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The Bound Structures of 17β‐Estradiol‐Binding Aptamers
Author(s) -
Hilder Tamsyn A.,
Hodgkiss Justin M.
Publication year - 2017
Publication title -
chemphyschem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.016
H-Index - 140
eISSN - 1439-7641
pISSN - 1439-4235
DOI - 10.1002/cphc.201700363
Subject(s) - aptamer , molecular dynamics , computational biology , chemistry , dna , binding selectivity , molecular recognition , nanotechnology , molecular binding , molecule , biophysics , biology , materials science , biochemistry , genetics , computational chemistry , organic chemistry
Abstract DNA aptamers can exhibit high affinity and selectivity towards their targets, but the aptamer–target complex structures are rarely available from crystallography and often difficult to elucidate. This is particularly true of small molecule targets, including 17β‐estradiol (E2), which is becoming one of the most widely encountered endocrine‐disrupting chemicals in the environment. Using molecular dynamics simulations, we demonstrate that E2 binds to a thymine loop region common to all E2‐specific aptamers in the literature. Analyzing these structures allows us to design new E2 binding sequences. As well as illuminating the essential sequence and structural factors for generating specificity for E2, we demonstrate the effectiveness of molecular dynamics simulations for aptamer science.