Hydrophobic catalysis and a potential biological role of dna pnas. Zdna and zrna in human disease communications biology. The adna structure is dominates in dehydrated samples and is similar to the doublestranded rna and dnarna hybrids. B at and gc base pairs shown for watsoncrick pairing a and hoogsteen pairing b. In aqueous enviromnents, including the majority of dna in a cell, bdna is the most common structure. Bdna displays either a hydration spine when the minor groove is. A small amount of the dna in a cell exists in the z form. Canonical, righthanded bdna can be transformed into noncanonical, lefthanded zdna in vitro at high salt concentrations or in vivo under physiological conditions. The helix has two nucleotides in the asymmetric unit and contains twelve base pairs per turn. This increase in emission, thus, appears to be an intrinsic property of zdna regardless of the fluorophore. High regularity of zdna revealed by ultra highresolution crystal. Z dna structure is lefthanded with 12 average base pairs per turn, distance between adjacent bases 0. Lavery, peter kollman, helen berman, nina pastor, z.
The structure of the bz junction has been revealed in a crystal structure ha et al. The information from the base composition of dna, the knowledge of dinucleotide structure, and the insight that the x. A similar enhancement of the fluorescence in zdna has previously also been observed for 2ap and was attributed to the disruption of the continuous base stacking of bdna, as the zdna architecture forms a discreet 4base stack 35,36. Each time a dna segment turns into zdna, two bz junctions form. The helical structure of dna is variable and depends on the sequence as well as the environment. Zdna is a radically different duplex structure, with the two strands coiling in lefthanded helices and a pronounced zigzag hence the name pattern in the phosphodiester backbone. This was tethered in the zform by being bound to domains of a zdnabinding protein, with the effect that eight base pairs are in the zform and six are in a bdna conformation fig. A stretched conformation of dna with a biological role. A, b and zdna helix families david w ussery,danish technical university, lyngby, denmark there are three major families of dna helices. Abstract there are three major families of dna helices.
The b form described by james watson and francis crick is believed to predominate in cells. A form helix senseright hand repeating units1 bp rotationbp33. Molecular dynamics simulations of bdna wesleyan university. Zdna is a rarer structure found in dna bound to certain proteins. High salt concentrations are required to minimize electrostatic repulsion between the backbone phosphates, which are closer to each other than in a and bdna. Source of the article published in description is wikipedia. Z dna is one of the many possible double helical structures of dna. Zi, with the phosphate groups inclined towards the inside of the helix, and zii, with the phosphate. The helical structure of dna is variable and depends on the sequence as well as the. Pictures of the double helix of deoxyribonucleic acid dna havebecomesocommonthateveryoneisfamiliar with its overall shape and structure figure 1a.
A dna, b dna and z dna this lecture explains about the difference between a dna, b dna and z dna. This bform of dna has approximately 10 nucleotides per turn of the. The conversion of bdna to zdna was associated with a flipping over of the base pairs so that they had an upside down orientation relative to that of bdna. During the manual inspection sessions, one spermine molecule was modeled and water. This z dna is formed by stretches of alternating purines and pyrimidines, e. The various types of conformations that the dna can adopt depend on different factors such as. It is a righthanded double helix fairly similar to the more common bdna form, but with a shorter, more compact helical structure whose base pairs are not perpendicular to the helixaxis as in bdna. The adna structure is dominates in dehydrated samples and is similar to the doublestranded rna and dna rna hybrids. Dna transkription in rna, weiter translatiert in proteine. The b to adna transition and the reorganization of solvent at the. The dna structure that watson and crick proposed was the b form of dna bdna, and this is the physiological form of dna. Under physiological conditions, most dna is in the b form.
The molecular mechanism of this drastic conformational transition is still unknown despite numerous studies. At least three dna conformations are believed to be found in nature, adna, bdna, and zdna. Methylation of cytosine at the 5carbon position 5mc is observed in both prokaryotes and eukaryotes. Zdna is a conformer of bdna stabilized both by negative superhelical stress and by binding of the z. In humans, dna methylation at cpg sites plays an important role in gene regulation and has been implicated in development, gene silencing, and cancer. Molecular structure of a lefthanded double helical dna fragment at. Zdna can form when the dna is in an alternating purinepyrimidine sequence such as gcgcgc, and indeed the g and c nucleotides are in different conformations. These have been examined extensively, but their structure was unknown. Note the difference in groove width and the relative displacements of the base pairs from the central axis. Each family has its own intrinsic restrictions on chain folding and structure.
A comparison table dna, the genetic information carrier molecule of the cell, is a long polymer of nucleotides and can adopt different types of structural conformations. This was performed by measuring the intensity values between the donor and acceptor fluorescent dyes, also known as fluorophore s, in relation to each other as they exchange electrons, while tagged onto a dna molecule. Besides chirality, zdna and bdna differ by their helical pitch, zdna being more elongated. Zdna is a high energy conformer of bdna that forms in vivo during transcription as a result of torsional strain generated by a moving polymerase. The role of methylation in the intrinsic dynamics of b. In addition, the cpg dinucleotide is a known hot spot for pathologic mutations genomewide. Z dna is thought to be one of three biologically active doublehelical structures along with aand b dna. In 2018, the pathway from bdna to zdna was experimentally proven using smfret assays. The double helix makes one complete turn about its axis every 10. Dna helix families ussery major reference works wiley online library. However, the dodecamer molecule shows a high level of flexibility, especially of the backbone phosphate groups, with six out of 11 phosphates modeled in double orientations corresponding to the two previously observed zdna conformations. The exact biological function of zdna is not clear. Adna is thought to be one of three biologically active double helical structures along with bdna and zdna.
Collapse of dna in packaging and cellular transport. It explains the structural differences between a,b and z. All helices on the picture are formed by 22 base pairs. The bform is the normal dna found in most biological aqueous contexts. Under reduced water conditions the aform is favoured, and under. The crystal structure of a zdna hexamer duplex dcgcgcg2 determined at ultra high. At least one example has been examined from each of the three known families of dna helix. What is the difference between a, b, and z forms of dna.
Zdna occurs in a dynamic state, forming as a result of physiological processes then relaxing to the righthanded bdna. The structure a dna molecule depends on its environment. The b to z helical transformation can be induced in supercoiled dna by untwisting the macromolecule. Zdna is one of the many possible double helical structures of dna. It has been tantalizing to propose that this different structure is involved in some way in regulation of some cellular function. Zdna is thought to be one of three biologically active double helical structures along with a and bdna.
The zdna form is adopted by short oligonucleotides that have sequences of alternating pyrimidines and purines. It is a lefthanded double helical structure in which the double helix winds to the left in a zigzag pattern instead of to the right, like the more common bdna form. Z junction and the previous zipper model, we show here, with the aid of. An understanding of the biological role of zdna has advanced with the discovery that the rna editing enzyme doublestranded rna adenosine deaminase type i adar1 has motifs specific for the zdna conformation. It is a lefthanded double helical structure in which the helix winds to the left in a zigzag pattern, instead of to the right, like the more common b dna form. Adna adna is one of the possible double helical structure which dna can adopt along with other two biologically active helix structureb dna,zdna. Flow ld confirms bdna and indicates shorter persistence length in diglyme. The transition between the b and z conformations of dna. A, b and zdna double helices in the canonical conformations. Different forms of dna a form, b form, z form molecular. The helix has an opposite rotation, composed of c and g nucleotides and is less symmetrical. Unveiling the pathway to zdna in the proteininduced bz. The zdna is usually located upstream of the start site of a gene and thus it may have some role in the regulation of gene expression. This structure is known as bdna, and represents an average conformation of dna, based on.