Paranemic Crossover Dna: There and Back Again

Papers

The overwinding and underwinding of duplex segments between junctions accept been used in designing... more The overwinding and underwinding of duplex segments between junctions take been used in designing both left-handed and right-handed Deoxyribonucleic acid origami nanostructures. For a multifariousness of DNA tubes obtained from self-assembled tiles, only a theoretical arroyo of the intrinsic curvature of the DNA tile (specified as the intrinsic tile curvature) has been previously used to explicate their formation. Details regarding the quantitative and structural descriptions of the tile curvature and its evolution in Deoxyribonucleic acid tubes by the coupling of the twist of the inter-tile arm (specified as the arm twist) have never been addressed. In this work, we designed three types of tile cores built effectually a circular 128 nucleotide scaffold past using longitudinal weaving (LW), bridged longitudinal weaving (bLW) and transverse weaving (TW). Joining the tiles with inter-tile artillery having the length of an odd number of DNA one-half-turns (termed O-tiling) almost resulted into planar 2D lattices, whereas joining the tiles with t...

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The tensegrity triangle motif utilizes Watson-Crick sticky end cohesion to self-assemble into a r... more The tensegrity triangle motif utilizes Watson-Crick sticky end cohesion to self-get together into a rhombohedral crystal lattice using complementary 5'-GA and 5'-TC sticky ends. Here, we report that using noncanonical 5'-AG and 5'-TC sticky ends in otherwise isomorphic tensegrity triangles results in crystal self-assembly in the P63 hexagonal space grouping as revealed by X-ray crystallography. In this structure, the DNA double helices bend at the crossover positions, a characteristic that was not observed in the original design. Instead of propagating linearly, the tilt between base pairs of each correct-handed helix results in a left-handed superstructure along the spiral axis, forming a microtubule-like construction equanimous of three double helices with an unbroken aqueduct at the center. This hexagonal lattice has a cavity bore of xi nm and a unit of measurement cell volume of 886 000 Å3-far larger than the rhombohedral counterpart (5 nm, 330 000 Å3).

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Deoxyribonucleic acid overwinding and underwinding betwixt side by side Holliday junctions have been practical in Deoxyribonucleic acid ori... more DNA overwinding and underwinding between adjacent Holliday junctions have been practical in Dna origami constructs to design both left-handed and right-handed nanostructures. For a diversity of DNA tubes assembled from pocket-sized tiles, only an abstract concept of the intrinsic tile curvature was previously used to explicate their formation. Details regarding the quantitative and structural descriptions of the intrinsic tile curvature and its development in DNA tubes past coupling with arm twists have been lacking. In this piece of work, we designed three types of tile cores from a circular 128 nucleotide scaffold by longitudinal weaving (LW), bridging longitudinal weaving (bLW), and transverse weaving (TW) and assembled their 2D planar or tubular nanostructures via inter-tile artillery with a distance of an odd or even number of Deoxyribonucleic acid half-turns. The biotin/streptavidin (SA) labeling technique was applied to define the tube configuration with addressable inside and exterior surfaces and thus their component tile ...

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Periodical of biomolecular structure & dynamics , 2015

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Angewandte Chemie

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Cell Chemical Biology , Nov 1, 2017

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Chemical reviews , Jan 18, 2018

Over the past 35 years, DNA has been used to produce various nanometer-scale constructs, nanomech... more Over the by 35 years, DNA has been used to produce various nanometer-calibration constructs, nanomechanical devices, and walkers. Construction of complex Dna nanostructures relies on the creation of rigid DNA motifs. Paranemic crossover (PX) DNA is one such motif that has played many roles in Deoxyribonucleic acid nanotechnology. Specifically, PX cohesion has been used to connect topologically airtight molecules, to gather a three-dimensional object, and to create two-dimensional Dna crystals. Additionally, a sequence-dependent nanodevice based on conformational change between PX and its topoisomer, JX, has been used in robust nanoscale assembly lines, every bit a primal component in a DNA transducer, and to dictate polymer assembly. Furthermore, the PX motif has recently found a new role direct in basic biology, by maybe serving equally the molecular structure for double-stranded Dna homology recognition, a prominent feature of molecular biology and essential for many crucial biological processes. This review dis...

