DNA-stacking interactions determine the sequence specificity of the deoxyribonuclease activity of 1,10-phenanthroline-copper ion

被引:30
作者
Schaeffer, F [1 ]
Rimsky, S [1 ]
Spassky, A [1 ]
机构
[1] INST CURIE,CNRS URA 400,LAB PHYS & CHIM BIOMOL,F-75231 PARIS 05,FRANCE
关键词
nuclease specificity; orthophenanthroline; copper ion; DNA-stacking; base-pair steps;
D O I
10.1006/jmbi.1996.0419
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Bis(1,10-phenanthroline)-copper(I) ion (OP2Cu+) binds reversibly to B-DNA and makes single-stranded cuts by oxidative attack on the deoxyribose moiety. The deoxyribonuclease activity is sequence-dependent yet not nucleotide-specific at the cutting site. OP2Cu+ sequence specificity was analysed in terms of local variations of DNA stability. Kinetic constants of strand cleavage were measured at sequence positions on the two strands and converted into activation free energies of the cleavage reaction. DNA unwinding free energies were calculated from the base sequence using B-DNA stacking parameters for calculations. The two free-energy variations were statistically compared for a series of DNA restriction fragments bearing the binding sites of regulatory proteins and representing a total of 345 DNA base positions. This study shows that the mean activation free energy of strand cleavage at a pair of opposing sugars across the DNA minor groove varies like the unwinding free energy of the DNA sequence delimited by opposing sugars (3 to 4 bp). A statistical equality between the two free-energy variations is demonstrated when considering the sum of the two cleavage events at the opposing sugars. Systematic deviations between the two free-energy distributions were observed at specific sequences, including polypurine-polypyrimidine tracts (A(n)T(m)/A(m)T(n), CnTmCp/G(p)A(m)G(n)), alternating purine-pyrimidine tracts ((TA)(n)/(TA)(n), (TG)(n)/(CA)(n)) and at certain Gi+C-rich triplets (GGC, GCC and CGC). The physical significance of these observations is discussed and a model of OP2Cu+ binding and cleavage specificity based on the free-energy equality is proposed. (C) 1996 Academic Press Limited
引用
收藏
页码:523 / 539
页数:17
相关论文
共 66 条
[11]   RECOGNITION AND CLEAVAGE SITE OF THE INTRON-ENCODED OMEGA TRANSPOSASE [J].
COLLEAUX, L ;
DAURIOL, L ;
GALIBERT, F ;
DUJON, B .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1988, 85 (16) :6022-6026
[12]   THE ANATOMY OF A-DNA, B-DNA, AND Z-DNA [J].
DICKERSON, RE ;
DREW, HR ;
CONNER, BN ;
WING, RM ;
FRATINI, AV ;
KOPKA, ML .
SCIENCE, 1982, 216 (4545) :475-485
[13]   CRYSTAL-LATTICE PACKING IS IMPORTANT IN DETERMINING THE BEND OF A DNA DODECAMER CONTAINING AN ADENINE TRACT [J].
DIGABRIELE, AD ;
SANDERSON, MR ;
STEITZ, TA .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1989, 86 (06) :1816-1820
[14]   NEGATIVE SUPERCOILING INDUCES SPONTANEOUS UNWINDING OF A BACTERIAL PROMOTER [J].
DREW, HR ;
WEEKS, JR ;
TRAVERS, AA .
EMBO JOURNAL, 1985, 4 (04) :1025-1032
[15]   DNA STRUCTURAL VARIATIONS IN THE ESCHERICHIA-COLI TYRT-PROMOTER [J].
DREW, HR ;
TRAVERS, AA .
CELL, 1984, 37 (02) :491-502
[16]  
FLEISHER MB, 1988, NUCLEIC ACIDS MOL BI, V2, P65
[17]   CRYSTAL-STRUCTURE OF CATGGCCATG AND ITS IMPLICATIONS FOR A-TRACT BENDING MODELS [J].
GOODSELL, DS ;
KOPKA, ML ;
CASCIO, D ;
DICKERSON, RE .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1993, 90 (07) :2930-2934
[18]   LOCATIONS OF FREQUENTLY OPENING REGIONS ON NATURAL DNAS AND THEIR RELATION TO FUNCTIONAL LOCI [J].
GOTOH, O ;
TAGASHIRA, Y .
BIOPOLYMERS, 1981, 20 (05) :1043-1058
[19]  
GOTOH O, 1983, ADV BIOPHYS, V16, P1
[20]   STABILITIES OF NEAREST-NEIGHBOR DOUBLETS IN DOUBLE-HELICAL DNA DETERMINED BY FITTING CALCULATED MELTING PROFILES TO OBSERVED PROFILES [J].
GOTOH, O ;
TAGASHIRA, Y .
BIOPOLYMERS, 1981, 20 (05) :1033-1042