The geometry of the phosphodiester backbone was analyzed for 7739 dinucleotides from 447 selected crystal structures of naked and complexed DNA. Ten torsion angles of a near-dinucleotide unit have been studied by combining Fourier averaging and clustering. Besides the known variants of the A-, B- and Z-DNA forms, we have also identified combined A + B backbone-deformed conformers, e.g. with alpha/gamma switches, and a few conformers with a syn orientation of bases occurring e.g. in G-quadruplex structures. A plethora of A- and B-like conformers show a close relationship between the A- and B-form double helices. A comparison of the populations of the conformers occurring in naked and complexed DNA has revealed a significant broadening of the DNA conformational space in the complexes, but the conformers still remain within the limits defined by the A- and B- forms. Possible sequence preferences, important for sequence-dependent recognition, have been assessed for the main A and B conformers by means of statistical goodness-of-fit tests. The structural properties of the backbone in quadruplexes, junctions and histone-core particles are discussed in further detail.

• MeSH
• A-DNA chemie   MeSH
• cytosin chemie   MeSH
• deoxyribonukleotidy chemie   MeSH
• DNA vazebné proteiny chemie   MeSH
• DNA chemie   MeSH
• G-kvadruplexy MeSH
• konformace nukleové kyseliny MeSH
• křížová struktura DNA chemie   MeSH
• ligandy MeSH
• nukleozomy chemie   MeSH
• RNA chemie   MeSH
• sekvence nukleotidů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• A-DNA MeSH
• cytosin MeSH
• deoxyribonukleotidy MeSH
• DNA vazebné proteiny MeSH
• DNA MeSH
• křížová struktura DNA MeSH
• ligandy MeSH
• nukleozomy MeSH
• RNA MeSH

[Fe(2)L(3)](4+) (L = C(25)H(20)N(4)) is a synthetic tetracationic supramolecular cylinder (with a triple helical architecture) that targets the major groove of DNA and can bind to DNA Y-shaped junctions. To explore the DNA-binding mode of [Fe(2)L(3)](4+), we examine herein the interactions of pure enantiomers of this cylinder with DNA by biochemical and molecular biology methods. The results have revealed that, in addition to the previously reported bending of DNA, the enantiomers extensively unwind DNA, with the M enantiomer being the more efficient at unwinding, and exhibit preferential binding to regular alternating purine-pyrimidine sequences, with the M enantiomer showing a greater preference. Also, interestingly, the DNA binding of bulky cylinders [Fe(2)(L-CF(3))(3)](4+) and [Fe(2)(L-Ph)(3)](4+) results in no DNA unwinding and also no sequence preference of their DNA binding was observed. The observation of sequence-preference in the binding of these supramolecular cylinders suggests that a concept based on the use of metallosupramolecular cylinders might result in molecular designs that recognize the genetic code in a sequence-dependent manner with a potential ability to affect the processing of the genetic code.

• MeSH
• deoxyribonukleasa I MeSH
• DNA footprinting MeSH
• DNA chemie   metabolismus   MeSH
• ethidium chemie   MeSH
• kompetitivní vazba MeSH
• konformace nukleové kyseliny MeSH
• pyridiny chemie   MeSH
• restrikční enzymy metabolismus   MeSH
• sekvence nukleotidů MeSH
• stereoizomerie MeSH
• superhelikální DNA chemie   MeSH
• železnaté sloučeniny chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• deoxyribonukleasa I MeSH
• DNA MeSH
• ethidium MeSH
• pyridiny MeSH
• restrikční enzymy MeSH
• superhelikální DNA MeSH
• železnaté sloučeniny MeSH

