Sequence-Specific Ultrasonic Cleavage of DNA

被引:34
作者
Grokhovsky, Sergei L. [1 ]
Il'icheva, Irina A. [1 ]
Nechipurenko, Dmitry Yu [2 ]
Golovkin, Michail V. [1 ]
Panchenko, Larisa A. [3 ]
Polozov, Robert V. [4 ]
Nechipurenko, Yury D. [1 ,2 ]
机构
[1] Russian Acad Sci, Engelhardt Inst Mol Biol, Moscow, Russia
[2] Moscow MV Lomonosov State Univ, Dept Phys, Moscow, Russia
[3] Moscow MV Lomonosov State Univ, Dept Biol, Moscow, Russia
[4] Russian Acad Sci, Inst Theoret & Expt Biophys, Pushchino, Russia
基金
俄罗斯基础研究基金会;
关键词
NUCLEIC-ACID CONFORMATIONS; NF-KAPPA-B; DEOXYRIBONUCLEIC ACID; SONIC DEGRADATION; FLEXIBILITY; BACKBONE; DYNAMICS; RECOGNITION; BINDING; PROTEIN;
D O I
10.1016/j.bpj.2010.10.052
中图分类号
Q6 [生物物理学];
学科分类号
071011 ;
摘要
We investigated the phenomenon of ultrasonic cleavage of DNA by analyzing a large set of cleavage patterns of DNA restriction fragments using polyacrylamide gel electrophoresis. The cleavage intensity of individual phosphodiester bonds was found to depend on the nucleotide sequence and the position of the bond with respect to the ends of the fragment. The relative intensities of cleavage of the central phosphodiester bond in 16 dinucleotides and 256 tetranucleotides were determined by multivariate statistical analysis. We observed a remarkable enhancement of the mean values of the relative intensities of cleavage (cleavage rates) in phosphodiester bonds following deoxycytidine, which diminished in the row of dinucleotides: d(CpG) > d(CpA) > d(CpT) >> d(CpC). The cleavage rates for all pairs of complementary dinucleotides were significantly different from each other. The effect of flanking nucleotides in tetranucleotides on cleavage rates of all 16 types of central dinucleotides was also statistically significant. The sequence-dependent ultrasonic cleavage rates of dinucleotides are consistent with reported data on the intensity of the conformational motion of their 5'-deoxyribose. As a measure of local conformational dynamics, cleavage rates may be useful for characterizing functional regions of the genome.
引用
收藏
页码:117 / 125
页数:9
相关论文
共 58 条
[1]   DNA structures from phosphate chemical shifts [J].
Abi-Ghanem, Josephine ;
Heddi, Brahim ;
Foloppe, Nicolas ;
Hartmann, Brigitte .
NUCLEIC ACIDS RESEARCH, 2010, 38 (03) :1119-1128
[2]  
[Anonymous], 1999, Biostatistical Analysis
[3]  
[Anonymous], 1982, Molecular cloning
[4]   EFFECTS OF BASE SUBSTITUTIONS ON THE BINDING OF A DNA-BENDING PROTEIN [J].
BAILLY, C ;
WARING, MJ ;
TRAVERS, AA .
JOURNAL OF MOLECULAR BIOLOGY, 1995, 253 (01) :1-7
[5]   DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone [J].
Balasubramanian, B ;
Pogozelski, WK ;
Tullius, TD .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (17) :9738-9743
[6]  
Basedow A.M., 1977, ADV POLYM SCI, V22, P83
[7]   Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials [J].
Becker, Nils B. ;
Wolff, Lars ;
Everaers, Ralf .
NUCLEIC ACIDS RESEARCH, 2006, 34 (19) :5638-5649
[8]   SEQUENCE-DEPENDENT STRUCTURAL VARIATIONS OF DNA REVEALED BY DNASE-I [J].
BRUKNER, I ;
JURUKOVSKI, V ;
SAVIC, A .
NUCLEIC ACIDS RESEARCH, 1990, 18 (04) :891-894
[9]   Single-molecule studies of DNA mechanics [J].
Bustamante, C ;
Smith, SB ;
Liphardt, J ;
Smith, D .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 2000, 10 (03) :279-285
[10]   Conformational variation of the central CG site in d(ATGACGTCAT)2 and d(GAAAACGTTTTC)2 -: An NMR, molecular modelling and 3D-homology investigation [J].
Cordier, C ;
Marcourt, L ;
Petitjean, M ;
Dodin, G .
EUROPEAN JOURNAL OF BIOCHEMISTRY, 1999, 261 (03) :722-733