scholarly journals DNA information: from digital code to analogue structure

2012 ◽  
Vol 370 (1969) ◽  
pp. 2960-2986 ◽  
Author(s):  
A. A. Travers ◽  
G. Muskhelishvili ◽  
J. M. T. Thompson
Keyword(s):  
Dimensional Space ◽  
Double Helix ◽  
Three Dimensional ◽  
Base Pairs ◽  
Nucleosome Core ◽  
Histone Octamer ◽  
Regulatory Mode ◽  
Sequence Periodicity ◽  
Recent Developments ◽  
Dna Double Helix

The digital linear coding carried by the base pairs in the DNA double helix is now known to have an important component that acts by altering, along its length, the natural shape and stiffness of the molecule. In this way, one region of DNA is structurally distinguished from another, constituting an additional form of encoded information manifest in three-dimensional space. These shape and stiffness variations help in guiding and facilitating the DNA during its three-dimensional spatial interactions. Such interactions with itself allow communication between genes and enhanced wrapping and histone–octamer binding within the nucleosome core particle. Meanwhile, interactions with proteins can have a reduced entropic binding penalty owing to advantageous sequence-dependent bending anisotropy. Sequence periodicity within the DNA, giving a corresponding structural periodicity of shape and stiffness, also influences the supercoiling of the molecule, which, in turn, plays an important facilitating role. In effect, the super-helical density acts as an analogue regulatory mode in contrast to the more commonly acknowledged purely digital mode. Many of these ideas are still poorly understood, and represent a fundamental and outstanding biological question. This review gives an overview of very recent developments, and hopefully identifies promising future lines of enquiry.

Symmetry-adapted digital modeling II. The double-helix B-DNA

2016 ◽  
Vol 72 (3) ◽  
pp. 312-323 ◽  
Author(s):  
A. Janner
Keyword(s):  
Dimensional Space ◽  
Double Helix ◽  
Three Dimensional ◽  
Reduction Factor ◽  
Lattice Points ◽  
Three Dimensions ◽  
Coarse Grained ◽  
Digital Modeling ◽  
Dna Strands ◽  
Dna Double Helix

The positions of phosphorus in B-DNA have the remarkable property of occurring (in axial projection) at well defined points in the three-dimensional space of a projected five-dimensional decagonal lattice, subdividing according to the golden mean ratio τ:1:τ [with τ = (1+\sqrt {5})/2] the edges of an enclosing decagon. The corresponding planar integral indicesn1,n2,n3,n4(which are lattice point coordinates) are extended to include the axial indexn5as well, defined for each P position of the double helix with respect to the single decagonal lattice ΛP(aP,cP) withaP= 2.222 Å andcP= 0.676 Å. A finer decagonal lattice Λ(a,c), witha=aP/6 andc=cP, together with a selection of lattice points for each nucleotide with a given indexed P position (so as to define a discrete set in three dimensions) permits the indexing of the atomic positions of the B-DNA d(AGTCAGTCAG) derived by M. J. P. van Dongen. This is done for both DNA strands and the single lattice Λ. Considered first is the sugar–phosphate subsystem, and then each nucleobase guanine, adenine, cytosine and thymine. One gets in this way a digital modeling of d(AGTCAGTCAG) in a one-to-one correspondence between atomic and indexed positions and a maximal deviation of about 0.6 Å (for the value of the lattice parameters given above). It is shown how to get a digital modeling of the B-DNA double helix for any given code. Finally, a short discussion indicates how this procedure can be extended to derive coarse-grained B-DNA models. An example is given with a reduction factor of about 2 in the number of atomic positions. A few remarks about the wider interest of this investigation and possible future developments conclude the paper.

The unique structure of A-tracts and intrinsic DNA bending

2009 ◽  
Vol 42 (1) ◽  
pp. 41-81 ◽  
Author(s):  
Tali E. Haran ◽  
Udayan Mohanty
Keyword(s):  
Current Knowledge ◽  
Double Helix ◽  
Dna Bending ◽  
Helical Axis ◽  
Base Pairs ◽  
Regulatory Regions ◽  
Unique Structure ◽  
Distinct Structure ◽  
Global Curvature ◽  
Dna Double Helix

AbstractShort runs of adenines are a ubiquitous DNA element in regulatory regions of many organisms. When runs of 4–6 adenine base pairs (‘A-tracts’) are repeated with the helical periodicity, they give rise to global curvature of the DNA double helix, which can be macroscopically characterized by anomalously slow migration on polyacrylamide gels. The molecular structure of these DNA tracts is unusual and distinct from that of canonical B-DNA. We review here our current knowledge about the molecular details of A-tract structure and its interaction with sequences flanking them of either side and with the environment. Various molecular models were proposed to describe A-tract structure and how it causes global deflection of the DNA helical axis. We review old and recent findings that enable us to amalgamate the various findings to one model that conforms to the experimental data. Sequences containing phased repeats of A-tracts have from the very beginning been synonymous with global intrinsic DNA bending. In this review, we show that very often it is the unique structure of A-tracts that is at the basis of their widespread occurrence in regulatory regions of many organisms. Thus, the biological importance of A-tracts may often be residing in their distinct structure rather than in the global curvature that they induce on sequences containing them.

