SUNY at Albany
June 19-23, 2001
Structural investigation of flexible motifs of DNA .
On the basis of statistical analysis of nucleotide sequences of transcriptional regulatory sites (using accessible open data bases) the fact was revealed of increased frequency of pyrimidine-purine dinucleotide repeats compared with coding sequences and some other interesting features. Among these repeats the overpowering frequency of occurrence corresponds to CA/TG dinucleotides.
We investigated experimentally the flexibility of synthetic oligonucleotides incorporating some motifs with (CA)n (n<=3) per 10 Ð11 bp, YCAX per 5-6 bp or 10-11 bp (Y,X- one of the four nucleotides) and their combinations. The methods used were ligation-cyclization procedure of initial oligonucleotides (determination of j-factors which is the characteristics of cyclization effectiveness of multimers), analysis of multimers electrophoresis migration and atomic forth microscopy (AFM) for visualization of minicircles.
It was demonstrated that the electrophoretic mobility slightly increased with n, j-factors depend upon n and combinations of Y,X.
The last fact possibly reflects the information of dependence of conformational parameters of CA/TG dinucleotides upon neighbouring nucleotides determined by other methods.
Fedoseyeva V.B.(1), Alexandrov A.A., Korobko V.G.(2), Nekrasova O.V.(2), Klinov D.V.(2)
Institute of Molecular Genetics RAS, Kurchatov Sq. Moscow 123182, Russia;
Ovchinikov Ju.A. and Shemyakin M.M. Institute of Bioorganic
Chemistry RAS(2), Miklukho-Maklaya St.16/10, Moscow 117871,Russia