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Shape readout of AT‐rich DNA by carbohydrates
Author(s) -
Kumar Sunil,
Newby Spano Meredith,
Arya Dev P.
Publication year - 2014
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.22448
Subject(s) - isothermal titration calorimetry , chemistry , binding constant , dna , circular dichroism , crystallography , molecule , titration , ionic strength , binding site , intercalation (chemistry) , binding selectivity , biophysics , biochemistry , aqueous solution , inorganic chemistry , organic chemistry , biology
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 2 A 6 T 6 C 2 ‐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 8 M −1 . ITC‐derived binding enthalpies were used to obtain the binding‐induced change in heat capacity (ΔC p ) 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 2 A 6 T 6 C 2 ‐3′]) >B form alternate AT‐rich DNA (d[5′‐G 2 (AT) 6 C 2‐ 3′]) > A form GC‐rich DNA (d[5′‐A 2 G 6 C 6 T 2 ‐3′]), demonstrating the preference of ligand 1 for B* form DNA. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 720–732, 2014.