Raman spectroscopic study of triplex-like complexes of polyuridylic acid with the isopolar, non-isosteric phosphonate analogues of diadenosine monophosphate

Abstract

The formation of poly(rU) complexes with diadenosine monophosphate (3 -5 ) and its four isopolar, nonisosteric phosphonate analogues was studied by means of Raman spectroscopic titration. A set of mixed samples containing the diadenosine monophosphate or monophosphonate and the poly(rU) at various concentration ratios was prepared. The room temperature spectra of mixed solutions were treated by factor analysis and decomposition of the Raman marker bands. For all the species studied, the results revealed an exclusive presence of the triplex-like complexes, i.e. complexes with a 1 : 2 stoichiometric ratio of the adenosine to uridine units, the Raman spectra of which exhibit all the features typical of the poly(rU)·poly(rA)·poly(rU) triple-helical structure. The individual molar fractions of the free ApA dimer, the free poly(rU) and the triplex-like complex do not fit classical equilibrium equation, because the binding ability of the adenosine dimers to poly(rU) falls significantly for small ApA molar fractions. This tendency is strongest for the natural diadenosine phosphate (3 -5 ) and weakest for two analogues in which the -CH 2 -group in the modified internucleotide linkage is situated closer to the 5 -position.

Synthesis and Properties of ApA Analogues with Shortened Phosphonate Internucleotide Linkage

“…Therefore, in order to obtain the basic data giving information about the properties of the modified internucleotide linkage, in comparison with other relevant types of linkages, we opted for the study of the thermal stability of duplex-(or triplex-) like structures of the appropriately modified "dimers" (i.e., diribonucleoside monophosphates) with polynucleotides using spectroscopic methods in view of the fact that a variety of modified dinucleoside monophosphates [13] and their enantiomers, [14] neutral phosphotriester [15] and methylphosphonate [16] dimers, and a series of the isopolar internucleotide linkage-modified ApAs [17][18][19][20] have been employed as model compounds to study changes in hybridization properties due to the presence of particular modifications. These studies encouraged us to undertake a study dealing with the following specific tasks: (i) the synthesis of a unique set of phosphonate ApA analogues in ribo and 2 -deoxyribo series with chiral α-hydroxy-phosphonate C3 -O-P-CH(OH)-C4 internucleotide linkage and non-chiral C3 (2 )-O-P-CH 2 -C4 one, (ii) the hybridization of the modified ApAs with polyU, (iii) the nuclear magnetic resonance (NMR) conformational investigation of the modified sugar-phosphate backbone, and (iv) the structural characteristics obtainable on this topics from the evaluation by molecular dynamics simulation (MDS).…”

“…Similar results, in fact, were also obtained with both natural ApAs and also with a series of another, earlier studied phosphonate analogues of ApA. [18][19][20][21] In all cases, the thermal characteristics showed single transition profiles only (data not shown), with considerably different T m values ( Table 1).…”

SVD‐based method for intensity normalization, background correction and solvent subtraction in Raman spectroscopy exploiting the properties of water stretching vibrations

“…Our approach of non-Raman baseline correction, normalization and subtraction of the solvent contribution is based on factor analysis (singular value decomposition (SVD)), [8,22] a mathematical procedure projecting experimental spectra from dataset [Y i (ν)] into orthonormal set of functions [S j (ν)] (denoted hereafter as subspectra) according to Eqn (1), where singular values W j are statistical weights of S j (ν) and elements V ij (denoted hereafter as coefficients) represent relative spectral contributions of S j (ν) to the spectrum Y i (ν). Typical results of SVD are shown in Figs 2 and 3.…”

“…Small singular values W j (usually below 0.5% of the maximal value) that decrease linearly with the order j are related to subspectra describing only white noise. [8,22] …”

Unfolding Thermodynamics of the Δ-Domain in the Prohead I Subunit of Phage HK97: Determination by Factor Analysis of Raman Spectra

“…In the case of protein melting, the set M is expected to include the native and unfolded states of the protein. The results of SVD can be fitted to the concentrations of the individual states γ in via a rotation matrix ρ nj , which relates the factors S j (ν) and the spectra Z n (ν) 42. In our analysis, we assumed a weak linear dependence of Z n (ν) on temperature to allow for protein chain flexibility or protein-solvent interactions that may occur without significant changes in the average secondary or tertiary structures 39,43…”