scholarly journals Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Shu-ichi Nakano ◽  
Masayuki Fujii ◽  
Naoki Sugimoto
Keyword(s):  
Nucleic Acid ◽  
Base Pair ◽  
Double Helix ◽  
Nucleoside Analogs ◽  
Structural Analog ◽  
Base Pairs ◽  
Nucleic Acid Analogs ◽  
Dna Double Helix ◽  
Nucleic Acid Interactions ◽  
Site Selective

Unnatural nucleosides have been explored to expand the properties and the applications of oligonucleotides. This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions. We also describe the nucleoside analogs of a base pair-mimic structure that we have examined. Although the base pair-mimic nucleosides possess a simplified stacking moiety of a phenyl or naphthyl group, they can be used as a structural analog of Watson-Crick base pairs. Remarkably, they can adopt two different conformations responding to their interaction energies, and one of them is the stacking conformation of the nonpolar aromatic group causing the site-selective flipping of the opposite base in a DNA double helix. The base pair-mimic nucleosides can be used to study the mechanism responsible for the base stacking and the flipping of bases out of a nucleic acid duplex.

5-Aza-7-deaza-2′-deoxyguanosine and 2′-Deoxycytidine Form Programmable Silver-Mediated Base Pairs with Metal Ions in the Core of the DNA Double Helix

2018 ◽  
Vol 24 (35) ◽  
pp. 8883-8892 ◽  
Author(s):  
Xiurong Guo ◽  
Peter Leonard ◽  
Sachin A. Ingale ◽  
Jiang Liu ◽  
Hui Mei ◽  
...  
Keyword(s):  
Metal Ions ◽  
Double Helix ◽  
Base Pairs ◽  
The Core ◽  
Dna Double Helix

The bending of DNA in nucleosomes and its wider implications

1987 ◽  
Vol 317 (1187) ◽  
pp. 537-561 ◽  
Keyword(s):  
Dna Sequences ◽  
Nucleosome Core Particle ◽  
Base Pairs ◽  
Structural Explanation ◽  
Bent Dna ◽  
Nucleosome Core ◽  
Histone Octamer ◽  
Naturally Occurring ◽  
Superhelical Turn ◽  
Intrinsically Bent Dna

The DNA of a nucleosome core particle is wrapped tightly around a histone octamer with approximately 80 base pairs per superhelical turn. Studies of both naturally occurring and reconstituted systems have shown that DNA sequences very often adopt well-defined locations with respect to the octamer. Recent work in this laboratory has provided a structural explanation for this sequence-dependent positioning in terms of the differential flexibility of different sequences and of departures from smooth bending. The ‘rules’ that are emerging for DNA bendability and, from the results of other workers, on intrinsically bent DNA, are likely to be useful in considering looping and bending of DNA in other processes in which it is thought to be wrapped around a protein core.

scholarly journals Solution structure of a DNA double helix with consecutive metal-mediated base pairs

2010 ◽  
Vol 2 (3) ◽  
pp. 229-234 ◽  
Author(s):  
Silke Johannsen ◽  
Nicole Megger ◽  
Dominik Böhme ◽  
Roland K. O. Sigel ◽  
Jens Müller
Keyword(s):  
Solution Structure ◽  
Double Helix ◽  
Base Pairs ◽  
Dna Double Helix

scholarly journals Destabilization of DNA duplexes by oxidative damage at guanine: implications for lesion recognition and repair

2008 ◽  
Vol 5 (suppl_3) ◽  
pp. 191-198 ◽  
Author(s):  
Supat Jiranusornkul ◽  
Charles A Laughton
Keyword(s):  
Oxidative Damage ◽  
Structural Changes ◽  
Double Helix ◽  
Dependent Manner ◽  
Dna Duplexes ◽  
Lesion Site ◽  
Base Pairs ◽  
Energetic Analysis ◽  
Dynamics Simulations ◽  
Dna Double Helix

We have used molecular dynamics simulations to study the structure and dynamics of a range of DNA duplexes containing the 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapydG) lesion that can result from oxidative damage at guanine. Compared to the corresponding undamaged DNA duplexes, FapydG-containing duplexes show little gross structural changes—the damaged base remains stacked in to the DNA double helix and retains hydrogen bonds to its cytosine partner. However, the experimentally observed reduction in DNA stability that accompanies lesion formation can be explained by a careful energetic analysis of the simulation data. Irrespective of the nature of the base pairs on either side of the lesion site, conversion of a guanine to a FapydG base results in increased dynamical flexibility in the base (but not in the DNA as a whole) that significantly weakens its hydrogen-bonding interactions. Surprisingly, the stacking interactions with its neighbours are not greatly altered. The formamido group adopts a non-planar conformation that can interact significantly and in a sequence-dependent manner with its 3′-neighbour. We conclude that the recognition of FapydG lesions by the repair protein formamidopyrimidine-DNA glycosylase probably does not involve the protein capturing an already-extrahelical FapydG base, but rather it relies on detecting alterations to the DNA structure and flexibility created by the lesion site.

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