Three-dimensional structures of a representative set of more than 30 hydrogen-bonded nucleic acids pairs have been studied by reliable ab initio quantum mechanical methods. We show that many hydrogen-bonded nucleic acid base pairs are intrinsically nonplanar, mainly due to the partial sp3 hybridization of nitrogen atoms of their amino groups and secondary electrostatic interactions. This finding extends the variability of intermolecular interactions of DNA bases in that i) flexibility of the base pairs is larger than has been assumed before, and ii) attractive proton-proton acceptor interactions oriented out of the base pair plane are allowed. For example, all four G-A mismatch base pairs are propeller twisted, and the energy preferences for the nonplanar structures range from less than 0.1 kcal/mol to 1.8 kcal/mol. We predict that nonplanarity of the amino group of guanine in the G(anti)...A(anti) pair of the ApG step of the d(CCAAGATTGG)2 crystal structure is an important stabilizing factor that improves the energy of this structure by almost 3 kcal/mol. Currently used empirical potentials are not accurate enough to properly cover the interactions associated with amino-group and base-pair nonplanarity.

• MeSH
• deoxyribonukleotidy chemie   MeSH
• DNA chemie   MeSH
• konformace nukleové kyseliny * MeSH
• kvantová teorie MeSH
• molekulární modely MeSH
• molekulární sekvence - údaje MeSH
• sekvence nukleotidů MeSH
• vodíková vazba MeSH
• zastoupení bazí MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, P.H.S. MeSH
• Názvy látek
• deoxyribonukleotidy MeSH
• DNA MeSH

To investigate the principles driving recognition between proteins and DNA, we analyzed more than thousand crystal structures of protein/DNA complexes. We classified protein and DNA conformations by structural alphabets, protein blocks [de Brevern, Etchebest and Hazout (2000) (Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Prots. Struct. Funct. Genet., 41:271-287)] and dinucleotide conformers [Svozil, Kalina, Omelka and Schneider (2008) (DNA conformations and their sequence preferences. Nucleic Acids Res., 36:3690-3706)], respectively. Assembling the mutually interacting protein blocks and dinucleotide conformers into 'interaction matrices' revealed their correlations and conformer preferences at the interface relative to their occurrence outside the interface. The analyzed data demonstrated important differences between complexes of various types of proteins such as transcription factors and nucleases, distinct interaction patterns for the DNA minor groove relative to the major groove and phosphate and importance of water-mediated contacts. Water molecules mediate proportionally the largest number of contacts in the minor groove and form the largest proportion of contacts in complexes of transcription factors. The generally known induction of A-DNA forms by complexation was more accurately attributed to A-like and intermediate A/B conformers rare in naked DNA molecules.

• MeSH
• DNA vazebné proteiny chemie   MeSH
• DNA chemie   MeSH
• fosfáty MeSH
• interpretace statistických dat MeSH
• konformace nukleové kyseliny MeSH
• konformace proteinů MeSH
• molekulární modely MeSH
• vazba proteinů MeSH
• voda chemie   MeSH
• výpočetní biologie MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA vazebné proteiny MeSH
• DNA MeSH
• fosfáty MeSH
• voda MeSH

The cytotoxicity of chloropolypyridyl ruthenium complexes of structural formulas [Ru(terpy)-(bpy)Cl]Cl, cis-[Ru(bpy)2Cl2], and mer-[Ru(terpy)Cl3] (terpy = 2,2':6'2"-terpyridine, bpy = 2,2'-bipyridyl) has been studied in murine and human tumor cell lines. The results show that mer-[Ru(terpy)Cl3] exhibits a remarkably higher cytotoxicity than the other complexes. Moreover, investigations of antitumor activity in a standard tumor screen have revealed the highest efficiency for mer-[Ru(terpy)Cl3]. In a cell-free medium, the ruthenium complexes coordinate to DNA preferentially at guanine residues. The resulting adducts can terminate DNA synthesis by thermostable VentR DNA polymerase. The reactivity of the complexes to DNA, their efficiency to unwind closed, negatively supercoiled DNA, and a sequence preference of their DNA adducts (studied by means of replication mapping) do not show a correlation with biological activity. On the other hand, the cytotoxic mer-[Ru(terpy)Cl3] exhibits a significant DNA interstrand cross-linking, in contrast to the inactive complexes which exhibit no such efficacy. The results point to a potential new class of metal-based antitumor compounds acting by a mechanism involving DNA interstrand cross-linking.

