Interaction of tobacco mosaic virus protein with synthetic polynucleotides containing a fluorescent label: optical properties of poly (A,εA) and poly (C,εC) copolymers and energy migration from the tryptophan to 1,N⁶or 3,N⁴-ethenocytosine residues in RNP

Abstract

A spectrophotometric method for determination of the modification degrees and molar extinction coefficients for poly(A, epsilonA) and poly(C, epsilonC) copolymers has been developed. Dependence of some absorption and fluorescence parameters of the copolymers on the modification degree has been studied. Distribution of modified residues in copolymers differs from random and depends on modification conditions. Interaction between the TMV protein and copolymers has been investigated. The protein interacts with poly(A, epsilonA) of low or medium modification degree and displays no activity with respect to poly(epsilonA). On the contrary, introduction of epsilonC to the polynucleotide promotes complex formation between poly(C, epsilonC) and TMV protein. Analysis of the fluorescence emission and excitation spectra has revealed energy transfer from tryptophan to epsilonA or epsilon C in the RNP to occur and permits one to estimate the average distance between Trp (presumably Trp 52)o and the RNA base binding region in the virus to be 17 to 20 A.

Purification and characterization of XRad51.1 protein, Xenopus RAD51 homologue: recombinant XRad51.1 promotes strand exchange reaction

“…The concentration of poly(d A) was calculated according to the formula as described previously (Ledneva et al 1978). More than 94% of the bases were modified in the polynucleotides.…”

Functional and Structural Heterogeneity of the DNA Binding Site of the Escherichia coli Primary Replicative Helicase DnaB Protein

“…The etheno-derivatives of nucleic acids were obtained by modification with chloroacetaldehyde (12,18). Oligomer dT(pT) 19 , labeled at the 5Ј-end with fluorescein, 5Ј-Fl-dT(pT) 19 , was synthesized using fluorescein phosphoramidate (Glen Research). Labeling of the 3Ј-end was performed by synthesizing dT(pT) 19 with the last residue at the 3Ј-end of the oligomer having the amino group on a six-carbon linker.…”

Fluorescence study of secondary structure of DNA within bacteriophage λ

“…At m < 1% RQY for DNA1 is close to the value 0.6-0.7. This value is characteristic for poly(A,eA) at a low percentage of eA [7]. RQY for some heterogeneous polynucleotides containing EA are known to be significantly less and to vary about the mean value 0.1 [7].…”

“…This value is characteristic for poly(A,eA) at a low percentage of eA [7]. RQY for some heterogeneous polynucleotides containing EA are known to be significantly less and to vary about the mean value 0.1 [7]. This suggests that the intraphage DNA sites with disturbed complementary interactions of the bases have the adjacent adenine residues in the same DNA chain.…”

“…Further modification causes the RQY for CA in DNA1 to fall sharply ( fig.2, se > 1%). This may be due to further modification of adenines in sites -A-•A-A-, that gives rise to structures: -A--EA-CAand then -eA-CA-CA-, wherein RQY can be estimated as 0.1 and 0.02, respectively [7]. Using the formalism developed in earlier papers [7,10] one can estimate that probability of eA formation out of the sites of initial modification of the intraphage DNA does not exceed 0.01.…”