Published in J Biomol Struct Dyn on June 01, 2010
A brief review of nucleosome structure. FEBS Lett (2015) 1.00
Working the kinks out of nucleosomal DNA. Curr Opin Struct Biol (2011) 0.95
Transcriptional activation of yeast genes disrupts intragenic nucleosome phasing. Nucleic Acids Res (2012) 0.91
Nucleosome adaptability conferred by sequence and structural variations in histone H2A-H2B dimers. Curr Opin Struct Biol (2015) 0.87
Rotational positioning of nucleosomes facilitates selective binding of p53 to response elements associated with cell cycle arrest. Nucleic Acids Res (2013) 0.84
Histone Sprocket Arginine Residues Are Important for Gene Expression, DNA Repair, and Cell Viability in Saccharomyces cerevisiae. Genetics (2015) 0.81
Novel nucleosomal particles containing core histones and linker DNA but no histone H1. Nucleic Acids Res (2015) 0.80
Codons support the maintenance of intrinsic DNA polymer flexibility over evolutionary timescales. Genome Biol Evol (2012) 0.80
An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression. BMC Struct Biol (2011) 0.79
Prediction of nucleosome rotational positioning in yeast and human genomes based on sequence-dependent DNA anisotropy. BMC Bioinformatics (2014) 0.78
Functional specificity of a protein-DNA complex mediated by two arginines bound to the minor groove. J Bacteriol (2012) 0.77
Molecular interactions and protein-induced DNA hairpin in the transcriptional control of bacteriophage ø29 DNA. Int J Mol Sci (2010) 0.75
Can nucleosomal DNA be described by an elastic model?: comment on "Sequence-dependent collective properties of DNAs and their role in biological systems" by Pasquale De Santis and Anita Scipioni. Phys Life Rev (2013) 0.75
Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature (1997) 44.55
The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q Rev Biophys (1978) 14.75
Definition of a consensus binding site for p53. Nat Genet (1992) 12.76
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res (2003) 10.63
Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J Mol Biol (2002) 8.42
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci U S A (1998) 8.14
Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol Cell (2005) 6.17
Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG. J Biol Chem (1982) 5.63
The role of DNA shape in protein-DNA recognition. Nature (2009) 5.52
The nucleosomal core histone octamer at 3.1 A resolution: a tripartite protein assembly and a left-handed superhelix. Proc Natl Acad Sci U S A (1991) 4.76
Recognition of a DNA operator by the repressor of phage 434: a view at high resolution. Science (1988) 4.60
Transcriptional regulation by p53 through intrinsic DNA/chromatin binding and site-directed cofactor recruitment. Mol Cell (2001) 3.74
Steroid-dependent interaction of transcription factors with the inducible promoter of mouse mammary tumor virus in vivo. Cell (1987) 3.74
Mechanics of sequence-dependent stacking of bases in B-DNA. J Mol Biol (1982) 3.72
Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. J Mol Biol (1999) 3.72
Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning. J Mol Biol (2004) 3.43
Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell (2007) 3.34
Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites. Mol Cell Biol (2001) 3.15
Anisotropic flexibility of DNA and the nucleosomal structure. Nucleic Acids Res (1979) 2.71
A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning. J Mol Biol (2007) 2.46
Nucleosome core displacement in vitro via a metastable transcription factor-nucleosome complex. Science (1992) 2.40
Structure and dynamic behavior of nucleosomes. Curr Opin Genet Dev (2003) 2.15
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps. Biophys J (2005) 2.09
Transcription factor access to chromatin. Nucleic Acids Res (1997) 2.02
Analysis of local helix geometry in three B-DNA decamers and eight dodecamers. J Mol Biol (1991) 1.91
Effects of DNA sequence and histone-histone interactions on nucleosome placement. J Mol Biol (1990) 1.91
The conformation of C-DNA. J Mol Biol (1975) 1.90
The assessment of the geometry of dinucleotide steps in double-helical DNA; a new local calculation scheme. J Mol Biol (1995) 1.88
Asymmetries in the nucleosome core particle at 2.5 A resolution. Acta Crystallogr D Biol Crystallogr (2000) 1.86
Static and statistical bending of DNA evaluated by Monte Carlo simulations. Proc Natl Acad Sci U S A (1991) 1.72
BI-BII transitions in B-DNA. Nucleic Acids Res (1993) 1.56
Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems. Chem Rev (2000) 1.55
Two distinct modes of protein-induced bending in DNA. J Mol Biol (1998) 1.47
Sequence-dependent anisotropic flexibility of B-DNA. A conformational study. J Biomol Struct Dyn (1984) 1.46
Sequence-dependent DNA deformability studied using molecular dynamics simulations. Nucleic Acids Res (2007) 1.41
Measuring the geometry of DNA grooves. Biopolymers (1994) 1.40
[Atom--atomic potential functions for conformational calculations of nucleic acids]. Mol Biol (Mosk) (1980) 1.30
DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences. Biophys J (2009) 1.23
