Sugar puckering usually dna one observes equilibrium of the s and n forms sugar repuckering. Base pair switching by interconversion of sugar puckers in. Glycosyl bond and sugar puckering in dna unacademy. These results can be correlated with the change in the intensities of zform dna which adopts a c 2 endo puckering. Z dna is one of the many possible double helical structures of dna. Neglect of diatomic differential overlap nddo and selfconsistent densityfunctional tightbinding sccdftb semiempirical models commonly employed in combined quantum mechanicalmolecular mechanical simulations fail to adequately describe the. The geometry of the dna forms can be used to describe the differences seen. Oisopropylideneadenosine structural studies on the two forms of 8bromo2. Each sugar is assigned into one of the following ten puckering modes, by dividing the phase. S, f s several methods for analysis exist, graphical and the more rigorous simulation. A dna is fairly similar to b dna given that it is a righthanded double helix with major and minor grooves. Sugar pucker correlates with phosphorusbase distance 3dna. Principles of nucleic acid structure, springerverlag, 1984.
Structural effects of cytosine methylation on dna sugar. The o2 stericly disfavors the c2endo conformation favored in b dna. Sugar pucker synonyms, sugar pucker pronunciation, sugar pucker translation, english dictionary definition of sugar pucker. Conformationally rigid nucleoside probes help understand the. So, again, we said the first component in dna deoxyribose.
The second thing we discussed just now were the nitrogens bases and now the third component in dna is going to be a phosphate group. Because of steric and energetic reasons some puckers are preferred over the others. Conformational variation arises from restricted bond rotations within the sugar ring, giving rise to different ribose ring pucker, and torsional angles at bonds connecting phosphate to ribose. B dna base pairs are nearly perpendicular to the helix axis. Sugar pucker definition of sugar pucker by the free. The interplay of sugar puckering and metal ion coordination may be an important mechanism to balance binding affinities of rna and dna interactions in general. In practice the desired outcome determines the effort to. Sugar rings play a central role in biological systems. Ribose ring pucker arises because a flat pentagon puts all ring c atoms into eclipsed conformations, despite the fact that the pentagon angle of 108 o is very close to the c tetrahedral angle of 109.
The sugar pucker pseudorotation phase pucker and helicoidal parameters were calculated from the average. How the sugar binds in the helix formation determines the tightness of the helix, so it will be a form or b form. Insight into the stabilization of adna by specific ion. A dna is one of the possible double helical structures which dna can adopt. Our thermodynamic findings led to a series of experiments with dna ligase that reveal, contrary to expectation based upon observed tms, that the duplex. Jan 26, 2017 consequently, the sugar phosphate backbone is shorter in comparison to the c2endo conformation, resulting in a double helix in which the base pairs are somewhat displaced. The structural properties of these locked pseudosugars are therefore useful for exploring the role of the sugar pucker and the glycosyl bond orientation in the stabilization of gquartet dna structures. One exception to this was found in the structures of icicicic 2.
Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombinbinding aptamer hisao saneyoshi1, stefania mazzini2, anna avin. Thesugar puckers in dna rna structures are predominately in either c3. On the role of uniform and mixed sugar puckers in dna double. The ribose ring is not aplanar and usually presents c2endo south or c3endo north conformation. The benchmark calculations are compared with semiempirical models. But like that slogan, the sugar conformation mantra needs revision, because it ignores what we see in the crystallographic data. The precise conformation of a deoxyribose ring can be completely specified by the five endocyclic torsion angles within it fig. Sugar the sugars in dna and rna are pentoses 5 carbons. Improvement of dna and rna sugar pucker pro les from. A dna, is similar to b dna, but with different sugar conformation leading to different base position with respect to the helical axis. A common substituent placed on the base is a methyl group on the c5 carbon. The 2oh of ribose shown in white in this view favors the c3endo sugar pucker necessary for aform geometry. The exact biological function of z dna is not clear.
Metal ions and sugar puckering balance singlemolecule. Sugar puckering there are two preferred ways of arranging the base in relation to the ribose, synand anti figs. In these two sugar conformations, the distance between neighboring phosphorus p atoms and the orientation of p relative to the sugarbases are. It also states the role of sugar puckering for better hydrogen bonding between complementary bases. Resolving sugar puckers in rna excited states exposes slow. Oh position, can change due to mispair formation, as well as from changes in the glycosidic torsion angle 1923. Sugar pucker geometries at the intercalation site of. In these two sugar conformations, the distance between neighboring phosphorus p atoms and the orientation of p relative to the sugar bases are also dramatically different figure below, right. All xray single crystal diffraction studies of chimeric duplexes have shown that sugar puckering invariably occurs in the c3.
