The isohydricity (pH constancy) as the property referred to mixtures of acids or bases, is illustrated on a simple example of the solutions: HL (C0, mol/L) and HL (C mol/L) mixed according to titrimetric mode (pH titration). A new derivation of the Michałowski formula 1 2 0 10 pK C C C    expressing this property is presented, and its applicability for determination of pK1 = – logK1 value is...

Urea titration of RNA by urea is an effective approach to investigate the forces stabilizing this biologically important molecule. We used all atom molecular dynamics simulations using two urea force fields and two RNA constructs to elucidate in atomic detail the destabilization mechanism of folded RNA in aqueous urea solutions. Urea denatures RNA by forming multiple hydrogen bonds with the RNA...

A class of hairpin polyamides linked by 3,4-diaminobutyric acid, resulting in a beta-amine residue at the turn unit, showed improved binding affinities relative to their alpha-amino-gamma-turn analogs for particular sequences. We incorporated beta-amino-gamma-turns in six-ring polyamides and determined whether there are any sequence preferences under the turn unit by quantitative footprinting t...

In aqueous solution above pH 2.4 with 4% (vol/vol) CH3CN, the complex [Ru(II)(bda)(isoq)2] (bda is 2,2'-bipyridine-6,6'-dicarboxylate; isoq is isoquinoline) exists as the open-arm chelate, [Ru(II)(CO2-bpy-CO2(-))(isoq)2(NCCH3)], as shown by (1)H and (13)C-NMR, X-ray crystallography, and pH titrations. Rates of water oxidation with the open-arm chelate are remarkably enhanced by added proton acc...

We have developed a sensitive continuous assay for nucleases using proton release. The assay has been applied to the determination of the kinetics of DNase I acting on short, defined deoxyoligonucleotides. The dependence of Kcat/K(m) on sequence and structure of short oligonucleotide substrates has been measured: increasing lengths of AnTn sequences decrease the rate of cleavage. G.A mismatches...

The interactions of actinomycin D (ACTD) with the oligonucleotides 5'-CAAAGCTTTG-3', 5'-CATGGCCATG-3' and 5'-TATGGCCATA-3' were investigated by means of acid-base titrations and mole-ratio and melting experiments monitored by molecular absorption and circular dichroism (CD) spectroscopies. For each experiment, CD and molecular absorption spectra were recorded at each point in the experiment, an...

An NMR titration method has been used to simultaneously measure the acid dissociation constant (pKa) and the intramolecular NHO prototropic constant ΔKNHO on a set of Schiff bases. The model compounds were synthesized from benzylamine and substituted ortho-hydroxyaldehydes, appropriately substituted with electron-donating and electron-withdrawing groups to modulate the acidity of the intramolec...

This paper reports results of a continuing investigation to evaluate coulometric methods of analysis and to develop highly precise and accurate analytical methods for important materials, based upon this technique. Earlier papers described the coulometric titrations of acids and bases [1] 1 and of halides [2]. The present research is concerned with a typical oxidation-reduction titration, the a...

The L-21 ScaI ribozyme derived from the Tetrahymena thermophila pre-rRNA group I intron catalyzes a site-specific endonucleolytic cleavage of RNA, DNA, and chimeric RNA/DNA oligonucleotides: CCCUCUA5 + G-->CCCUCU + GA5. The pH-rate dependence was determined for the reaction of the E.G complex with the oligonucleotide substrate d(CCCUC)r(U)d(A5) [(kcat/Km)S conditions]. Although it was shown tha...

Duplexes are the most fundamental elements of nucleic acid folding. Although it has become increasingly clear that duplex formation can be associated with a significant change in heat capacity (deltaC(p)), this parameter is typically overlooked in thermodynamic studies of nucleic acid folding. Analogy to protein folding suggests that base stacking events coupled to duplex formation should give ...