Thermodynamics of nucleic acid "shape readout" by an aminosugar.
Thermodynamics of nucleic acid "shape readout" by an aminosugar.
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DOI：
10.1021/bi201077h
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发表时间：
2011-10-25
期刊：
影响因子：
2.9
通讯作者：
Arya, Dev P.
中科院分区：
文献类型：
--
作者：
Xi, Hongjuan;Davis, Erik;Ranjan, Nihar;Xue, Liang;Hyde-Volpe, David;Arya, Dev P.
Recognition of nucleic acids is important for our understanding of nucleic acid structure as well as for our understanding of nucleic acid-protein interactions. In addition to the direct readout mechanisms of nucleic acids such as H-bonding, shape recognition of nucleic acids is being increasingly recognized to play an equally important role in DNA recognition. Competition Dialysis, UV, Flourescent Intercalator displacement (FID), Computational Docking, and calorimetry studies were conducted to study the interaction of neomycin with a variety of nucleic acid conformations (shapes). At pH 5.5, these results suggest: (1) Neomycin binds three RNA structures (16S A site rRNA, poly(rA)•poly(rA), and poly(rA)•poly(rU)) with high affinities, Ka~107M−1. (2) The binding of neomycin to A-form GC-rich oligomer d(A2G15C15T2)2 has comparable affinity to RNA structures. (3) The binding of neomycin to DNA•RNA hybrids shows a three-fold variance attributable to their structural differences (poly(dA) •poly(rU), Ka=9.4×106M−1 and poly(rA)•poly(dT), Ka=3.1×106M−1). (4) The interaction of neomycin with DNA triplex poly(dA)•2poly(dT) yields a binding affinity of Ka=2.4×105M−1. (5) Poly(dA-dT)2 showed the lowest association constant for all nucleic acids studied (Ka=<105). (6) Neomycin binds to G-quadruplexes with Ka~104-105M−1. (7) Computational studies show that the decrease in major groove width in the B to A transition correlates with increasing neomycin affinity. Neomycin’s affinity for various nucleic acid structures can be ranked as follows, RNAs and GC-rich d(A2G15C15T2)2 structures > poly(dA)•poly(rU) > poly(rA)•poly(dT) > T•A-T triplex , G-quadruplexes, B-form AT-rich or GC-rich DNA sequences. The results illustrate the first example of a small molecule based ‘shape readout’ of different nucleic acid conformations.
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影响因子：
3.4
作者：
Barbieri, CM;Pilch, DS
通讯作者：
Pilch, DS
DOI：
10.2174/1568011054222292
发表时间：
2005-07-01
期刊：
Current Medicinal Chemistry - Anti-Cancer Agents
影响因子：
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作者：
Chaires, Jonathan B.
通讯作者：
Chaires, Jonathan B.
影响因子：
3.4
作者：
Dadarlat, VM;Saxena, VK
通讯作者：
Saxena, VK
影响因子：
3.9
作者：
Chaires, Jonathan B.
通讯作者：
Chaires, Jonathan B.
影响因子：
15
作者：
Boger, DL;Fink, BE;Hedrick, MP
通讯作者：
Hedrick, MP