How sequence defines structure: A crystallographic map of DNA structure and conformation

Hays, Franklin A.; Teegarden, A.T.; Jones, Z.J.R.; Harms, Michael J.; Raup, D.; Watson, J.; Cavaliere, E.; Ho, P Shing

doi:10.1073/pnas.0409455102

Cited by 138 publications

(196 citation statements)

References 32 publications

(29 reference statements)

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“…The three junctions are nearly identical in structure, with significant structural perturbations localized at the core of the junction, consistent with the intramolecular interactions being the primary determinant of the stability (11,12) and the isomeric form of the junction. Interestingly, the X-and H-bonding pyrimidine bases of N 7 overlay almost exactly in all three structures (Fig.…”

Section: Resultsmentioning

confidence: 57%

“…The Br⅐⅐⅐O distances for Br 2 J and Br 1 J are closer than the sums of their respective van der Waals radii, indicating the formation of X-bonds, and they are closer than the analogous methyl to phosphate distance in the ATC-J junction. ATC-J is amphimorphic (crystallizing as both junction and B-DNA duplex) (12), suggesting that the thymine to phosphate electrostatic interaction is significantly weaker than either the X-or H-bonds. In Br 2 J and Br 1 J, the phosphate oxygens are drawn toward the bromines to establish the respective X-bonds, similar to the H-bond in H 2 J.…”

Section: Resultsmentioning

confidence: 99%

“…The pairs of stacked duplex arms are highlighted with cylinders. Details of the molecular interactions that stabilize junctions are in crystals are shown, with the essential H-bond from the C 8 cytosine to the phosphate of the cross-over C7 nucleotide in the blue box, and the weaker H-bond from C7 to A6 in the ACC-J or the weak electrostatic interaction from the methyl of T7 to A6 in d(CCGATATCGG) (ATC-J) in the red boxes (12,16).…”

mentioning

confidence: 99%

“…2) (13-15). The presence of an X-or H-bond at the junction cross-over will be ref lected, in this assay, by the preference for one of the two isomer forms.A cytosine to phosphate H-bond at the N 7 nucleotide position has been shown to help stabilize the junction in the sequence d(CCGGTACCGG) (ACC-J) in crystals (11,12,16) and in solution (17). The stability of this junction, formed by a single inverted repeat sequence, depends entirely on this set of intramolecular interactions.…”

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confidence: 99%

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Directing macromolecular conformation through halogen bonds

Voth

Hays

2007

Proc. Natl. Acad. Sci. U.S.A.

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329

310

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The halogen bond, a noncovalent interaction involving polarizable chlorine, bromine, or iodine molecular substituents, is now being exploited to control the assembly of small molecules in the design of supramolecular complexes and new materials. We demonstrate that a halogen bond formed between a brominated uracil and phosphate oxygen can be engineered to direct the conformation of a biological molecule, in this case to define the conformational isomer of a four-stranded DNA junction when placed in direct competition against a classic hydrogen bond. As a result, this bromine interaction is estimated to be Ϸ2-5 kcal/mol stronger than the analogous hydrogen bond in this environment, depending on the geometry of the halogen bond. This study helps to establish halogen bonding as a potential tool for the rational design and construction of molecular materials with DNA and other biological macromolecules.biomolecular engineering ͉ DNA structure ͉ molecular interactions H alogen bonds have recently seen a resurgence of interest as a tool for ''bottom-up'' molecular design. Chlorines, bromines, and iodines in organic and inorganic compounds are known to polarize along their covalent bonds to generate an electropositive crown; the halogen thus acts as a Lewis acid to pair with Lewis bases, including oxygens and nitrogens. These electrostatic pairs, originally called charge-transfer bonds (1), are now known as halogen bonds (X-bonds), recognizing their similarities to hydrogen bonds (H-bonds) in their strength and directionality (2). In chemistry, X-bonds are being exploited in the design and engineering of supramolecular assemblies (3) and molecular crystals (for review, see ref. 4), with an iodine X-bond estimated to be Ϸ3.5 kcal/mol more stable than an O-H⅐⅐⅐O H-bond in organic crystals (5).The X-bond, however, has not generally been a part of the biologist's lexicon. Although halogens are widely used in drug design and to probe molecular interactions, X-bonds have only recently been recognized as a distinct interaction in ligand recognition and molecular folding and in the assembly of proteins and nucleic acids (6, 7). With the growing application of biological molecules (biomolecule), particularly nucleic acids (for review, see ref. 8), in the design of nanomechanical devices, we ask here whether specific X-bonds can be engineered to direct conformational switching in a biomolecule.To compare X-and H-bonds in the complex environment of a biomolecule, we have designed a crystallographic assay to determine whether an intramolecular X-bond could be engineered to direct the conformational isomerization of a DNA Holliday junction by competing an X-bond against a classic H-bond and, consequently, we are able to compare the stabilization energies afforded by these two types of interactions. The stacked-X form of the DNA Holliday junction (Fig. 1), seen in high-salt solutions (9) and in crystal structures (10 -12), is a simple and well controlled biomolecular assay system that can isomerize between two nearly isoenergetic an...

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Section: Resultsmentioning

confidence: 57%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Directing macromolecular conformation through halogen bonds

Voth

Hays

2007

Proc. Natl. Acad. Sci. U.S.A.

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329

310

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“…This in turn opened the door for the determination of DNA crystal structures [5][6][7]. DNA crystal structures are responsible for a great deal of our knowledge about the diversity of DNA structure, its sequence-dependent heterogeneity [8,9], and how it interacts with other biological molecules to express the information stored in its molecular structure/sequence [10,11].…”

Section: Introductionmentioning

confidence: 99%

3D DNA Crystals and Nanotechnology

Paukstelis

Seeman

2016

Crystals

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DNA's molecular recognition properties have made it one of the most widely used biomacromolecular construction materials. The programmed assembly of DNA oligonucleotides has been used to create complex 2D and 3D self-assembled architectures and to guide the assembly of other molecules. The origins of DNA nanotechnology are rooted in the goal of assembling DNA molecules into designed periodic arrays, i.e., crystals. Here, we highlight several DNA crystal structures, the progress made in designing DNA crystals, and look at the current prospects and future directions of DNA crystals in nanotechnology.

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Watson–Crick Base Pairs: Character and Recognition

Olson

Colasanti

et al. 2008

Wiley Encyclopedia of Chemical Biology

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The unique Watson–Crick arrangement of hydrogen‐bonded bases in DNA accommodates two different, complementary purine–pyrimidine pairs, A·T = T·A and G·C = C·G, in a common spatial setting. Nature takes advantage of these isomorphous structures, which store genetic information in terms of the proton donor and acceptor atoms that hold the bases in place. As outlined here, the Watson–Crick base pairs carry other chemical signals that are used to recognize and to process specific sequences of bases. The relative stabilities of G·C versus A·T pairs reflect their different electronic structures. The distributions of electronic charge on the exposed major‐groove and minor‐groove edges of the base pairs present unique motifs for direct sequence recognition, and the deformations of the paired bases from ideal, planar configurations provide subtle, indirect recognition elements. The biologic significance of the latter signals is not fully understood but is becoming clearer as more and more high‐resolution structures of DNA and RNA are determined.

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How sequence defines structure: A crystallographic map of DNA structure and conformation

Abstract: www.pnas.org/cgi

Cited by 138 publications

References 32 publications

Directing macromolecular conformation through halogen bonds

Directing macromolecular conformation through halogen bonds

3D DNA Crystals and Nanotechnology

Watson–Crick Base Pairs: Character and Recognition

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