Distance Dependent Interhelical Couplings of Organic Rods Incorporated in DNA 4-Helix Bundles

Andersen, Casper S.; Knudsen, Martin M.; Chhabra, Rajendra S.; Liu, Yan; Gothelf, Kurt V.

doi:10.1021/bc900078c

Cited by 8 publications

(5 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Although interactions and synergy of proteins can be successfully predicted by computer simulations, − the influence of distance constraints on binding and activity of biomolecules has been reported in only very few cases . In addition, current computer simulations do not account for variations of physical properties, such as entropy, that are known to be crucial for molecular recognition. − Nanostructures based on self-assembled DNA have been used to study interligand distances resulting from the simultaneous binding of multiple ligands. , However, self-assembled DNA structures behave as rigid scaffolds, which induce a decrease in binding due to spatial mismatches. , To the best of our knowledge, there are very few model scaffolds that can specifically bind multiple proteins with controlled distances between binding sites, and none has used polymer-based scaffolds.…”

Section: Introductionmentioning

confidence: 99%

“…20−23 Nano-structures based on self-assembled DNA have been used to study interligand distances resulting from the simultaneous binding of multiple ligands. 24,25 However, self-assembled DNA structures behave as rigid scaffolds, which induce a decrease in binding due to spatial mismatches. 24,25 To the best of our knowledge, there are very few model scaffolds that can specifically bind multiple proteins with controlled distances between binding sites, and none has used polymer-based scaffolds.…”

Section: ■ Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Poly(N-isopropylacrylamide-co-tris-nitrilotriacetic acid acrylamide) for a Combined Study of Molecular Recognition and Spatial Constraints in Protein Binding and Interactions

Liu

Spulber

et al. 2014

J. Am. Chem. Soc.

View full text Add to dashboard Cite

Many biological processes require precise regulation and synergy of proteins, and consequently involve molecular recognition and spatial constraints between biomolecules. Here, a library of poly(N-isopropylacrylamide-co-tris-nitrilotriacetic acid acrylamide) (PNTs) has been synthesized and complexed with Cu(2+) in order to serve as models for investigation of the combined effects of molecular recognition and spatial constraints in biomolecular interactions. The average distance between Cu(2+)-trisNTA binding sites in PNTs polymers was varied from 4.3 to 31.5 nm by adjusting their trisNTA contents. His tag (His6), His-tagged enhanced yellow fluorescent protein (His6-eYFP), and His6-tagged collagenase G (His6-ColG), with sizes ranging from 1 to 11 nm, were used as models to assess whether the binding ability is influenced by a cooperative topology based on molecular recognition interactions with Cu(2+)-trisNTA binding sites, and spatial constraints created by decreasing average distance between trisNTAs. His-tagged molecules bound to all PNTs polymers due to their molecular recognition interaction involving histidines and Cu(2+)-trisNTA pockets, but with a binding ability that was highly modulated by the average distance between the trisNTA binding sites. Small molecular mass molecules (His6) exhibit a high binding ability to all PNTs polymers, whereas his-tagged proteins bind to PNTs efficiently only when the average distance between trisNTA binding sites is larger than the protein dimensions.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

Poly(N-isopropylacrylamide-co-tris-nitrilotriacetic acid acrylamide) for a Combined Study of Molecular Recognition and Spatial Constraints in Protein Binding and Interactions

Liu

Spulber

et al. 2014

J. Am. Chem. Soc.

View full text Add to dashboard Cite

show abstract

“…While the synthesis was simpler than LOM/TOM approach, it was limited by low yields and inability to form structures more complex than a dimer. In the continuous search for DNA structures that can serve as templates for DNAdirected couplings of conjugated organic molecules, interhelical couplings in a DNA 4-helix bundle (4-HB) have been investigated [21]. A conjugated linear molecule containing terminal salicylaldehyde groups and a central activated ester was synthesized.…”

Section: Modular Self-assembly Of Molecular Componentsmentioning

confidence: 99%

Controlling Single Molecule Conjugated Oligomers and Polymers with DNA

Hansen

Gothelf

2023

Natural Computing Series

View full text Add to dashboard Cite

The unique specificity of DNA interactions and our ability to synthesize artificial functionalized DNA sequences makes it the ideal material for controlling self-assembly and chemical reactions of components attached to DNA sequences. Inspired by the field of molecular electronics and the lack of methods to assemble molecular components, we have explored the organization of conjugated molecular components using DNA-based self-assembly. In this chapter, we provide an overview of our efforts first to assemble and chemically couple conjugated molecules directed by DNA, and more recently to assemble conjugated polymers in DNA nanostructures. At the end of the chapter, we provide a short overview of work by other groups in the field.

show abstract

“…ICLs over greater distances have also been reported. 16,18 Although several groups have used different methods to introduce ICLs to xed distances such as adjacent base pairs, 19,20 one base pair apart, 21 and two base pairs apart, 22 most current methods do not readily allow for the coupling of specic nucleotides in a nucleic acid structure, especially at varying distances. For example, psoralen is one of the most frequently used agents for cross-linking.…”

Section: Introductionmentioning

confidence: 99%

Site-specific inter-strand cross-links of DNA duplexes

et al. 2013

View full text Add to dashboard Cite

We report the development of technology that allows inter-strand coupling across various positions within one turn of DNA. Four 2′-modified nucleotides were synthesized as protected phosphoramidites and incorporated into DNA oligonucleotides. The modified nucleotides contain either 5-atom or 16-atom linker components, with either amine or carboxylic acid functional groups at their termini, forming 10 or 32 atom (11 or 33 bond) linkages. Chemical coupling of the amine and carboxylate groups in designed strands resulted in the formation of an amide bond. Coupling efficiency as a function of trajectory distance between the individual linker components was examined. For those nucleotides capable of forming inter-strand cross-links (ICLs), coupling yields were found to depend on temperature, distance, and linker length, enabling several approaches that can control regioselective linkage. In the most favorable cases, the coupling yields are quantitative. Spectroscopic measurements of strands that were chemically cross-linked indicate that the global structure of the DNA duplex does not appear to be distorted from the B form after coupling. Thermal denaturing profiles of those strands were shifted to somewhat higher temperatures than those of their respective control duplexes. Thus, the robust amide ICLs formed by this approach are site-specific, do not destabilize the rest of the duplex, and only minimally perturb the secondary structure.

show abstract

Distance Dependent Interhelical Couplings of Organic Rods Incorporated in DNA 4-Helix Bundles

Cited by 8 publications

References 56 publications

Poly(N-isopropylacrylamide-co-tris-nitrilotriacetic acid acrylamide) for a Combined Study of Molecular Recognition and Spatial Constraints in Protein Binding and Interactions

Poly(N-isopropylacrylamide-co-tris-nitrilotriacetic acid acrylamide) for a Combined Study of Molecular Recognition and Spatial Constraints in Protein Binding and Interactions

Controlling Single Molecule Conjugated Oligomers and Polymers with DNA

Site-specific inter-strand cross-links of DNA duplexes

Contact Info

Product

Resources

About