The effect of sugar puckering on the sequencedependent protein dna interactions has not been studied systematically, however. Anyway, now that weve discussed the nitrogen bases that make up dna lets go back to actually putting our dna together and the various components in it. The ribose sugar geometry is defined by the following five endocyclic torsion angles. Pdf metal ions and sugar puckering balance singlemolecule. Whereas a dna crystal structures show little deviation from c39endo sugar puckering 14, 15, b dna structures have a broad distribution of sugar puckers centered on c29endo but extending from c49exoto c39endo and. It is a righthanded double helix fairly similar to the more common b dna form, but with a shorter, more compact helical structure whose base pairs are not perpendicular to the helixaxis as in b dna. There are several important differences between dna and rna. A dna base pairs inclined with respect to helical axis and untwisted cf. Thus, sequences r14,15 and fa14,15 were modified with two riboguanosines and two 2fluoro.
The rmsd values were calculated using the program midasplus and the canonical a dna and b dna models were created as described in the materials and methods. Puckering relieves the steric conflict due to eclipsed. Crystal structure and conformation of a dnarna hybrid duplex. Ring pucker also affects nonbonded hh separations, which can be measured by noesy. Unless one form greatly dominates the local analysis requires quite a few parameters. These alterations permit dna to bend into its wide groove, eventually resulting in the formation of the mixed puckered kink i. This dna structure lecture explains the sugar puckering chemistry. Conformationally rigid nucleoside probes help understand. Essentially all helical rna is in a form, but dna can also be found in a form under certain conditions particularly in rna dna hybrids. Sugar pucker modulates the crosscorrelated relaxation. The dependence of n19 and c1 chemical shielding cs tensors on the glycosidic bond orientation.
Structural effects of cytosine methylation on dna sugar pucker studied by ftir banyay, martina. This failure limits the application of these methods to rna and dna systems. Z dna is one of the biologically active forms of dna found in vivo in the cells. Improvement of dna and rna sugar pucker profiles from semiempirical quantum methods article in journal of chemical theory and computation 104. The results indicate that these cstensors exhibit a significant degree of conformational.
Video description in this video, we describe the mechanistic details of dna sugar puckering at molecular level. A dna, is a form of the dna duplex observed under dehydrating conditions. The magnotudes of such angles are all interrelated and, therefore, the geometry of the ribose ring can be defined from two parameters. The two substitutions promoted a structural rearrangement to a topology with the 5terminal g residue located in the central tetrad and the two modified residues linked by a v. Biophysical chemistry 1, fall 2010 reading assignment. A dna is thought to be one of three biologically active double helical structures along with b dna and z dna.
The sugar pucker which determines the shape of the ahelix, whether the helix will exist in the aform or in the bform, occurs at the c2endo. Dec 22, 2009 while sugar conformation can be biased by sugar structure, sugar conformation can also be influenced by base pair configuration. The impact of sugar pucker on base pair and mispair stability ncbi. B dna c c2endo for pyrimidines and c3endo for purines. Proteindna hydrophobic recognition in the minor groove is. The structure of a stable intermediate in the a b dna helix. Confirming the excited state sugar puckers using an es2stabilizing tar mutant. Conformational energies of dna sugar phosphate backbone.
The sugar puckers in dnarna structures are predominately in either c3. The ring puckering arises from the effect of nonbonded interactions between substituents at the four ring carbon atoms the energetically most. Sugar puckering in rna is related to an aconformation that enables genetic transfer from dna via a. The two types of sugar pucker most commonly found in nucleic acids. Sugar pucker definition of sugar pucker by medical. Methylation of dna is an important functional signal in transcription, but its effect on dna. Cyclic conformation and nucleic acid sugar puckering.
Influence of metal on sugar puckering and stability of nglycosidic bond, a dft study. This video explains the types of sugar puckering found in dna and the effect of sugar puckering in maintaining the structure of double helix. The z dna is usually located upstream of the start site of a gene and thus it may have some role in the regulation of gene expression. The fivemembered deoxyribose sugar ring in dna is inherently nonplanar. This has improved the precision of the description of dna structure, but we will see there is still some ambiguity about the structure of z dna. Yoshifumi nishimura, masamichi tsuboi, toru nakano, shigesada higuchi, tomohiro sato, toshio shida, seiichi uesugi, eiko ohtsuka, morio ikehara, raman diagnosis of nucleic acid structure. Taken together, the rd data pinpoint slow sugar dynamics specifically to nucleotides that experience changes in base pairing upon forming an es and otherwise provide no evidence for slow modes of repuckering dynamics in a variety of structural contexts. Crystal structure and conformation of a dnarna hybrid.
