Properties of the nucleic-acid bases in free and Watson-Crick hydrogen-bonded states: computational insights into the sequence-dependent features of double-helical DNA

Srinivasan, A. R.; Sauers, Ronald R.; Fenley, Márcia O.; Boschitsch, Alexander H.; Matsumoto, Atsushi; Colasanti, Andrew V.; Olson, Wilma K.

doi:10.1007/s12551-008-0003-2

Cited by 36 publications

(30 citation statements)

References 48 publications

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“…Each of the PC corresponds to one of the lowest vibrational normal modes [31]. The ratio of ν buckle PC in the quantum simulation is significantly smaller than that in the classical simulation, while the ratio of the ν propeller mode in the quantum simulation is slightly larger than that in the classical simulation in AT-I.…”

Section: Principle Component Analysismentioning

confidence: 81%

“…PCA is a commonly used technique for analyzing statistical data. The variables of principle component (PC) represent dominant modes of the displacement from the reference coordinates [31]. The PCs are obtained as eigenvectors of the covariance matrix of displacements.…”

Section: Methods and Computational Detailsmentioning

confidence: 99%

“…These three modes are identified as corresponding inter-molecular vibrations between the adenine and thymine. We illustrate these inter-molecular three modes, so-called buckle, propeller and opening modes [31], in Fig. 2.…”

Section: Static Molecular Orbital Calculationmentioning

confidence: 99%

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Effects of monohydration on an adenine–thymine base pair

et al. 2015

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Section: Principle Component Analysismentioning

confidence: 81%

Section: Methods and Computational Detailsmentioning

confidence: 99%

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Effects of monohydration on an adenine–thymine base pair

et al. 2015

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“…Noncovalent interactions involved in the folding of the highly flexible and negatively charged sugarphosphate backbone of RNA molecules are far less understood, compared with those involved in protein folding (Č erný and Hobza 2007). These interactions are also relatively more complex than in regular DNA double helices, which are held together by canonical A:T and G:C WatsonCrick (WC) base pairs that are intrinsically suited for the structure and function of DNA (Srinivasan et al 2009). In keeping with their variety of functional roles, single-stranded RNA (ssRNA) molecules display far richer variation in basepairing types and geometries, which govern their ''folding on themselves'' into complex dynamic structures.…”

Section: Introductionmentioning

confidence: 99%

On the role of Hoogsteen:Hoogsteen interactions in RNA: Ab initio investigations of structures and energies

Sharma

Chawla²,

Sharma³

et al. 2010

RNA

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We use a combination of database analysis and quantum chemical studies to investigate the role of cis and trans Hoogsteen:Hoogsteen (H:H) base pairs and associated higher-order structures in RNA. We add three new examples to the list of previously identified base-pair combinations belonging to these families and, in addition to contextual classification and characterization of their structural and energetic features, we compare their interbase interaction energies and propensities toward participation in triplets and quartets. We find that some base pairs, which are nonplanar in their isolated minimum energy geometries, attain planarity and stability upon triplet formation. A:A H:H trans is the most frequent H:H combination in RNA structures. This base pair occurs at many distinct positions in known rRNA structures, where it helps in the interaction of ribosomal domains in the 50S subunit. It is also present as a part of tertiary interaction in tRNA structures. Although quantum chemical studies suggest an intrinsically nonplanar geometry for this base pair in isolated form, it has the tendency to attain planar geometry in RNA crystal structures by forming higher-order tertiary interactions or in the presence of additional basephosphate interactions. The tendency of this base pair to form such additional interactions may be helpful in bringing together different segments of RNA, thus making it suitable for the role of facilitator for RNA folding. This also explains the high occurrence frequency of this base pair among all H:H interactions.

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“…In 2009 Srinivasan et al reviewed the importance of the chemical structure of the nucleic acid bases to the polymeric properties of DNA. These authors focussed on the important contribution of ab initio computations to our understanding of the importance of nucleotide sequence dependence in the accumulation of charge on the major-and minor-groove edges of the Watson-Crick base pairs.…”

mentioning

confidence: 99%

Biophysical Reviews publications on DNA structure and function that complement this Special Issue on DNA supercoiling

Remedios

2016

Biophys Rev

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Although this Special Issue provides an in-depth analysis of the importance of DNA supercoiling, I would like to refer readers to several other relevant reviews published in Biophysical Reviews on the wider topic of DNA structure and function.In 2009 Srinivasan et al. reviewed the importance of the chemical structure of the nucleic acid bases to the polymeric properties of DNA. These authors focussed on the important contribution of ab initio computations to our understanding of the importance of nucleotide sequence dependence in the accumulation of charge on the major-and minor-groove edges of the Watson-Crick base pairs. They showed how optimizing the base-pair planes of DNA with the same handedness influences the binding of proteins to DNA.Three years later, this same laboratory (Olson et al. 2012) extended their computer simulations by highlighting the importance of communication between regulatory proteins attached to precisely constructed stretches of chromatin DNA. They developed new computational methods that provided insights into the roles played by individual proteins in reading and compacting the genome. As a consequence they were able to simulate the dynamic, three-dimensional structures of long, fluctuating, protein-decorated strands of DNA and take account of novel experimental measurements of enhancer-protein interactions. The states of chromatin captured in these simulations offered new insights into the ways DNA, histones and regulatory proteins contribute to long-range communication along the genome.The next year Biophysical Reviews reported (Qin and Zhou 2013) a freely-available suite of software, PI 2 PE (http://pipe. sc.fsu.edu) for predicting, inter alia, solvent accessibility of amino acids involved in protein folding and in protein-DNA complexes, as well as the binding rate constants of these complexes. The authors now have a new server that can predict these binding rate constants. These powerful web servers form a virtual pipeline between amino acid sequence data, tertiary structure, quaternary structure, and binding kinetics.Last year Yuri Lyubchenko (Lyubchenko 2015) reviewed the contributions of single-molecule time-lapse atomic force microscopy (AFM) to our understanding of the accessibility of DNA within complex bodies, called nucleosomes (these form the fundamental repeating units of eukaryotic chromatin). It turns out that these structures, which were once thought to be static, are in fact highly dynamic when examined on a millisecond time scale. They exhibit sliding and unwrapping, and even complete dissociation. Thus, AFM can provide new insights into the mechanisms that control spontaneous chromatin dynamics.Finally, in a hot-off-the-press review, Lois Pollack (Tokuda et al. 2016) reviews the way contrast variation in small angle X-ray scattering (SAXS) reveals new structural information on protein-DNA and ion-DNA interactions. Since DNA is essentially a long polyanion, its electrostatic interactions are mediated either by positively charged protein residues or by charge-comp...

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Properties of the nucleic-acid bases in free and Watson-Crick hydrogen-bonded states: computational insights into the sequence-dependent features of double-helical DNA

Cited by 36 publications

References 48 publications

Effects of monohydration on an adenine–thymine base pair

Effects of monohydration on an adenine–thymine base pair

On the role of Hoogsteen:Hoogsteen interactions in RNA: Ab initio investigations of structures and energies

Biophysical Reviews publications on DNA structure and function that complement this Special Issue on DNA supercoiling

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