Co-reporter:Stefjord Todolli, Pamela J. Perez, Nicolas Clauvelin, Wilma K. Olson
Biophysical Journal 2017 Volume 112, Issue 3(Volume 112, Issue 3) pp:
Publication Date(Web):7 February 2017
DOI:10.1016/j.bpj.2016.11.017
One of the critical unanswered questions in genome biophysics is how the primary sequence of DNA bases influences the global properties of very-long-chain molecules. The local sequence-dependent features of DNA found in high-resolution structures introduce irregularities in the disposition of adjacent residues that facilitate the specific binding of proteins and modulate the global folding and interactions of double helices with hundreds of basepairs. These features also determine the positions of nucleosomes on DNA and the lengths of the interspersed DNA linkers. Like the patterns of basepair association within DNA, the arrangements of nucleosomes in chromatin modulate the properties of longer polymers. The intrachromosomal loops detected in genomic studies contain hundreds of nucleosomes, and given that the simulated configurations of chromatin depend on the lengths of linker DNA, the formation of these loops may reflect sequence-dependent information encoded within the positioning of the nucleosomes. With knowledge of the positions of nucleosomes on a given genome, methods are now at hand to estimate the looping propensities of chromatin in terms of the spacing of nucleosomes and to make a direct connection between the DNA base sequence and larger-scale chromatin folding.
Co-reporter:Pamela J. Perez;Wilma K. Olson
Biophysical Reviews 2016 Volume 8( Issue 1 Supplement) pp:135-144
Publication Date(Web):2016 November
DOI:10.1007/s12551-016-0209-7
Genomic DNA is vastly longer than the space allotted to it in a cell. The molecule must fold with a level of organization that satisfies the imposed spatial constraints as well as allow for the processing of genetic information. Key players in this organization include the negative supercoiling of DNA, which facilitates the unwinding of the double-helical molecule, and the associations of DNA with proteins, which partition the DNA into isolated loops, or domains. In order to gain insight into the principles of genome organization and to visualize the folding of spatially constrained DNA, we have developed new computational methods to identify the preferred three-dimensional pathways of protein-mediated DNA loops and to characterize the topological properties of these structures. Here, we focus on the levels of supercoiling and the spatial arrangements of DNA in model nucleoprotein systems with two topological domains. We construct these systems by anchoring DNA loops in opposing orientations on a common protein–DNA assembly, namely the Lac repressor protein with two bound DNA operators. The linked pieces of DNA form a covalently closed circle such that the protein attaches to two widely spaced sites along the DNA. We examine the effects of operator spacing, loop orientation, and long-range contacts on overall chain configuration and topology, and discuss our findings in the context of classic experiments on the effects of supercoiling and operator spacing on Lac repressor-mediated looping and recent work on the role of proteins as barriers that divide genomes into independent topological domains.
Co-reporter:Michael A. Grosner;David Swigon;Wilma K. Olson;Juan Wei;Luke Czapla
PNAS 2014 Volume 111 (Issue 47 ) pp:16742-16747
Publication Date(Web):2014-11-25
DOI:10.1073/pnas.1405016111
Topological constraints placed on short fragments of DNA change the disorder found in chain molecules randomly decorated by
nonspecific, architectural proteins into tightly organized 3D structures. The bacterial heat-unstable (HU) protein builds
up, counter to expectations, in greater quantities and at particular sites along simulated DNA minicircles and loops. Moreover,
the placement of HU along loops with the “wild-type” spacing found in the Escherichia coli lactose (lac) and galactose (gal) operons precludes access to key recognition elements on DNA. The HU protein introduces a unique spatial pathway in the DNA
upon closure. The many ways in which the protein induces nearly the same closed circular configuration point to the statistical
advantage of its nonspecificity. The rotational settings imposed on DNA by the repressor proteins, by contrast, introduce
sequential specificity in HU placement, with the nonspecific protein accumulating at particular loci on the constrained duplex.
Thus, an architectural protein with no discernible DNA sequence-recognizing features becomes site-specific and potentially
assumes a functional role upon loop formation. The locations of HU on the closed DNA reflect long-range mechanical correlations.
The protein responds to DNA shape and deformability—the stiff, naturally straight double-helical structure—rather than to
the unique features of the constituent base pairs. The structures of the simulated loops suggest that HU architecture, like
nucleosomal architecture, which modulates the ability of regulatory proteins to recognize their binding sites in the context
of chromatin, may influence repressor–operator interactions in the context of the bacterial nucleoid.