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Journal of the American Chemic Lodge , Aug 22, 2016

Structural DNA nanotechnology combines branched Dna junctions with sticky-ended cohesion to creat... more Structural Dna nanotechnology combines branched Dna junctions with sticky-ended cohesion to create self-assembling macromolecular architectures. One of the cardinal goals of structural DNA nanotechnology is to construct three-dimensional (3D) crystalline lattices. Hither nosotros nowadays a new Deoxyribonucleic acid motif and a strategy that has led to the assembly of a 3D lattice. We have adamant the X-ray crystal structure of two related constructs to 3.ane Å resolution using bromine-derivatized crystals. The motif nosotros used employs a 5 nucleotide repeating sequence that weaves through a series of 2-plow Deoxyribonucleic acid duplexes. The duplexes are tied into a layered structure that is organized and dictated by a concert of four-arm junctions; these in plough assemble into continuous arrays facilitated by sequence-specific sticky-ended cohesion. The 3D X-ray construction of these DNA crystals holds promise for designing new structural motifs to create programmable 3D Deoxyribonucleic acid lattices with atomic spatial resolution. The ii arrays diffe...

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Journal of Biomolecular Structure and Dynamics , 2015

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Journal of Biomolecular Structure and Dynamics , 2013

Abstract Dna has been used as a tool for the self-assembly of nano-sized objects and arrays in tw... more ABSTRACT Dna has been used as a tool for the cocky-assembly of nano-sized objects and arrays in 2 and three-dimensions. Triplex-forming oligonucleotides (TFOs) can be exploited to recognize and introduce functionality at precise duplex regions inside these Deoxyribonucleic acid nanostructures (Rusling et al., 2012). Hither nosotros accept examined the feasibility of using TFOs to bind to specific locations within a three-plough DNA tensegrity triangle motif. The tensegrity triangle is a rigid DNA motif with three-fold rotational symmetry, consisting of iii helices directed along 3 linearly independent directions (Liu et al., 2004). The triangles class a three-dimensional crystalline lattice stabilized via viscous-end cohesion (Zheng et al., 2009). The TFO five′-TTCTTTCTTCTCT was used to target the tensegrity motif containing an appropriately embedded oligopurine–oligopyrimidine bounden site. Formation of Dna triplex in the motif was characterized by an electrophoretic mobility shift assay (EMSA), UV melting studies and FRET analysis. Not-denaturing gel analysis of annealed Deoxyribonucleic acid motifs showed a ring with slower mobility but in the presence of TFO and but when the Dna motif contained the triplex binding site. Experiments were undertaken at pH 5.0, since the formation of a triplex with cytidine-containing TFOs requires slightly acidic weather condition (pHK a worked at a more neutral pH, also evidenced by EMSA. UV melting studies revealed that the melting point of the iii-turn triangle was 64 °C and the TFO binding increased the melting indicate to 80 °C. FRET analysis was washed by labeling the triangle with fluorescein and the TFO with a cyanine dye (Cy5). The FRET melting curve revealed that a signal was observed only when the TFO was bound to the Dna motif and the results were consistent with UV melting studies. These results indicate that a TFO can be specifically targeted to the tensegrity triangle motif.

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Angewandte Chemie International Edition , 2014

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ACS Nano

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Jail cell chemical biological science , January 16, 2017

There is an increasing appreciation for structural multifariousness of DNA that is of interest to both D... more At that place is an increasing appreciation for structural diversity of DNA that is of interest to both Deoxyribonucleic acid nanotechnology and bones biology. Here, we take explored how DNA responds to torsional stress by building on a previously reported two-turn DNA tensegrity triangle and demonstrating that we could introduce an extra nucleotide pair (np) into the original sequence without affecting assembly and crystallization. The extra np imposes a significant torsional stress, which is accommodated by global changes throughout the B-Dna duplex and the Deoxyribonucleic acid lattice. The work reveals a most-diminutive structure of naked DNA under a torsional stress of approximately 14%, and thus provides an instance of DNA distortions that occur without a requirement for either an external free energy source or the free energy available from poly peptide or drug binding.

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Journal of Crystal Growth

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Journal of the American Chemical Society , Sep nineteen, 2016

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Chemic communications (Cambridge, England) , January 28, 2016

The tensegrity triangle is a robust DNA motif that can self-assemble to generate macroscopic thre... more The tensegrity triangle is a robust DNA motif that tin can self-assemble to generate macroscopic three-dimensional crystals. However, the stability of these crystals is dependent on the high ionic weather condition used for crystal growth. Here nosotros demonstrate that a triplex-forming oligonucleotide tin be used to direct the specific intercalation, and subsequent photo-cross-linking, of four,5',8-trimethylpsoralen to single or multiple loci inside or between the tiles of the crystal. Cantankerous-linking between the tiles of the crystal improves their thermal stability. Such an approach is likely to facilitate the removal of crystals from their mother liquor and may evidence useful for applications that require greater crystal stability.

