Analyzing and Building Nucleic Acid Structures with 3DNA

Colasanti, Andrew V.; Lu, Xiang‐Jun; Olson, Wilma K.

doi:10.3791/4401

Cited by 53 publications

(66 citation statements)

References 35 publications

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“…The 80-nucleotide (nt) A-form RNA duplex and 48-nt B-form DNA helix are generated using the latest version (version 2.1) of the program X3DNA. 73 Other RNA structures, such as the 76-nt yeast tRNA Phe (PDB ID: 1TRA 74 ), 58-nt fragment of rRNA and rRNA-protein complex (PDB ID: 1HC8 75 ), and 72-nt Adenine riboswitch (A-riboswitch; PDB ID: 1Y26 76 ), are generated from the Protein Data Bank coordinate files. 77 For the 5BSL3.2:3X complex in the HCV genomic RNA, cell-based viral replication assays 68–70 have suggested that the kissing complex is formed between 5BSL3.2 and the SL2 hairpin loop in the 3′X.…”

Section: The Pctbi Modelmentioning

confidence: 99%

Predicting Ion Effects in an RNA Conformational Equilibrium

et al. 2017

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We develop a partial charge-based Tightly Bound Ion (PCTBI) model for the ion effects in RNA folding. Based on the Monte Carlo Tightly Bound Ion (MCTBI) approach, the model can account for ion fluctuation and correlation effects, and can predict the ion distribution around the RNA. Furthermore, unlike the previous coarse-grained RNA charge models, where negative charges are placed on the phosphates only, the current new model considers the detailed all-atom partial charge distribution on the RNA. Thus, the model not only keeps the advantage of the MCTBI model but also has the potential to provide important detailed information unattainable by the previous MCTBI models. For example, the model predicts the reduction in ion binding upon protein binding and ion-induced conformational switches. For Hepatitis C virus (HCV) genomic RNA, the model predicts a Mg2+-induced stabilization of a kissing motif for a cis-acting regulatory element in the genomic RNA. Extensive theory-experiment comparisons support the reliability of the theoretical predictions. Therefore, the model may serve as a robust starting point for further development of an accurate method for ion effects in RNA conformational equilibrium and RNA-cofactor interactions.

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Section: The Pctbi Modelmentioning

confidence: 99%

Predicting Ion Effects in an RNA Conformational Equilibrium

et al. 2017

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“…We take advantage of a new feature in the 3DNA suite of programs that allows a user to look at multiple structures from a common perspective. 32 The software aligns the individual DNA pathways in the multi-model NMR structure files on a common reference frame. Here we position the G·C base pair at the centers of the three natural operators on the corresponding base pair in the O 1 -containing crystal structure and the highly kinked CG base-pair step at the centers of the symmetric operator models on the corresponding base pair in the O sym crystal complex (PDB entry 1efa 18 ).…”

Section: Methodsmentioning

confidence: 99%

“…We take advantage of another new feature of 3DNA that facilitates the analysis of ensembles of related structures in collecting the components of the local helical axes. 32 The twisting of DNA is based on a discrete ribbon constructed from the origins and reference frames of successive base pairs. 35 In contrast to the twist angle included in the six rigid-body parameters specifying the relative spatial arrangements of successive base pairs, 36 the twist reported here, the so-called twist of supercoiling, can be combined with the writhing number of a closed structure to obtain the correct linking number.…”

Section: Methodsmentioning

confidence: 99%

Weak operator binding enhances simulated lac repressor‐mediated DNA looping

et al. 2013

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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.

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“…S6B,C). As chemical shifts and NOE patterns were not significantly affected upon magnesium addition, the same dihedral and distances restraints were used to generate a model of Five stems were defined using the 3DNA software (Colasanti et al 2013). Helical axes for the five stems were generated using MOLMOL software and are indicated in pink (Koradi et al 1996).…”

Section: Effect Of Magnesium On Hpi Structurementioning

confidence: 99%

“…Quality factors (Q) and root-mean-square deviations (RMSD) between input and calculated RDCs were calculated with the PALES software for the 10 final converged structures before and after refinement with the opls force field (Table 1; Zweckstetter and Bax 2000). Structures were visualized and analyzed with MOLMOL, Pymol and 3DNA software packages (Koradi et al 1996;Delano 2005;Colasanti et al 2013). …”

Section: Structure Calculationsmentioning

confidence: 99%

Solution structure of the 5′-terminal hairpin of the 7SK small nuclear RNA

Bourbigot¹,

Dock-Brégeon²,

Eberling³

et al. 2016

RNA

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The small nuclear 7SK RNA regulates RNA polymerase II (RNA Pol II) transcription, by sequestering and inhibiting the positive transcription elongation factor b (P-TEFb). P-TEFb is stored in the 7SK ribonucleoprotein (RNP) that contains the three nuclear proteins Hexim1, LaRP7, and MePCE. P-TEFb interacts with the protein Hexim1 and the 7SK RNA. Once P-TEFb is released from the 7SK RNP, it activates transcription by phosphorylating the C-terminal domain of RNA Pol II. P-TEFb also plays a crucial role in the replication of the human immunodeficiency virus HIV-1, through its recruitment by the viral transactivator Tat. Previous work demonstrated that the protein Tat promotes the release of P-TEFb from the 7SK RNP through direct binding to the 7SK RNA. Hexim1 and Tat proteins both comprise conserved and similar arginine-rich motifs that were identified to bind the 7SK RNA at a repeated GAUC site located at the top of the 5 ′ -terminal hairpin (HPI). Here, we report the solution structure of this region as determined by nuclear magnetic resonance, to identify HPI structural features recognized by Hexim1 and Tat. The HPI solution structure displays an elongated shape featuring four helical segments interrupted by one internal loop and three bulges with distinct folds. In particular, the repeated GAUC motif adopts a pre-organized geometry. Our results suggest that the binding of Hexim1 and Tat to the 7SK RNA could originate from a conformational selection of this motif, highlighting how RNA local structure could lead to an adaptive recognition of their partners.

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Analyzing and Building Nucleic Acid Structures with 3DNA

Cited by 53 publications

References 35 publications

Predicting Ion Effects in an RNA Conformational Equilibrium

Predicting Ion Effects in an RNA Conformational Equilibrium

Weak operator binding enhances simulated lac repressor‐mediated DNA looping

Solution structure of the 5′-terminal hairpin of the 7SK small nuclear RNA

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