Co-reporter:Andrew V. Colasanti;Michael A. Grosner;Pamela J. Perez;Nicolas Clauvelin;Xiang-Jun Lu;Wilma K. Olson
Biopolymers 2013 Volume 99( Issue 12) pp:1070-1081
Publication Date(Web):
DOI:10.1002/bip.22336
ABSTRACT
The 50th anniversary of Biopolymers coincides closely with the like celebration of the discovery of the Escherichia coli (lac) lactose operon, a classic genetic system long used to illustrate the influence of biomolecular structure on function. The looping of DNA induced by the binding of the Lac repressor protein to sequentially distant operator sites on DNA continues to serve as a paradigm for understanding long-range genomic communication. Advances in analyses of DNA structures and in incorporation of proteins in computer simulations of DNA looping allow us to address long-standing questions about the role of protein-mediated DNA loop formation in transcriptional control. Here we report insights gained from studies of the sequence-dependent contributions of the natural lac operators to Lac repressor-mediated DNA looping. Novel superposition of the ensembles of protein-bound operator structures derived from NMR measurements reveals variations in DNA folding missed in conventional structural alignments. The changes in folding affect the predicted ease with which the repressor induces loop formation and the ways that DNA closes between the protein headpieces. The peeling of the auxiliary operators away from the repressor enhances the formation of loops with the 92-bp wildtype spacing and hints of a structural reason behind their weak binding. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 1070–1081, 2013.
Co-reporter:Tahir I. Yusufaly, Yun Li, and Wilma K. Olson
The Journal of Physical Chemistry B 2013 Volume 117(Issue 51) pp:16436-16442
Publication Date(Web):December 6, 2013
DOI:10.1021/jp409887t
van der Waals density functional theory is integrated with analysis of a non-redundant set of protein–DNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5-methylation. Principal component analysis of the steps reveals the dominant collective motions to correspond to a tensile “opening” mode and two shear “sliding” and “tearing” modes in the orthogonal plane. The stacking interactions of the methyl groups globally inhibit CG:CG step overtwisting while simultaneously softening the modes locally via potential energy modulations that create metastable states. Additionally, the indirect effects of the methyl groups on possible base-pair steps neighboring CG:CG are observed to be of comparable importance to their direct effects on CG:CG. The results have implications for the epigenetic control of DNA mechanics.
Co-reporter:Wilma K. Olson;Nicolas Clauvelin;Andrew V. Colasanti;Gautam Singh
Biophysical Reviews 2012 Volume 4( Issue 3) pp:171-178
Publication Date(Web):2012 September
DOI:10.1007/s12551-012-0093-8
Within the nucleus of each cell lies DNA—an unfathomably long, twisted, and intricately coiled molecule—segments of which make up the genes that provide the instructions that a cell needs to operate. As we near the 60th anniversary of the discovery of the DNA double helix, crucial questions remain about how the physical arrangement of the DNA in cells affects how genes work. For example, how a cell stores the genetic information inside the nucleus is complicated by the necessity of maintaining accessibility to DNA for genetic processing. In order to gain insight into the roles played by various proteins in reading and compacting the genome, we have developed new methodologies to simulate the dynamic, three-dimensional structures of long, fluctuating, protein-decorated strands of DNA. Our a priori approach to the problem allows us to determine the effects of individual proteins and their chemical modifications on overall DNA structure and function. Here, we present our recent treatment of the communication between regulatory proteins attached to precisely constructed stretches of chromatin. Our simulations account for the enhancement in communication detected experimentally on chromatin compared to protein-free DNA of the same chain length, as well as the critical roles played by the cationic ‘tails’ of the histone proteins in this signaling. The states of chromatin captured in the simulations offer new insights into the ways that the DNA, histones, and regulatory proteins contribute to long-range communication along the genome.
Co-reporter:Heather E. Peckham;Wilma K. Olson
Biopolymers 2011 Volume 95( Issue 4) pp:254-269
Publication Date(Web):
DOI:10.1002/bip.21570
Abstract
The growing numbers of very well resolved nucleic-acid crystal structures with anisotropic displacement parameters provide an unprecedented opportunity to learn about the natural motions of DNA and RNA. Here we report a new Monte-Carlo approach that takes direct account of this information to extract the distortions of covalent structure, base pairing, and dinucleotide geometry intrinsic to regularly organized double-helical molecules. We present new methods to test the validity of the anisotropic parameters and examine the apparent deformability of a variety of structures, including several A, B, and Z DNA duplexes, an AB helical intermediate, an RNA, a ligand-DNA complex, and an enzyme-bound DNA. The rigid-body parameters characterizing the positions of the bases in the structures mirror the mean parameters found when atomic motion is taken into account. The base-pair fluctuations intrinsic to a single structure, however, differ from those extracted from collections of nucleic-acid structures, although selected base-pair steps undergo conformational excursions along routes suggested by the ensembles. The computations reveal surprising new molecular insights, such as the stiffening of DNA and concomitant separation of motions of contacted nucleotides on opposite strands by the binding of Escherichia coli endonuclease VIII, which suggest how the protein may direct enzymatic action. © 2010 Wiley Periodicals, Inc. Biopolymers 95: 254–269,2011.