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Http Dx Doi Org 10 1080 07391102 2013 786374 , May 29, 2013

Abstract Our laboratory has reported a cocky-assembled 3-D crystal based on a DNA tensegrity trian... more than ABSTRACT Our laboratory has reported a self-assembled 3-D crystal based on a DNA tensegrity triangle. The tensegrity triangle is a rigid Deoxyribonucleic acid motif with three-fold rotational symmetry consisting of iii helices whose axes are directed forth three linearly contained directions (ane). The triangles form a crystalline lattice stabilized via sticky ends (2). The length of the mucilaginous ends reported previously was two nucleotides (nt) GA:TC. Although diffracting to four Å resolution at the APS-ID19 beam line, they diffract simply to 4.9 Å at the NSLS-X25 beam line. In the electric current written report, we have analysed the event of sticky end length and sequence on crystal formation and the resolution of the X-ray diffraction pattern on NSLS-X25. Tensegrity triangle motifs having one-, two-, and 3-nt sticky ends accept all formed crystals. Ten-ray diffraction data from the same beam line revealed that the crystal resolution was somewhat better for the 2-nt glutinous end having an AA:TT base pair (4.75 Å) than GA:CT and CC:GG (8.0 Å). Moreover, the 1-nt glutinous cease (C:G) yielded a diffraction pattern whose resolution (three.five Å) compared favorably with all the three two-nt sticky end systems. However, the triangle motif having a 1-nt viscous end with an A:T base pair did not yield any crystals. For motifs with 3-nt sticky ends, the sequence GAG:CTC produced small crystals (ten–20 μm), while larger crystals (150 μm) were obtained with the sequences TAG:ATC and TAT:ATA. Our results point that not merely do the lengths and sequences of the sticky ends ascertain the interactions between motifs, simply they too have an touch on on the resulting resolution. We expect redesigned assemblies to form 3-D crystals with better resolution that can help in the scaffolding of biological macromolecules for crystallographic structure decision. Applications in many areas of Deoxyribonucleic acid nanotechnology are expected to do good from a complete analysis of the effects of sticky end length, sequence, and free free energy.

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The overwinding and underwinding of duplex segments between junctions have been used in designing... more than The overwinding and underwinding of duplex segments between junctions accept been used in designing both left-handed and right-handed DNA origami nanostructures. For a variety of Dna tubes obtained from self-assembled tiles, simply a theoretical approach of the intrinsic curvature of the Deoxyribonucleic acid tile (specified every bit the intrinsic tile curvature) has been previously used to explain their formation. Details regarding the quantitative and structural descriptions of the tile curvature and its evolution in Deoxyribonucleic acid tubes by the coupling of the twist of the inter-tile arm (specified as the arm twist) have never been addressed. In this work, nosotros designed 3 types of tile cores built around a circular 128 nucleotide scaffold by using longitudinal weaving (LW), bridged longitudinal weaving (bLW) and transverse weaving (TW). Joining the tiles with inter-tile arms having the length of an odd number of Deoxyribonucleic acid half-turns (termed O-tiling) almost resulted into planar 2D lattices, whereas joining the tiles with t...

PaperRank:

The tensegrity triangle motif utilizes Watson-Crick sticky finish cohesion to self-assemble into a r... more The tensegrity triangle motif utilizes Watson-Crick glutinous cease cohesion to cocky-gather into a rhombohedral crystal lattice using complementary v'-GA and 5'-TC pasty ends. Here, we study that using noncanonical 5'-AG and five'-TC mucilaginous ends in otherwise isomorphic tensegrity triangles results in crystal cocky-assembly in the P63 hexagonal space group equally revealed by X-ray crystallography. In this structure, the DNA double helices bend at the crossover positions, a feature that was non observed in the original design. Instead of propagating linearly, the tilt between base pairs of each correct-handed helix results in a left-handed superstructure forth the screw axis, forming a microtubule-similar structure composed of 3 double helices with an unbroken channel at the center. This hexagonal lattice has a cavity diameter of 11 nm and a unit jail cell volume of 886 000 Å3-far larger than the rhombohedral analogue (five nm, 330 000 Å3).