Case study i dna sugar pucker is sensitive to many substituents that are placed on the deoxyribose nitrogenous base. The sugar phosphate backbone of the two antiparallel chains forms ridges on the edges of the helix. Dna can exist in a number of configurations, of which b dna is the predominant form. Nevertheless, dssr also contains an undocumented option, sugar pucker westhof83, to output. B dna e c2endo for purines and c3endo for pyrimidines. The effect of sugar puckering on the sequencedependent proteindna interactions has not been studied systematically, however.
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. Dna structures are now determined using crystals of synthetic oligonucletides. Pdf improvement of dna and rna sugar pucker profiles. Z dna, a lefthanded form, was also prepared, although its biological relevance is still the subject of investigation. The impact of sugar pucker on base pair and mispair stability. Learn vocabulary, terms, and more with flashcards, games, and other study tools. The crystal structure of dacccgcgggt 2 was obtained from the nucleic acid databank, pdb entry code pdb220d. Sugar pucker and nucleic acid structure martin egli department of biochemistry, vanderbilt university, nashville, tn 37232 the world is made of sugar and dirt doblin, 1929 dna and rna are acids, contain bases, form salts and are held together by sugars. Previously, other investigators have observed that the placement of 2. The backbone of rna and dna consists of the alternating phosphateribose or 2deoxyribose chain. During this modeling, we found that the interconversion of sugar puckers between the ntype and the stype rotates bases horizontally, while maintaining the deoxyribosebase stacking interaction. However, as shown in the comparison table below, there is a slight increase in the number of base pairs bp per turn resulting in a smaller twist angle, and smaller rise per base pair making a dna 2025% shorter than b dna.
Information readout in the dna minor groove is accompanied by substantial dna deformations, such as sugar switching between the two conformational domains, blike c20endo and alike c30endo. Improvement of dna and rna sugar pucker profiles from. To more generally assess the role of a north sugar pucker for v. Glycosyl bond and suger puckering hindi dna stucture. In an ideal dna double helix, there are approximately 10 base pairs per turn of dna. Usually, the helical conformation is righthanded, that is, it twists to the right as do the threads on most screws. T1 an efficient nmr experiment for analyzing sugar puckering in unlabeled dna. Apr 17, 2014 this stereochemistry video lecture explains the mechanism of sugar puckering in dna ribose sugar. The existence of z dna was discovered by andres wang and alexander rich. Methylation, sugar puckering and zform status of dna from a.
Dec 06, 2002 read structural effects of cytosine methylation on dna sugar pucker studied by ftir, journal of molecular biology on deepdyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips. They are one of the building blocks of carbohydrates 1. Z dna is thought to be one of three biologically active doublehelical structures along with aand b dna. Sugar pucker and nucleic acid structure martin egli the world is made of sugar and dirt doblin, 1929 dna and rna are acids, contain bases, form salts and are held together by sugars. The sugar puckers in dna rna structures are predominately in either c3. Z dna d c2endo for purines and c3endo for pyrimidines.
An efficient nmr experiment for analyzing sugarpuckering. The prevalence of stype sugar puckering over ntype conformation indicates an elevated level of zform dna in heavy metalacclimated groups, in agreement with our result in the dna backbone. T2 application to the 26kda dead ringer dna complex. In this work, we provide benchmark ab initio gasphase twodimensional potential energy scans of the rna and dna sugar puckering. We chose to use rna secondary structure to probe chemical shift trends, since there are often few direct constraints on the sugar puckers in nmr structures, noting that most helical nucleotides adopt the c3. While sugar conformation can be biased by sugar structure, sugar conformation can also be influenced by base pair configuration. A nucleic acid that carries the genetic information in cells and some viruses, consisting of two long. Structural impact of other modifications at position 14 and 15. Determination of the dna sugar pucker using c nmr spectroscopy. In this form the molecule is twisted into a righthanded double helix, with a complete turn every tenth base.
Aug 12, 2017 video description in this video, we describe the mechanistic details of dna sugar puckering at molecular level. This is often done naturally by the cell as an epigenetic marker for many cellular processes in both, prokaryotes and eukaryotes. This point may be help you for your question sugar pucker correlates with phosphorusbase distance. Z dna is a lefthanded double helical conformation of dna in which the double helix winds to the left in a zigzag pattern.
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