Single-Stranded DNA Oligonucleotides Retain Rise Coordinates Characteristic of Double Helices

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Abstract
The structures of single stranded DNA oligonucleotides from dimeric to hexameric sequences have been thoroughly investigated. Computations performed at the density functional level of theory including dispersion forces and solvation show that single stranded helices adopt conformations very close to crystallographic B-DNA, with rise coordinates amounting up to 3.33 Ansgtrom. Previous results, suggesting that single strands should be shorter than double helices were largely originated by the incompleteness of the adopted basis set. Although sensible deviations with respect to standard B-DNA are predicted, computations indicate that sequences rich of stacked adenines are the most ordered ones, favoring the B-DNA pattern and inducing regular arrangements also on flanking nucleobases. Several structural properties of double helices rich of adenine are indeed already reflected by the corresponding single strands.
Funding Information
  • Universit? degli Studi di Salerno

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