Co-reporter:Guohui Zheng, Luke Czapla, A. R. Srinivasan and Wilma K. Olson
Physical Chemistry Chemical Physics 2010 vol. 12(Issue 6) pp:1399-1406
Publication Date(Web):23 Dec 2009
DOI:10.1039/B916183J
The natural stiffness of DNA, which contributes to the interactions of the many proteins involved in its biological processing and packaging, also plays an important role in modern nanotechnology. Here we report new Monte-Carlo simulations of deformable DNA molecules of potential utility in understanding the behavior of the long, double-helical polymer in the tight confines of a cell and in the design of novel nanomaterials and molecular devices. We directly determine the fluctuations in end-to-end extension associated with the conventional elastic-rod representation of DNA and with more realistic models that take account of the precise deformability of the constituent base-pair steps. Notably, the variance of end-to-end distance shows a quadratic increase with chain length in short chains of both types. We also consider the contributions to chain extension from the chemical linkages used to attach small molecular probes to DNA. The distribution of computed distances is sensitive to the intrinsic structure and allowed deformations of the tether. Surprisingly, the enhancement in end-to-end variance associated with the presence of the probe depends upon chain length, even when the probe is rigidly connected to DNA. We find that the elastic rod model of DNA in combination with a slightly fluctuating tether accounts satisfactorily for the distributions of end-to-end distances extracted from the small-angle X-ray scattering of gold nanocrystals covalently linked to the ends of short DNAs. There is no need to introduce additional structural fluctuations to reproduce the measured uptake in end-to-end fluctuations with chain length.
Co-reporter:A. R. Srinivasan;Ronald R. Sauers;Marcia O. Fenley
Biophysical Reviews 2009 Volume 1( Issue 1) pp:
Publication Date(Web):2009 March
DOI:10.1007/s12551-008-0003-2
The nucleic-acid bases carry structural and energetic signatures that contribute to the unique features of genetic sequences. Here, we review the connection between the chemical structure of the constituent nucleotides and the polymeric properties of DNA. The sequence-dependent accumulation of charge on the major- and minor-groove edges of the Watson–Crick base pairs, obtained from ab initio calculations, presents unique motifs for direct sequence recognition. The optimization of base interactions generates a propellering of base-pair planes of the same handedness as that found in high-resolution double-helical structures. The optimized base pairs also deform along conformational pathways, i.e., normal modes, of the same type induced by the binding of proteins. Empirical energy computations that incorporate the properties of the base pairs account satisfactorily for general features of the next level of double-helical structure, but miss key sequence-dependent differences in dimeric structure and deformability. The latter discrepancies appear to reflect factors other than intrinsic base-pair structure.
Co-reporter:Victor B. Zhurkin, Wilma K. Olson
Physics of Life Reviews (March 2013) Volume 10(Issue 1) pp:70-72
Publication Date(Web):1 March 2013
DOI:10.1016/j.plrev.2013.01.009
Co-reporter:Luke Czapla, David Swigon, Wilma K. Olson
Journal of Molecular Biology (3 October 2008) Volume 382(Issue 2) pp:353-370
Publication Date(Web):3 October 2008
DOI:10.1016/j.jmb.2008.05.088
The histone-like HU (heat unstable) protein plays a key role in the organization and regulation of the Escherichia coli genome. The nonspecific nature of HU binding to DNA complicates analysis of the mechanism by which the protein contributes to the looping of DNA. Conventional models of the looping of HU-bound duplexes attribute the changes in biophysical properties of DNA brought about by the random binding of protein to changes in the effective parameters of an ideal helical wormlike chain. Here, we introduce a novel Monte Carlo approach to study the effects of nonspecific HU binding on the configurational properties of DNA directly. We randomly decorated segments of an ideal double-helical DNA with HU molecules that induce the bends and other structural distortions of the double helix find in currently available X-ray structures. We find that the presence of HU at levels approximating those found in the cell reduces the persistence length by roughly threefold compared with that of naked DNA. The binding of protein has particularly striking effects on the cyclization properties of short duplexes, altering the dependence of ring closure on chain length in a way that cannot be mimicked by a simple wormlike model and accumulating at higher-than-expected levels on successfully closed chains. Moreover, the uptake of protein on small minicircles depends on chain length, taking advantage of the HU-induced deformations of DNA structure to facilitate ligation. Circular duplexes with bound HU show much greater propensity than protein-free DNA to exist as negatively supercoiled topoisomers, suggesting a potential role of HU in organizing the bacterial nucleoid. The local bending and undertwisting of DNA by HU, in combination with the number of bound proteins, provide a structural rationale for the condensation of DNA and the observed expression levels of reporter genes in vivo.