• MeSH
• 2,2'-dipyridyl analogy a deriváty   toxicita   MeSH
• adukty DNA * MeSH
• DNA-dependentní DNA-polymerasy metabolismus   MeSH
• HeLa buňky MeSH
• konformace nukleové kyseliny MeSH
• leukemie L1210 MeSH
• lidé MeSH
• molekulární sekvence - údaje MeSH
• myši MeSH
• organokovové sloučeniny toxicita   MeSH
• protinádorové látky farmakologie   toxicita   MeSH
• reagencia zkříženě vázaná MeSH
• replikace DNA účinky léků   MeSH
• sekvence nukleotidů MeSH
• superhelikální DNA účinky léků   MeSH
• testy toxicity MeSH
• vztah mezi dávkou a účinkem léčiva MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Názvy látek
• 2,2'-dipyridyl MeSH
• adukty DNA * MeSH
• chloro(2,2'-6',2''-terpyridine)(2,2'-bipyridine)ruthenium MeSH Prohlížeč
• dichlorobis(2,2'-bipyridine)ruthenium MeSH Prohlížeč
• DNA-dependentní DNA-polymerasy MeSH
• organokovové sloučeniny MeSH
• protinádorové látky MeSH
• reagencia zkříženě vázaná MeSH
• superhelikální DNA MeSH
• Tli polymerase MeSH Prohlížeč
• trichloro(2,2'-6',2''-terpyridine)ruthenium MeSH Prohlížeč

By analyzing almost 120 000 dinucleotides in over 2000 nonredundant nucleic acid crystal structures, we define 96+1 diNucleotide Conformers, NtCs, which describe the geometry of RNA and DNA dinucleotides. NtC classes are grouped into 15 codes of the structural alphabet CANA (Conformational Alphabet of Nucleic Acids) to simplify symbolic annotation of the prominent structural features of NAs and their intuitive graphical display. The search for nontrivial patterns of NtCs resulted in the identification of several types of RNA loops, some of them observed for the first time. Over 30% of the nearly six million dinucleotides in the PDB cannot be assigned to any NtC class but we demonstrate that up to a half of them can be re-refined with the help of proper refinement targets. A statistical analysis of the preferences of NtCs and CANA codes for the 16 dinucleotide sequences showed that neither the NtC class AA00, which forms the scaffold of RNA structures, nor BB00, the DNA most populated class, are sequence neutral but their distributions are significantly biased. The reported automated assignment of the NtC classes and CANA codes available at dnatco.org provides a powerful tool for unbiased analysis of nucleic acid structures by structural and molecular biologists.

• MeSH
• biokatalýza MeSH
• DNA chemie   klasifikace   MeSH
• konformace nukleové kyseliny * MeSH
• nukleotidové motivy * MeSH
• nukleotidy chemie   klasifikace   MeSH
• reprodukovatelnost výsledků MeSH
• riboswitch MeSH
• ribozomy chemie   metabolismus   MeSH
• RNA katalytická chemie   metabolismus   MeSH
• RNA chemie   klasifikace   MeSH
• vazebná místa MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA MeSH
• nukleotidy MeSH
• riboswitch MeSH
• RNA katalytická MeSH
• RNA MeSH

