| 1. |
- Ratilainen, Tommi, 1970, et al.
(author)
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A simple model for gene targeting
- 2001
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In: Biophysical Journal. - 0006-3495 .- 1542-0086. ; 81:5, s. 2876-2885
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Journal article (peer-reviewed)abstract
- Sequence-specific binding to genomic-size DNA sequences by artificial agents is of major interest for the development of gene-targeting strategies, gene-diagnostic applications, and biotechnical tools. The binding of one such agent, peptide nucleic acid (PNA), to a randomized human genome has been modeled with statistical mass action calculations. With the length of the PNA probe, the average per-base binding constant k(0), and the binding affinity loss of a mismatched base pair as main parameters, the specificity was gauged as a "therapeutic ratio" G = maximum safe [PNA](tot)/minimal efficient [PNA](tot). This general, though simple, model suggests that, above a certain threshold length of the PNA, the microscopic binding constant k(0) is the primary determinant for optimal discrimination, and that only a narrow range of rather low k(0) values gives a high therapeutic ratio G. For diagnostic purposes, the value of k(0) could readily be modulated by changing the temperature, due to the substantial DeltaH(o) associated with the binding equilibrium. Applied to gene therapy, our results stress the need for appropriate control of the binding constant and added amount of the gene-targeting agent, to meet the varying conditions (ionic strength, presence of competing DNA-binding molecules) found in the cell.
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| 2. |
- Jabak, Adam A., et al.
(author)
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Effect of Chirality on the Elastic Properties of the DNA-Threading Binuclear Ruthenium Complex
- 2020
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In: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 118:3, Supplement 1, s. 617a-
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Conference paper (peer-reviewed)abstract
- Transition metal-based small molecules have been promising candidates for cancer treatments. A certain type of these molecules falls into a category known as threading intercalators, that have a dumbbell shape with a flat intercalating section in between bulky side chains. In order to bind to DNA, they must thread one of their bulky side chains through the DNA base pairs. The ruthenium-based molecule, ΛΛ-[μ-bidppz(phen)4Ru2]4+ (ΛΛ-P for short), is a transition metal-based threading intercalator. We use optical tweezers to study the interactions of ΛΛ-P with DNA to compare it with the previously studied ΔΔ-P, a complex that has the same chemical components but an opposite chirality. In these studies, we use the optical tweezers to trap a single DNA molecule and stretch it in the presence of various concentrations of ΛΛ-P. The DNA stretches obtained at saturated concentrations of ΛΛ-P at various forces allows us to obtain the effective elastic properties of the DNA-ΛΛ-P complex. This allows us to compare these properties to the previously studied ΔΔ-P complex to determine whether chirality has an effect. This type of comparison may lead us towards a better understanding of the role chirality has towards DNA binding.
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| 3. |
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| 4. |
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| 5. |
- Ainla, Alar, 1982, et al.
(author)
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Lab on a Biomembrane
- 2014
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In: Biophysical Journal. - 0006-3495 .- 1542-0086. ; 106:2, s. 209A-209A
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Journal article (other academic/artistic)
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| 6. |
- Ali Doosti, Baharan, 1991, et al.
(author)
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Ca2+ Gradient Induces Membrane Bending and Formation of Nanotubes in Giant Lipid Vesicles
- 2016
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In: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 110:3, s. 584A-584A
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Journal article (peer-reviewed)abstract
- Reshaping and bending of the cell membrane is imperative in many processes such as cell division, filopodia formation, and endocytosis. Understanding these shape transitions, will help to elucidate the underlying mechanisms of these essential cellular processes. In our work, we investigate an interplay between cell membrane morphology and chemical stimulation by constructing a biomimetic model system. More specifically, giant lipid vesicles were exposed to a chemical gradient of Ca2+, which was established over the membrane surface.
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| 8. |
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| 9. |
- Alizadehheidari, Mohammadreza, 1987, et al.
(author)
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Unfolding of nanoconfined circular DNA
- 2015
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In: BIOPHYSICAL JOURNAL. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 108:2 Supplement 1
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Journal article (other academic/artistic)
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| 10. |
- Almaqwashi, A. A., et al.
(author)
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Dissecting the Dynamic Pathways of Stereoselective DNA Threading Intercalation
- 2016
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In: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 110:6, s. 1255-1263
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Journal article (peer-reviewed)abstract
- DNA intercalators that have high affinity and slow kinetics are developed for potential DNA-targeted therapeutics. Although many natural intercalators contain multiple chiral subunits, only intercalators with a single chiral unit have been quantitatively probed. Dumbbell-shaped DNA threading intercalators represent the next order of structural complexity relative to simple intercalators, and can provide significant insights into the stereoselectivity of DNA-ligand intercalation. We investigated DNA threading intercalation by binuclear ruthenium complex [mu-dppzip(phen)(4)Ru-2](4+) (Piz). Four Piz stereoisomers are defined by the chirality of the intercalating subunit (Ru(phen)(2)dppz) and the distal subunit (Ru(phen)(2)ip), respectively, each of which can be either right-handed (Delta) or left-handed (Lambda). We used optical tweezers to measure single DNA molecule elongation due to threading intercalation, revealing force-dependent DNA intercalation rates and equilibrium dissociation constants. The force spectroscopy analysis provided the zero-force DNA binding affinity, the equilibrium DNA-ligand elongation Delta x(eq), and the dynamic DNA structural deformations during ligand association x(on) and dissociation x(off). We found that Piz stereoisomers exhibit over 20-fold differences in DNA binding affinity, from a K-d of 27 +/- 3 nM for (Delta,Lambda)-Piz to a K-d of 622 +/- 55 nM for (Lambda,Delta)-Piz. The striking affinity decrease is correlated with increasing Delta x(eq) from 0.30 +/- 0.02 to 0.48 +/- 0.02 nm and x(on) from 0.25 +/- 0.01 to 0.46 +/- 0.02 nm, but limited x(off) changes. Notably, the affinity and threading kinetics is 10-fold enhanced for right-handed intercalating subunits, and 2- to 5-fold enhanced for left-handed distal subunits. These findings demonstrate sterically dispersed transition pathways and robust DNA structural recognition of chiral intercalators, which are critical for optimizing DNA binding affinity and kinetics.
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