 atoms of the guanine bases are the primary binding site for platinum [3, 41, chelation of the N7 atoms of adjacent guanines by cisPt seems most likely. Such a binding mode emerged, for example, from studies of exonuclease digestion of DNAs treated with cisPt [5, 61. This enzymatic digestion was found to stop at (dG), (n 2 2) sequences. Another study showed that cleavage of pSMl DNA at a cutting site for a restriction endonuclease near a (dG), . (dC), sequence is selectively inhibited by low doses of cisPt [7]. One of the products obtained upon enzymatic digestion of DNA treated with cisPt was recently shown to be d(pGpG) . cisPt 181. Recently, Chottard et al. [9] and Girault et al. [lo] studied the interaction of cisPt with a variety of dinucleoside monophosphates. It was found that GpG, Ipl, ApA, d(GpG) and d(pGpG) form chelates with cisPt. Two self-complementary hexanucleotides were recently shown to form chelates with the N7 positions of adjacent guanines [ l l , 121. In these chelates the N7 atoms of both purines of the dinucleotide are coordinated to platinum.

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Sites and thermodynamic quantities associated with proton and metal ion interaction with ribonucleic acid, deoxyribonucleic acid, and their constituent bases, nucleosides, and and nucleotides

Cited by 756 publications

References 32 publications

Self-Assembling of cytosine nucleoside into triply-bound dimers in acid Media. A comprehensive evaluation of proton-bound pyrimidine nucleosides by electrospray tandem mass spectrometry, X-rays diffractometry, and theoretical calculations

Self-Assembling of cytosine nucleoside into triply-bound dimers in acid Media. A comprehensive evaluation of proton-bound pyrimidine nucleosides by electrospray tandem mass spectrometry, X-rays diffractometry, and theoretical calculations

Enthalpies of solution of the nucleic acid bases. 4. Uracil in water

Interaction of platinum compounds with short oligodeoxynucleotides containing guanine and cytosine

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