We have used CD spectroscopy, polyacrylamide gel electrophoresis, and UV absorption spectroscopy to study conformational properties of DNA fragments containing (CCA)n and (TGG)n repeats, which are the most length-polymorphic microsatellite sequences of the human genome. The (CCA)n fragments are random single strands at neutral and alkaline pH but they fold into intramolecular intercalated cytosine tetraplexes at mildly acid pH values. More acid values stabilize intermolecular tetraplex formation. The behavior of (TGG)n repeats is more complex. They form hairpins or antiparallel homoduplexes in low salt solutions which, however, are transformed into parallel-stranded guanine tetraplexes at physiological KCl concentrations. Their molecularity depends on the repeat number: (TGG)4 associates into an octameric complex, (TGG)8 forms tetramolecular complexes. (TGG)n with odd repeat numbers (5, 7, and 9) generate bimolecular and tetramolecular tetraplexes. The only (TGG)7 folds into an intramolecular tetraplex at low KCl concentrations, which is antiparallel-stranded. Moreover, the (TGG)(n) fragments provide various mutually slipped conformers whose population increases with salt concentration and with the increasing repeat number. However, the self-structures of both strands disappear in the presence of the complementary strand because both (TGG)n and (CCA)n prefer to associate into the classical heteroduplex. We suppose that the extreme conformational variability of the DNA strands stands behind the length polymorphism which the (CCA)n/(TGG)n repeats exhibit in the human genome.

• MeSH
• chlorid draselný farmakologie   MeSH
• cirkulární dichroismus MeSH
• cytosin chemie   MeSH
• denaturace nukleových kyselin MeSH
• DNA chemie   MeSH
• EDTA chemie   MeSH
• elektroforéza v polyakrylamidovém gelu MeSH
• genom lidský MeSH
• koncentrace vodíkových iontů MeSH
• konformace nukleové kyseliny MeSH
• konformace proteinů MeSH
• lidé MeSH
• mikrosatelitní repetice MeSH
• oligonukleotidy MeSH
• polymorfismus genetický MeSH
• soli farmakologie   MeSH
• spektrofotometrie MeSH
• teplota MeSH
• trinukleotidové repetice MeSH
• ultrafialové záření MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• chlorid draselný MeSH
• cytosin MeSH
• DNA MeSH
• EDTA MeSH
• oligonukleotidy MeSH
• soli MeSH

Large-scale molecular dynamics (MD) simulations have been utilized to study G-DNA quadruplex molecules containing mixed GCGC and all-guanine GGGG quartet layers. Incorporation of mixed GCGC quartets into G-DNA stems substantially enhances their sequence variability. The mixed quadruplexes form rigid assemblies that require integral monovalent cations for their stabilization. The interaction of cations with the all-guanine quartets is the leading contribution for the stability of the four-stranded assemblies, while the mixed quartets are rather tolerated within the structure. The simulations predict that two cations are preferred to stabilize a four-layer quadruplex stem composed of two GCGC and two all-guanine quartets. The distribution of cations in the structure is influenced by the position of the GCGC quartets within the quadruplex, the presence and arrangement of thymidine loops connecting the guanine/cytosine stretches forming the stems, and the cation type present (Na(+) or K(+)). The simulations identify multiple nanosecond-scale stable arrangements of the thymidine loops present in the molecules investigated. In these thymidine loops, several structured pockets are identified capable of temporarily coordinating cations. However, no stable association of cations to a loop has been observed. The simulations reveal several paths through the thymidine loop regions that can be followed by the cations when exchanging between the central ion channel in the quadruplex stem and the surrounding solvent. We have carried out 20 independent simulations while the length of simulations reaches a total of 90 ns, rendering this study one of the most extensive MD investigations carried out on nucleic acids so far. The trajectories provide a largely converged characterization of the structural dynamics of these four-stranded G-DNA molecules.

• MeSH
• chemické modely * MeSH
• chlorid draselný chemie   MeSH
• chlorid sodný chemie   MeSH
• cytosin chemie   MeSH
• DNA chemie   MeSH
• guanin chemie   MeSH
• kationty jednomocné MeSH
• konformace nukleové kyseliny * MeSH
• molekulární modely MeSH
• oligonukleotidy chemie   MeSH
• počítačová simulace MeSH
• roztoky MeSH
• sekvence nukleotidů MeSH
• termodynamika MeSH
• thymidin chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• chlorid draselný MeSH
• chlorid sodný MeSH
• cytosin MeSH
• DNA MeSH
• guanin MeSH
• kationty jednomocné MeSH
• oligonukleotidy MeSH
• roztoky MeSH
• thymidin MeSH