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Dna overwinding and underwinding between adjacent Holliday junctions have been applied in Deoxyribonucleic acid ori... more DNA overwinding and underwinding between side by side Holliday junctions have been applied in DNA origami constructs to design both left-handed and right-handed nanostructures. For a diverseness of DNA tubes assembled from small tiles, simply an abstract concept of the intrinsic tile curvature was previously used to explain their germination. Details regarding the quantitative and structural descriptions of the intrinsic tile curvature and its evolution in Deoxyribonucleic acid tubes by coupling with arm twists accept been defective. In this work, we designed three types of tile cores from a circular 128 nucleotide scaffold by longitudinal weaving (LW), bridging longitudinal weaving (bLW), and transverse weaving (TW) and assembled their 2D planar or tubular nanostructures via inter-tile arms with a altitude of an odd or even number of DNA half-turns. The biotin/streptavidin (SA) labeling technique was applied to define the tube configuration with addressable inside and exterior surfaces and thus their component tile ...

PaperRank:

Periodical of biomolecular structure & dynamics , 2015

PaperRank:

Angewandte Chemie

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Cell Chemic Biology , November one, 2017

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Chemical reviews , Jan 18, 2018

Over the past 35 years, Deoxyribonucleic acid has been used to produce various nanometer-scale constructs, nanomech... more than Over the past 35 years, Deoxyribonucleic acid has been used to produce various nanometer-scale constructs, nanomechanical devices, and walkers. Structure of complex Deoxyribonucleic acid nanostructures relies on the creation of rigid Dna motifs. Paranemic crossover (PX) Dna is one such motif that has played many roles in Deoxyribonucleic acid nanotechnology. Specifically, PX cohesion has been used to connect topologically closed molecules, to assemble a 3-dimensional object, and to create two-dimensional Deoxyribonucleic acid crystals. Additionally, a sequence-dependent nanodevice based on conformational change between PX and its topoisomer, JX, has been used in robust nanoscale assembly lines, equally a key component in a DNA transducer, and to dictate polymer associates. Furthermore, the PX motif has recently establish a new role directly in bones biological science, by possibly serving as the molecular structure for double-stranded DNA homology recognition, a prominent characteristic of molecular biology and essential for many crucial biological processes. This review dis...

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Journal of the American Chemical Society , Aug 22, 2016

Structural DNA nanotechnology combines branched Dna junctions with gluey-ended cohesion to creat... more Structural DNA nanotechnology combines branched Deoxyribonucleic acid junctions with gummy-ended cohesion to create self-assembling macromolecular architectures. One of the primal goals of structural DNA nanotechnology is to construct three-dimensional (3D) crystalline lattices. Here nosotros nowadays a new DNA motif and a strategy that has led to the associates of a 3D lattice. We take adamant the X-ray crystal structure of two related constructs to 3.1 Å resolution using bromine-derivatized crystals. The motif nosotros used employs a 5 nucleotide repeating sequence that weaves through a series of 2-plow DNA duplexes. The duplexes are tied into a layered structure that is organized and dictated by a concert of iv-arm junctions; these in plough assemble into continuous arrays facilitated past sequence-specific sticky-ended cohesion. The 3D X-ray structure of these DNA crystals holds promise for designing new structural motifs to create programmable 3D DNA lattices with atomic spatial resolution. The two arrays diffe...

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Journal of Biomolecular Construction and Dynamics , 2015

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Journal of Biomolecular Construction and Dynamics , 2013

Abstruse DNA has been used equally a tool for the self-assembly of nano-sized objects and arrays in tw... more ABSTRACT DNA has been used as a tool for the self-assembly of nano-sized objects and arrays in two and three-dimensions. Triplex-forming oligonucleotides (TFOs) tin can be exploited to recognize and introduce functionality at precise duplex regions within these Deoxyribonucleic acid nanostructures (Rusling et al., 2012). Here nosotros have examined the feasibility of using TFOs to demark to specific locations within a three-plough Deoxyribonucleic acid tensegrity triangle motif. The tensegrity triangle is a rigid DNA motif with three-fold rotational symmetry, consisting of iii helices directed forth three linearly contained directions (Liu et al., 2004). The triangles form a three-dimensional crystalline lattice stabilized via sticky-end cohesion (Zheng et al., 2009). The TFO five′-TTCTTTCTTCTCT was used to target the tensegrity motif containing an appropriately embedded oligopurine–oligopyrimidine binding site. Germination of DNA triplex in the motif was characterized by an electrophoretic mobility shift assay (EMSA), UV melting studies and FRET analysis. Non-denaturing gel assay of annealed DNA motifs showed a ring with slower mobility simply in the presence of TFO and only when the Dna motif contained the triplex binding site. Experiments were undertaken at pH 5.0, since the formation of a triplex with cytidine-containing TFOs requires slightly acidic conditions (pHK a worked at a more neutral pH, also evidenced by EMSA. UV melting studies revealed that the melting point of the 3-turn triangle was 64 °C and the TFO bounden increased the melting signal to 80 °C. FRET analysis was done by labeling the triangle with fluorescein and the TFO with a cyanine dye (Cy5). The FRET melting curve revealed that a point was observed only when the TFO was leap to the DNA motif and the results were consistent with UV melting studies. These results bespeak that a TFO can exist specifically targeted to the tensegrity triangle motif.

