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Cooperative interactions in the tandem of oligonucleotide derivatives arranged at complementary target. Quantitative estimates and contribution of the target secondary structure
Author(s) -
Fedorova Olga S.,
Adeenah-Zadah Abdussalam,
Knorre Dmitri G.
Publication year - 1995
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/0014-5793(95)00733-p
Subject(s) - reagent , chemistry , tandem , residue (chemistry) , alkylation , stereochemistry , effector , oligonucleotide , crystallography , dna , materials science , organic chemistry , biochemistry , composite material , catalysis
The intraduplex reaction of the alkylating reagent CIRCH 2 NHpd(TTCCCA) (X, CIR is p‐( N ‐2‐chloroethyl‐ N ‐methylaminophenyl) residue) with the target 26‐mer d(TTGCCTTGAATGGGAAGAGGGTCATT) (P) in the presence of effectors was studied. The effectors used were Phn‐L‐pd(TTCAAGGC)p‐L‐Phn (E 1 ) and Phn‐L‐pd(TGACCCTC)p‐L‐Phn (E 2 ), where Phn is N ‐(2‐hydroxyethyl)‐phenazinium residue and L is NHCH 2 CH 2 NH spacer. The dependence of the alkylation extent of the target on the reagent concentration was treated using the equation derived earlier for the two‐component system (reagent+target) to calculate association constants of X with P, PE 1 , PE 2 and PE 1 E 2 . The latters were found to be K xe1 = 6.75 · 10 5 M −1 , K xe2 = 4.15 · 10 4 M − and K xe12 = 5.87 · 10 6 10 6 M −1 as compared with the affinity of X to P K x = 2.16 · 10 4 M −1 in the absence of effectors. Taking into account the internal structure of the target, co‐operativity parameters describing interactions in the tandem E 1 · X · E 2 arranged at the target were calculated as α 1 = 16, α 2 = 10 and α 12 = 139 for the duplexes PXE 1 , PXE 2 and PXE 1 E 2 .