Co-reporter:Sreekala Balasubramanian, Fei Xu, Wilma K. Olson
Biophysical Journal (18 March 2009) Volume 96(Issue 6) pp:
Publication Date(Web):18 March 2009
DOI:10.1016/j.bpj.2008.11.040
The folding of DNA on the nucleosome core particle governs many fundamental issues in eukaryotic molecular biology. In this study, an updated set of sequence-dependent empirical “energy” functions, derived from the structures of other protein-bound DNA molecules, is used to investigate the extent to which the architecture of nucleosomal DNA is dictated by its underlying sequence. The potentials are used to estimate the cost of deforming a collection of sequences known to bind or resist uptake in nucleosomes along various left-handed superhelical pathways and to deduce the features of sequence contributing to a particular structural form. The deformation scores reflect the choice of template, the deviations of structural parameters at each step of the nucleosome-bound DNA from their intrinsic values, and the sequence-dependent “deformability” of a given dimer. The correspondence between the computed scores and binding propensities points to a subtle interplay between DNA sequence and nucleosomal folding, e.g., sequences with periodically spaced pyrimidine-purine steps deform at low cost along a kinked template whereas sequences that resist deformation prefer a smoother spatial pathway. Successful prediction of the known settings of some of the best-resolved nucleosome-positioning sequences, however, requires a template with “kink-and-slide” steps like those found in high-resolution nucleosome structures.
Co-reporter:Michael Y. Tolstorukov, Andrew V. Colasanti, David M. McCandlish, Wilma K. Olson, Victor B. Zhurkin
Journal of Molecular Biology (17 August 2007) Volume 371(Issue 3) pp:725-738
Publication Date(Web):17 August 2007
DOI:10.1016/j.jmb.2007.05.048
How eukaryotic genomes encode the folding of DNA into nucleosomes and how this intrinsic organization of chromatin guides biological function are questions of wide interest. The physical basis of nucleosome positioning lies in the sequence-dependent propensity of DNA to adopt the tightly bent configuration imposed by the binding of the histone proteins. Traditionally, only DNA bending and twisting deformations are considered, while the effects of the lateral displacements of adjacent base pairs are neglected. We demonstrate, however, that these displacements have a much more important structural role than ever imagined. Specifically, the lateral Slide deformations observed at sites of local anisotropic bending of DNA define its superhelical trajectory in chromatin. Furthermore, the computed cost of deforming DNA on the nucleosome is sequence-specific: in optimally positioned sequences the most easily deformed base-pair steps (CA:TG and TA) occur at sites of large positive Slide and negative Roll (where the DNA bends into the minor groove). These conclusions rest upon a treatment of DNA that goes beyond the conventional ribbon model, incorporating all essential degrees of freedom of “real” duplexes in the estimation of DNA deformation energies. Indeed, only after lateral Slide displacements are considered are we able to account for the sequence-specific folding of DNA found in nucleosome structures. The close correspondence between the predicted and observed nucleosome locations demonstrates the potential advantage of our “structural” approach in the computer mapping of nucleosome positioning.
Co-reporter:Guohui Zheng, Luke Czapla, A. R. Srinivasan and Wilma K. Olson
Physical Chemistry Chemical Physics 2010 - vol. 12(Issue 6) pp:NaN1406-1406
Publication Date(Web):2009/12/23
DOI:10.1039/B916183J
The natural stiffness of DNA, which contributes to the interactions of the many proteins involved in its biological processing and packaging, also plays an important role in modern nanotechnology. Here we report new Monte-Carlo simulations of deformable DNA molecules of potential utility in understanding the behavior of the long, double-helical polymer in the tight confines of a cell and in the design of novel nanomaterials and molecular devices. We directly determine the fluctuations in end-to-end extension associated with the conventional elastic-rod representation of DNA and with more realistic models that take account of the precise deformability of the constituent base-pair steps. Notably, the variance of end-to-end distance shows a quadratic increase with chain length in short chains of both types. We also consider the contributions to chain extension from the chemical linkages used to attach small molecular probes to DNA. The distribution of computed distances is sensitive to the intrinsic structure and allowed deformations of the tether. Surprisingly, the enhancement in end-to-end variance associated with the presence of the probe depends upon chain length, even when the probe is rigidly connected to DNA. We find that the elastic rod model of DNA in combination with a slightly fluctuating tether accounts satisfactorily for the distributions of end-to-end distances extracted from the small-angle X-ray scattering of gold nanocrystals covalently linked to the ends of short DNAs. There is no need to introduce additional structural fluctuations to reproduce the measured uptake in end-to-end fluctuations with chain length.
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