Also, the phosphate conformations strongly influence groove width values. An increasing number of BII states narrows the major groove and broadens the minor groove, although minor and major groove widths are poorly anti-correlated Figure provided in Supporting Information S1. This minor groove opening is mechanically associated to the accumulation of negative rolls in BII-rich segments [21] , [28] , [30]. We recall that the roll angle measures the rotation between two successive base-pair planes about their long axis y-axis ; the roll is negative when it opens up on the major groove side of the bases.
In any decamer, the groove dimensions are defined over the 6 central base-pairs. The differential effects of BI- or BII-rich regions on the groove dimensions are illustrated on two representative decamers in Figure 3 , clearly showing a wider minor groove and a shallower major groove in the BII-rich decamer. BI and BII phosphate groups are in blue and green, respectively.
Top: the lateral view shows that the minor groove mG is considerably enlarged in the BII-rich structure right. Bottom: view along the major groove MG , showing its reduced concavity in the BII-rich structure right. The mechanism relating phosphate group behavior to groove dimensions is particularly interesting in regard to the minor groove width variations.
The next section examines this point. These scores were compared to the exhaustive minor groove width values recently published [6]. These minor groove width data were extracted from a large number of free oligomer X-ray structures, then sorted and averaged according to 59 out of the possible tetrameric sequences.
Despite a rather large dispersion, likely contributed by crystallographic biases, the tetramer TRX scores broadly reflect the minor groove width values Figure 4 -A. This parallel between the sequence-dependent DNA flexibilities in solution TRX scores and the minor groove widths in X-ray structures strongly supports the notion that this relation is a general intrinsic property of DNA.
To interpret this relation, one should keep in mind the origins of the quantities, both averaged but extracted from either static minor groove width values or dynamic TRX scores structures. In particular, high tetrameric TRX scores correspond to flexible tetrameric sequences, in which the phosphate linkages can explore all the BI and BII combinations listed in Table 1. Therefore, malleable sequences oscillate between wide and narrow grooves. The coupling uncovered in Figure 4 -A means that higher TRX scores increase the probability of wide minor groove conformations.
These values are plotted versus the TRX scores calculated on the same DNA sequences, with a sliding tetrameric window. The vertical bars correspond to the minor groove width standard deviations. The black curves are non-linear data fits. Overall, the TRX analysis provides a new and mechanistically based interpretation of the sequence-dependent propensities for wider minor groove in B-DNA. Next, we examine whether DNA binding proteins take advantage of this groove malleability. To investigate if proteins exploit the intrinsic sequence-dependent malleability of the DNA, we compared the TRX scores of free tetrameric sequences to the minor groove width values recently compiled [6] on tetramers in crystallographic DNA-protein complexes, and averaged according to the possible tetrameric sequences.
In this crystal structure dataset, the proteins bind either the major or minor groove of their DNA targets. On average, minor groove width values in protein-bound DNA are significantly wider 6. The minor groove width values of protein-bound DNA parallel well the corresponding TRX scores of intrinsic flexibility for tetrameric sequences Figure 4 -B.
This correlation is less dispersed than that obtained with minor groove width in free DNA Figure 4 -A. A possible reason is the larger size of the protein-bound DNA dataset. As shown above, stiff sequences favor narrow minor grooves while free malleable sequences can explore various conformations, from narrow to wide minor grooves. Figure 4 indicates that proteins exploit the ability of flexible tetramers to adopt wide minor grooves.
Such cases point out that proteins can sometimes overcome the intrinsic structural preference of DNA. Also, more specific and sequence-focused arguments reinforce the idea that proteins exploit the intrinsic DNA mechanical properties.
In protein-bound DNA, the malleable GC-rich and the stiff AT-rich tetramers are strongly associated to wide and narrow minor grooves, respectively. This stresses that, although the DNA mechanics is very influential, other factors also contribute to DNA-protein recognition.
Analyzing the observed minor groove width in terms of sequence-dependent intrinsic flexibility provides further insights regarding the dependence on the sequence context. So, our results show significant evidence that the DNA minor-groove deformation upon protein binding is commensurate with the intrinsic nucleotidic sequence-dependent malleability captured by the TRX scale.
Under the protein influence, such distortions can be enhanced beyond what is observed in free DNA, but these enhanced deformations still reflect the intrinsic sequence-dependence DNA flexibility. Analyzing the groove dimensions in DNA-protein complexes highlighted that the DNA minor groove width is especially variable [3] , [6] , [8] , [9]. Biology 3 months, 2 weeks ago. View Full Video Already have an account?
Joanna Q. Answer What is the major groove of a DNA helix? Discussion You must be signed in to discuss. Video Transcript What's his beat?
Upgrade today to get a personal Numerade Expert Educator answer! Ask unlimited questions. Test yourself. Join Study Groups. Create your own study plan. Join live cram sessions. Live student success coach. Top Biology Educators Emily T. University of Wisconsin - Madison. The latter conformation brings the 5' and 3' hydroxyls both esterified to the phosphates linking to the next nucleotides closer together than is seen in the C2' endoconfromation Figure 2.
A second major difference between A-form and B-form nucleic acid is the placement of base-pairs within the duplex.
The result is a ribbon-like helix with a more open cylindrical core in A-form. Z-DNA is a radically different duplex structure, with the two strands coiling in left-handed helices and a pronounced zig-zag hence the name pattern in the phosphodiester backbone.
The big difference is at the G nucleotide. It has the sugar in the C3' endoconformation like A-form nucleic acid, and in contrast to B-form DNA and the guanine base is in the synconformation.
This places the guanine back over the sugar ring, in contrast to the usual anticonformation seen in A- and B-form nucleic acid. Note that having the base in the anticonformation places it in the position where it can readily form H-bonds with the complementary base on the opposite strand. Even classic B-DNA is not completely uniform in its structure. The chemical groups on the edges of GC and AT base pairs that are available for interaction in the major left picture and minor grooves right picture , color-coded for different types of interactions, are shown in the pair of illustrations.
More information on the recognition elements in the major and minor grooves is found in the views "major groove recogniton" and "minor groove recognition".
Tutorial The sugar-phosphate backbones spiral around the outer surface of DNA.
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