We have compared the binding of human full-length p53 protein (p53; expressed in bacteria and insects) and its isolated core domain (p53CD, amino acids 94-312; expressed in bacteria) to negatively supercoiled (sc) DNA using gel electrophoresis and immunoblotting. Significant differences were observed; p53CD produced a relatively small and continuous retardation of scDNA, in contrast to the ladder of distinct bands formed by p53 in agarose gels. The ladder produced by full-length protein expressed in bacteria (p53b) was similar to that observed earlier with protein expressed in insect cells (p53i). Competition between scDNAs and their linearized (lin) forms showed a preference for scDNAs by both p53 and p53CD, but the ratios characterizing the distribution of the protein between sc and lin pBluescript DNAs were substantially higher for p53 (sc/lin > 60 in p53b) than for p53CD (sc/lin approximately 4). Strong binding of p53 to scDNA lacking the p53 consensus sequence may represent a new p53-binding mode, which we tentatively denote supercoil-selective (SCS) binding. This binding requires both the C-terminal domain and the core domain. Targets of this binding may include: (a) DNA segments defined both by the nucleotide sequence and local topology, and/or (b) strand crossings and/or bending. The binding preference of p53CD for scDNA may be due to the known nonspecific binding to internal single-stranded regions in scDNA (absent in relaxed DNA molecules) and/or to SCS binding albeit with reduced affinity due to the absence of contributions from other p53 domains.

• MeSH
• Baculoviridae metabolismus   MeSH
• DNA chemie   metabolismus   MeSH
• elektroforéza v agarovém gelu MeSH
• kompetitivní vazba MeSH
• konformace nukleové kyseliny MeSH
• nádorový supresorový protein p53 chemie   metabolismus   MeSH
• plazmidy metabolismus   MeSH
• superhelikální DNA metabolismus   MeSH
• terciární struktura proteinů MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• vysoká teplota MeSH
• vztah mezi dávkou a účinkem léčiva MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA MeSH
• nádorový supresorový protein p53 MeSH
• superhelikální DNA MeSH

The manner of packing of the terminal DNA loci into nucleosomes and higher order structures may strongly influence their functional interactions. Besides the structural flexibility of telomeric DNA sequences, conserved features of their chromatin including short nucleosome phasing (157 bp) and nucleosome sliding have been described previously. To gain a complementary knowledge of subtelomeres, we have analysed the chromatin structure of two subtelomeric tandem repeats from the plant Silene latifolia: X43.1 and 15Ssp. X43.1 shows two distinct nucleosome periodicities--157 and 188 bp. Preferred positions of its two nucleosomes have been mapped at both low and high resolution and the experimental results correspond to computer-predicted positions. 15Ssp is a newly-discovered sequence showing a telomere-associated position by PCR and a subtelomeric location by pulsed-field gel electrophoresis and fluorescence in situ hybridisation. Its 159 bp sequence unit shows a tandem arrangement and the presence of micrococcal nuclease-hypersensitive sites when either naked DNA or chromatin is digested. Use of a chemical nuclease results in a regular nucleosome ladder of 157 bp periodicity. Moreover, 15Ssp mononucleosomes show instability and absence of specific positioning, features typical for telomeric chromatin.

• MeSH
• DNA rostlinná chemie   genetika   metabolismus   MeSH
• genetické matrice MeSH
• heterochromatin chemie   genetika   metabolismus   MeSH
• hybridizace in situ fluorescenční MeSH
• konformace nukleové kyseliny * MeSH
• Magnoliopsida genetika   MeSH
• mikrokoková nukleasa metabolismus   MeSH
• molekulární sekvence - údaje MeSH
• nukleozomy chemie   genetika   metabolismus   MeSH
• restrikční mapování MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA MeSH
• Southernův blotting MeSH
• tandemové repetitivní sekvence genetika   MeSH
• telomery genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná MeSH
• heterochromatin MeSH
• mikrokoková nukleasa MeSH
• nukleozomy MeSH