Structures of (5′S)-8,5′-Cyclo-2′-deoxyguanosine Mismatched with dA or dT

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Effects of site-specific substitution of 5-fluorouridine on the stabilities of duplex DNA and RNA.

The effects of 5-fluorouridine (FUrd) and 5-fluorodeoxyuridine (FdUrd) substitution on the stabilities of duplex RNA and DNA have been studied to determine how FUrd substitution in nucleic acids may alter the efficiency of biochemical processes that require complementary base pairing for molecular recognition. The parent sequence, 5'-GCGAAUUCGC, contains two non-equivalent uridines. Eight oligonucleotides (four RNA and four DNA) were prepared with either zero, one or two Urd substituted by FUrd. The stability of each self-complementary duplex was determined by measuring the absorbance at 260 nm as a function of temperature. Tm values were calculated from the first derivative of the absorbance versus temperature profiles and values for delta H0 and delta S0 were calculated from the concentration dependence of the Tm. Individual absorbance versus temperature curves were also analyzed by a parametric approach to calculate thermodynamic parameters for the duplex to single-stranded transition. Analysis of the thermodynamic parameters for each oligonucleotide revealed that FUrd substitution had sequence-dependent effects in both A-form RNA and B-form DNA duplexes. Conservation of helix geometry in FUrd-substituted duplexes was determined by CD spectroscopy. FUrd substitution at a single site in RNA stabilized the duplex (delta delta G37 = 0.8 kcal/mol), largely due to more favorable stacking interactions. FdUrd substitution at a single site in DNA destabilized the duplex (delta delta G37 = 0.3 kcal/mol) as a consequence of less favorable stacking interactions. All duplexes melt via single cooperative transitions

Chemical ionization induced competing and consecutive heterolytic ring cleavages in the mass spectra of substituted tetrahydro-1,3,2-oxazaphosphorin-2-oxides

The chemical ionization mass spectra of some substituted heterocyclic systems, viz. tetrahydro-1,3,2-oxazaphosphorin-2-oxides, reveal polar cycloreversion reactions. The zwitterion intermediate formed by the heterolysis of the CO bond undergoes stepwise clean heterolysis further resulting in the expulsion of the potential nucleophilic and electrophilic groups. The competitive and consecutive heterolysis of the ring bonds leads to the formation of the protonated phenylimine ions. Competing with heterolysis, elimination reactions involving hydrogen transfer leading to the formation of α-phenylethyl ions are also observed. The chemical ionization mass spectrometry of the heterocyclic system shows many features of the Grob type of fragmentation mechanism

Intramolecular single and double hydrogen migrations in the mass spectra of substituted tetrahydro-1,3,2-oxazaphosphorin-2-oxides

The mass spectral fragmentation of substituted tetrahydro-1,3,2-oxazaphosphorin-2-oxides occurs by the cleavage of ring bonds. The ions due to simple cleavage, single and double hydrogen migration, seem to be triggered by C=O bond cleavage of the oxazaphosphorin ring. The variations in the relative abundance of ions arising due to similar fragmentation modes have been found to depend on the nature of the substituent and the stability of the particular fragment. The single hydrogen transfer process is supported by metastable ion and shift techniques