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Eva Fadrna et al.
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R. Lavery et al.
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Alberto Perez et al.
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Quan Du et al.
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Alberto Perez et al.
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J Sponer et al.
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A Pérez et al.
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A Pérez et al.
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X-ray and NMR studies of the DNA oligomer d(ATATAT):: Hoogsteen base pairing in duplex DNA
NGA Abrescia et al.
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J Sponer et al.
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DNA and its counterions:: a molecular dynamics study
P Várnai et al.
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DL Beveridge et al.
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A Noy et al.
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ZG Wu et al.
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M Orozco et al.
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E Cubero et al.
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I Andricioaei et al.
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Sequence-dependent elastic properties of DNA
F Lankas et al.
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