DFT study of minimal fragments of nucleic acid single chain for explication of sequence dependence of DNA duplex conformation

Poltev, V. I.; Anisimov, Victor M.; Danilov, V.I.; Deriabina, A.; Gonzalez, Emmanuel A.; García, Diosdado Baena; Rivas, Francisco; Jurkiewicz, Agata; Leś, Andrzej; Polteva, Nina

doi:10.1016/j.theochem.2009.03.022

Cited by 13 publications

(38 citation statements)

References 30 publications

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“…Table II contains same and different conformation families, we divided the 16 dDMPs into four groups depending on base sequence: purine-purine (PUR-PUR), pyrimidine-pyrimidine (PYR-PYR), purine-pyrimidine (PUR-PYR), and pyrimidine-purine (PYR-PUR) sequences. In our previous article, [4] we mentioned that calculations with the ADF program and a triple zeta basis set result in numerical values of the conformational characteristics close to those obtained with the DGAUSS program. In this work, we present the conformational characteristics obtained by both programs for selected nucleoside sequences to explicitly show the degree of variation happening due to the use of different computer programs.…”

Section: A-family Conformationssupporting

confidence: 56%

“…The conformational characteristics of the optimized structures having various base sequences will be compared with the corresponding characteristics of the BI-like dDMP structures obtained earlier [3,4]. In common, the three groups of the obtained structures (A, BI, and BII) correspond to anti parallel right-handed DNA duplexes with an anti conformation of the nucleosides.…”

Section: Resultsmentioning

confidence: 99%

“…The structural characteristics of dDMPs in the BI conformation pertaining to the geometry of nucleobases, amino group non-planarity, and bond lengths and bond angles of the sugar- phosphate backbone were analyzed in our previous work [3,4]. The corresponding characteristics of dDMPs in A and BII conformations remain essentially the same as in the BI form of dDMPs and thus do not show additional information.…”

Section: Resultsmentioning

confidence: 99%

“…The mutual base arrangement in dDMP is sequence dependent, namely two dDMPs with the same nucleoside content but different base sequence (e.g., dApdC and dCpdA) have drastically differed mutual base positions. These observations lead us to the conclusion of principal contribution of the sugar-phosphate backbone to the three-dimensional structure of the DNA single strand, and a minor contribution to these effects can be attributed to base-base stacking interactions [3,4]. Surely, dispersive base-base interactions contribute substantially to the DNA duplex stability and deformability, but they cannot explain the nearly parallel arrangements of the bases with nearly negligible overlap or the essential difference between purine-pyrimidine and pyrimidine-purine base arrangements.…”

Section: Introduction Dmentioning

confidence: 93%

“…In the light of these difficulties, our previous studies [3,4] were necessarily limited to consideration of the B-family-like structures of deoxydinucleoside monophosphates, while focusing the attention on elucidating the dependence of the three-dimensional structure of the dDMPs on their nucleotide sequence. Our DFT computations revealed that the characteristic BI-type conformation of DNA duplexes is initially predisposed in the single strand and namely in its dDMP conformational profile in the form of a local energy minimum.…”

Section: Introduction Dmentioning

confidence: 99%

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DFT study of polymorphism of the DNA double helix at the level of dinucleoside monophosphates

Poltev

Anisimov²,

Danilov

et al. 2010

Int J of Quantum Chemistry

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ABSTRACT:We apply DFT calculations to deoxydinucleoside monophosphates (dDMPs) which represent minimal fragments of the DNA chain to study the molecular basis of stability of the DNA duplex, the origin of its polymorphism and conformational heterogeneity. In this work, we continue our previous studies of dDMPs where we detected internal energy minima corresponding to the ''classical'' B conformation (BI-form), which is the dominant form in the crystals of oligonucleotide duplexes. We obtained BI local energy minima for all existing base sequences of dDMPs. In the present study, we extend our analysis to other families of DNA conformations, successfully identifying A, BI, and BII energy minima for all dDMP sequences. These conformations demonstrate distinct differences in sugar ring puckering, but similar sequence-dependent base arrangements. Internal energies of BI and BII conformers are close to each other for nearly all the base sequences. The dGpdG, dTpdG, and dCpdA dDMPs slightly favor the BII conformation, which agrees with these sequences being more frequently experimentally encountered in the BII form. We have found BII-like structures of dDMPs for the base sequences both existing in crystals in BII conformation and those not yet encountered in crystals till now. On the other hand, we failed to obtain dDMP energy minima corresponding to the Z family of DNA conformations, thus giving us the ground to conclude that these conformations are stabilized in both crystals and solutions by external factors, presumably by interactions with various components of the media. Overall the accumulated computational data demonstrate that the A, BI, and BII families of DNA conformations originate from the corresponding local energy minimum conformations of dDMPs, thus determining structural stability of a single DNA strand during the processes of unwinding and rewinding of DNA.