PaperRank:

Angewandte Chemie International Edition , 2014

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ACS Nano

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Prison cell chemical biological science , January 16, 2017

In that location is an increasing appreciation for structural variety of DNA that is of interest to both D... more At that place is an increasing appreciation for structural diverseness of Dna that is of involvement to both Dna nanotechnology and basic biology. Here, nosotros take explored how Deoxyribonucleic acid responds to torsional stress past building on a previously reported two-turn DNA tensegrity triangle and demonstrating that we could innovate an extra nucleotide pair (np) into the original sequence without affecting associates and crystallization. The actress np imposes a significant torsional stress, which is accommodated by global changes throughout the B-DNA duplex and the Dna lattice. The work reveals a virtually-diminutive structure of naked DNA under a torsional stress of approximately fourteen%, and thus provides an case of DNA distortions that occur without a requirement for either an external energy source or the complimentary energy available from protein or drug binding.

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Journal of Crystal Growth

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Journal of the American Chemical Society , Sep 19, 2016

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Chemical communications (Cambridge, England) , Jan 28, 2016

The tensegrity triangle is a robust DNA motif that tin cocky-assemble to generate macroscopic thre... more The tensegrity triangle is a robust Deoxyribonucleic acid motif that can self-assemble to generate macroscopic three-dimensional crystals. However, the stability of these crystals is dependent on the high ionic conditions used for crystal growth. Here we demonstrate that a triplex-forming oligonucleotide can be used to straight the specific intercalation, and subsequent photograph-cantankerous-linking, of iv,v',8-trimethylpsoralen to unmarried or multiple loci inside or between the tiles of the crystal. Cross-linking between the tiles of the crystal improves their thermal stability. Such an approach is probable to facilitate the removal of crystals from their mother liquor and may prove useful for applications that require greater crystal stability.

PaperRank:

Http Dx Doi Org 10 1080 07391102 2013 786374 , May 29, 2013

ABSTRACT Our laboratory has reported a self-assembled 3-D crystal based on a Dna tensegrity trian... more ABSTRACT Our laboratory has reported a self-assembled 3-D crystal based on a Dna tensegrity triangle. The tensegrity triangle is a rigid DNA motif with three-fold rotational symmetry consisting of three helices whose axes are directed along three linearly contained directions (1). The triangles grade a crystalline lattice stabilized via viscid ends (ii). The length of the viscid ends reported previously was two nucleotides (nt) GA:TC. Although diffracting to 4 Å resolution at the APS-ID19 beam line, they diffract only to 4.nine Å at the NSLS-X25 beam line. In the electric current study, we have analysed the effect of sticky cease length and sequence on crystal formation and the resolution of the X-ray diffraction blueprint on NSLS-X25. Tensegrity triangle motifs having i-, 2-, and 3-nt sticky ends take all formed crystals. X-ray diffraction data from the same beam line revealed that the crystal resolution was somewhat improve for the ii-nt sticky terminate having an AA:TT base pair (4.75 Å) than GA:CT and CC:GG (viii.0 Å). Moreover, the 1-nt sticky end (C:Thousand) yielded a diffraction blueprint whose resolution (iii.v Å) compared favorably with all the 3 2-nt pasty terminate systems. Even so, the triangle motif having a 1-nt sticky finish with an A:T base of operations pair did not yield any crystals. For motifs with iii-nt mucilaginous ends, the sequence GAG:CTC produced small crystals (x–20 μm), while larger crystals (150 μm) were obtained with the sequences TAG:ATC and TAT:ATA. Our results indicate that not but practice the lengths and sequences of the sticky ends define the interactions betwixt motifs, simply they also accept an impact on the resulting resolution. We await redesigned assemblies to form 3-D crystals with ameliorate resolution that can aid in the scaffolding of biological macromolecules for crystallographic structure conclusion. Applications in many areas of DNA nanotechnology are expected to benefit from a complete analysis of the effects of glutinous end length, sequence, and free energy.

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Paranemic Crossover Dna: There and Back Again

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