Shape readout of AT‐rich DNA by carbohydrates. Issue 7 (July 2014)

• Record Type: Journal Article
• Authors: Kumar, Sunil; Newby Spano, Meredith; Arya, Dev P.
• Is Part Of: Biopolymers. Volume 101:Issue 7(2014)
• Page Start: 720
• Page End: 732
• Publication Date: 2014-07
• Subjects: Biopolymers -- Periodicals; Peptides -- Periodicals; Spectrum analysis -- Periodicals; 572.33
• DOI: 10.1002/bip.22448
• Languages: English
• ISSNs: 0006-3525

Abstract

<abstract abstract-type="main"> <title>ABSTRACT</title> <p>Gene expression can be altered by small molecules that target DNA; sequence as well as shape selectivities are both extremely important for DNA recognition by intercalating and groove‐binding ligands. We have characterized a carbohydrate scaffold (1) exhibiting DNA "shape readout" properties. Thermodynamic studies with 1 and model duplex DNAs demonstrate the molecule's high affinity and selectivity towards B* form (continuous AT‐rich) DNA. Isothermal titration calorimetry (ITC), circular dichroism (CD) titration, ultraviolet (UV) thermal denaturation, and Differential Scanning Calorimetry were used to characterize the binding of 1 with a B* form AT‐rich DNA duplex d[5′‐G<sub>2</sub>A<sub>6</sub>T<sub>6</sub>C<sub>2</sub>‐3′]. The binding constant was determined using ITC at various temperatures, salt concentrations, and pH. ITC titrations were fit using a two‐binding site model. The first binding event was shown to have a 1:1 binding stoichiometry and was predominantly entropy‐driven with a binding constant of approximately 10<sup>8</sup> M<sup>−1</sup>. ITC‐derived binding enthalpies were used to obtain the binding‐induced change in heat capacity (ΔC<sub>p</sub>) of −225 ± 19 cal/mol·K. The ionic strength dependence of the binding constant indicated a significant electrolytic contribution in ligand:DNA binding, with approximately four to five ion pairs involved in binding. Ligand 1 displayed a significantly higher affinity towards AT‐tract DNA over sequences containing GC inserts, and binding experiments revealed the order of binding affinity for 1 with DNA duplexes: contiguous B* form AT‐rich DNA (d[5′‐G<sub>2</sub>A<sub>6</sub>T<sub>6</sub>C<sub>2</sub>‐3′]) >B form alternate AT‐rich DNA (d[5′‐G<sub>2</sub>(AT)<sub>6</sub>C<sub>2‐</sub>3′]) > A form GC‐rich DNA (d[5′‐A<sub>2</sub>G<sub>6</sub>C<sub>6</sub>T<sub>2</sub>‐3′]), demonstrating the preference of ligand 1 for B* form DNA. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 720–732, 2014.</p> </abstract>