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Section: A-family Conformationssupporting

confidence: 56%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introduction Dmentioning

confidence: 93%

Section: Introduction Dmentioning

confidence: 99%

See 3 more Smart Citations

DFT study of polymorphism of the DNA double helix at the level of dinucleoside monophosphates

Poltev

Anisimov²,

Danilov

et al. 2010

Int J of Quantum Chemistry

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Structural, Electronic, and Optical Properties of Metallo Base Pairs in Duplex DNA: A Theoretical Insight

Samanta

Manna

Pati

2012

Chemistry An Asian Journal

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Using density functional theory calculations, we investigated the structural, energetic, electronic, and optical properties of recently synthesized duplex DNA containing metal-mediated base pairs. The studied duplex DNA consists of three imidazole (Im) units linked through metal (Im-M-Im, M = metal) and four flanking A:T base pairs (two on each side). We examined the role of artificial base pairing in the presence of two distinctive metal ions, diamagnetic Ag(+) and magnetic Cu(2+) ions, on the stability of duplex DNA. We found that metal-mediated base pairs form stable duplex DNA by direct metal ion coordination to the Im bases. Our results suggest a higher binding stability of base pairing mediated by Cu(2+) ions than by Ag(+) ions, which is attributed to a larger extent of orbital hybridization. We furthermore found that DNA modified with Im-Ag(+)-Im shows the low-energy optical absorption characteristic of π-π*orbital transition of WC A:T base pairs. On the other hand, we found that the low-energy optical absorption peaks for DNA modified with Im-Cu(2+)-Im originate from spin-spin interactions. Additionally, this complex exhibits weak ferromagnetic coupling between Cu(2+) ions and strong spin polarization, which could be used for memory devices. Moreover, analyzing the role of counter ions (Na(+)) and the presence of explicit water molecules on the structural stability and electronic properties of the DNA duplex modified with Im-Ag(+)-Im, we found that the impact of these two factors is negligible. Our results are fruitful for understanding the experimental data and suggest a potential route for constructing effective metal-mediated base pairs in duplex DNA for optoelectronic applications.

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The role of molecular structure of sugar‐phosphate backbone and nucleic acid bases in the formation of single‐stranded and double‐stranded DNA structures

et al. 2014

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Our previous DFT computations of deoxydinucleoside monophosphate complexes with Na(+)-ions (dDMPs) have demonstrated that the main characteristics of Watson-Crick (WC) right-handed duplex families are predefined in the local energy minima of dDMPs. In this work, we study the mechanisms of contribution of chemically monotonous sugar-phosphate backbone and the bases into the double helix irregularity. Geometry optimization of sugar-phosphate backbone produces energy minima matching the WC DNA conformations. Studying the conformational variability of dDMPs in response to sequence permutation, we found that simple replacement of bases in the previously fully optimized dDMPs, e.g. by constructing Pyr-Pur from Pur-Pyr, and Pur-Pyr from Pyr-Pur sequences, while retaining the backbone geometry, automatically produces the mutual base position characteristic of the target sequence. Based on that, we infer that the directionality and the preferable regions of the sugar-phosphate torsions, combined with the difference of purines from pyrimidines in ring shape, determines the sequence dependence of the structure of WC DNA. No such sequence dependence exists in dDMPs corresponding to other DNA conformations (e.g., Z-family and Hoogsteen duplexes). Unlike other duplexes, WC helix is unique by its ability to match the local energy minima of the free single strand to the preferable conformations of the duplex.

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DFT study of minimal fragments of nucleic acid single chain for explication of sequence dependence of DNA duplex conformation

Cited by 13 publications

References 30 publications

DFT study of polymorphism of the DNA double helix at the level of dinucleoside monophosphates

DFT study of polymorphism of the DNA double helix at the level of dinucleoside monophosphates

Structural, Electronic, and Optical Properties of Metallo Base Pairs in Duplex DNA: A Theoretical Insight

The role of molecular structure of sugar‐phosphate backbone and nucleic acid bases in the formation of single‐stranded and double‐stranded DNA structures

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