8 Result(s)
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Article
High-resolution NMR structure of an AT-rich DNA sequence
We have determined, by proton NMR and complete relaxation matrix methods, the high-resolution structure of a DNA oligonucleotide in solution with nine contiguous AT base pairs. The stretch of AT pairs, TAATTAT...
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Chapter
Conformational Ensemble Calculations: Analysis of Protein and Nucleic Acid NMR Data
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Article
Conformational dynamics in mixed α/β-oligonucleotides containing polarity reversals: A molecular dynamics study using time-averaged restraints*
Nucleic acid duplexes featuring a single alpha-anomeric thymidine inserted into each DNA strand via 3′-3′ and 5′-5′ phosphodiester linkages exhibit local conformational dynamics that are not adequately depicte...
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Article
Determination of the populations and structures of multiple conformers in an ensemble from NMR data: Multiple-copy refinement of nucleic acid structures using floating weights
A new algorithm is presented for determination of structural conformers and their populations based on NMR data. Restrained Metropolis Monte Carlo simulations or restrained energy minimizations are performed f...
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Chapter
Dynamic Structure of Nucleic Acid Duplexes
Sequence-dependent structural variations in nucleic acids are important for the protein-nucleic acid and RNA-DNA interactions essential for life. Furthermore, structural variations are important factors in the...
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Article
Interproton distance bounds from 2D NOE intensities: Effect of experimental noise and peak integration errors
The effect of experimental and integration errors on the calculations in interproton distances from NOE intensities is examined. It is shown that NOE intensity errors can have a large impact on the distances d...
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Chapter and Conference Paper
Determination of High-Resolution, Sequence-Dependent DNA Duplex Structures in Solution
There can be rather subtle structural variations in the DNA double helix which are sequence-dependent; but these subtle structural differences may direct protein, mutagen or drug recognition. These subtle vari...
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Article
Metropolis Monte Carlo calculations of DNA structure using internal coordinates and NMR distance restraints: An alternative method for generating a high-resolution solution structure
A new method, a restrained Monte Carlo (rMC) calculation, is demonstrated for generating high-resolution structures of DNA oligonucleotides in solution from interproton distance restraints and bounds derived f...