The histone octamer is invisible when NF-kappaB binds to the nucleosome. J Biol Chem (2004) 1.15
Structure and conformation of helical nucleic acids: rebuilding program (SCHNArP). J Mol Biol (1997) 1.06
Flexibility of the B-DNA backbone: effects of local and neighbouring sequences on pyrimidine-purine steps. Nucleic Acids Res (1998) 0.99
p53 binding to nucleosomal DNA depends on the rotational positioning of DNA response element. J Biol Chem (2009) 0.99
Nucleosome DNA bendability matrix (C. elegans). J Biomol Struct Dyn (2009) 0.99
Sequence preference for BI/BII conformations in DNA: MD and crystal structure data analysis. J Biomol Struct Dyn (2005) 0.87
A snapshot of a dynamic nuclear building block. Nat Struct Biol (1997) 0.85
Nonsequence-specific arginine interactions in the nucleosome core particle. Biopolymers (2003) 0.84
A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning. J Mol Biol (2007) 2.46
A triple helix within a pseudoknot is a conserved and essential element of telomerase RNA. Mol Cell Biol (2007) 1.61
Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy. J Biomol NMR (2003) 1.53
The p53 tumor suppressor network is a key responder to microenvironmental components of chronic inflammatory stress. Cancer Res (2005) 1.42
Impact of Alu repeats on the evolution of human p53 binding sites. Biol Direct (2011) 1.25
A-tract clusters may facilitate DNA packaging in bacterial nucleoid. Nucleic Acids Res (2005) 1.21
"Antiparallel" DNA loop in gal repressosome visualized by atomic force microscopy. J Mol Biol (2003) 1.17
Solution structure of a consensus stem-loop D RNA domain that plays important roles in regulating translation and replication in enteroviruses and rhinoviruses. Biochemistry (2004) 1.08
DNA trajectory in the Gal repressosome. Genes Dev (2004) 1.08
Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching. J Mol Biol (2004) 1.08
Mitogen-activated protein kinase phosphatase 2: a novel transcription target of p53 in apoptosis. Cancer Res (2006) 1.08
nuScore: a web-interface for nucleosome positioning predictions. Bioinformatics (2008) 1.08
Pyrimidine motif triple helix in the Kluyveromyces lactis telomerase RNA pseudoknot is essential for function in vivo. Proc Natl Acad Sci U S A (2013) 1.08
Distinctive sequence patterns in metazoan and yeast nucleosomes: implications for linker histone binding to AT-rich and methylated DNA. Nucleic Acids Res (2009) 0.99
p53 binding to nucleosomal DNA depends on the rotational positioning of DNA response element. J Biol Chem (2009) 0.99
Combined micrococcal nuclease and exonuclease III digestion reveals precise positions of the nucleosome core/linker junctions: implications for high-resolution nucleosome mapping. J Mol Biol (2013) 0.97
Structure-based analysis of DNA sequence patterns guiding nucleosome positioning in vitro. J Biomol Struct Dyn (2010) 0.97
Working the kinks out of nucleosomal DNA. Curr Opin Struct Biol (2011) 0.95
NMR structures of loop B RNAs from the stem-loop IV domain of the enterovirus internal ribosome entry site: a single C to U substitution drastically changes the shape and flexibility of RNA. Biochemistry (2004) 0.92
Discovery of ligands for a novel target, the human telomerase RNA, based on flexible-target virtual screening and NMR. J Med Chem (2008) 0.92
Transcriptional activation of yeast genes disrupts intragenic nucleosome phasing. Nucleic Acids Res (2012) 0.91
Nucleocapsid protein-mediated maturation of dimer initiation complex of full-length SL1 stemloop of HIV-1: sequence effects and mechanism of RNA refolding. Nucleic Acids Res (2007) 0.89
Recombination R-triplex: H-bonds contribution to stability as revealed with minor base substitutions for adenine. Nucleic Acids Res (2006) 0.87
Formation of an intramolecular triple-stranded DNA structure monitored by fluorescence of 2-aminopurine or 6-methylisoxanthopterin. Nucleic Acids Res (2004) 0.85
Rotational positioning of nucleosomes facilitates selective binding of p53 to response elements associated with cell cycle arrest. Nucleic Acids Res (2013) 0.84
Iodine-125 radioprobing of E. coli RNA polymerase transcription elongation complexes. Methods Enzymol (2003) 0.83
Dynamic NMR structures of [Rp]- and [Sp]-phosphorothioated DNA-RNA hybrids: is flexibility required for RNase H recognition? Biophys J (2003) 0.78
NMR structure of the 3' stem-loop from human U4 snRNA. Nucleic Acids Res (2002) 0.78
Prediction of nucleosome rotational positioning in yeast and human genomes based on sequence-dependent DNA anisotropy. BMC Bioinformatics (2014) 0.78
Binding characteristics of small molecules that mimic nucleocapsid protein-induced maturation of stem-loop 1 of HIV-1 RNA. Biochemistry (2010) 0.77
Radioprobing the conformation of DNA in a p53-DNA complex. Int J Radiat Biol (2012) 0.75
Intramolecular recombination R-triplex in solution: stabilization by bis-intercalator YOYO. J Biomol Struct Dyn (2008) 0.75
7 Topological polymorphism of two-start nucleosome fibers. J Biomol Struct Dyn (2015) 0.75
6 Combined influence of linker DNA and histone tails on nucleosome dynamics as revealed by microsecond molecular dynamics simulations. J Biomol Struct Dyn (2015) 0.75