Density functional study of the influence of C5 cytosine substitution in base pairs with guanine

Moser, Adam; Guza, Rebecca; Tretyakova, Natalia; York, Darrin M.

doi:10.1007/s00214-008-0497-5

Cited by 19 publications

(18 citation statements)

References 60 publications

(59 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Several ab initio molecular orbital studies on the substitution effect on hydrogen-bond formation energy of adenine-uracile-X (A-U-X), X-adenine-uracile (X-A-U), guanine-cytosine-X (G-C-X), and X-guanine-cytosine (X-G-C) base pairs have already been reported by Kawahara et al [9][10][11][12][13]. Recently, a density functional study of the influence of C5 cytosine substitution in base pairs with guanine has been performed by Moser et al [14]. On the other hand, many studies have analyzed the interaction of different metal cations to G and their influence on base pairing [15][16][17][18][19][20][21][22][23][24].…”

Section: Introductionmentioning

confidence: 98%

The effect of CH3, F and NO2 substituents on the individual hydrogen bond energies in the adenine–thymine and guanine–cytosine base pairs

Ebrahimi

Habibi‐Khorassani

Delarami

et al. 2010

J Comput Aided Mol Des

View full text Add to dashboard Cite

The substituent effects on the geometrical parameters and the individual hydrogen bond (HB) energies of base pairs such as X-adenine-thymine (X-A-T), X-thymine-adenine (X-T-A), X-guanine-cytosine (X-G-C), and X-cytosine-guanine (X-C-G) have been studied by the quantum mechanical calculations at the B3LYP and MP2 levels with the 6-311++G(d,p) basis set. The electron withdrawing (EW) substituents (F and NO(2)) increase the total binding energy (DeltaE) of X-G-C derivatives and the electron donating (ED) substituent (CH(3)) decreases it when they are introduced in the 8 and 9 positions of G. The effects of substituents are reversed when they are located in the 1, 5, and 6 positions of C, with exception of CH(3) in the 1 position and F in the 5 position, which in both cases the DeltaE value decreases negligibly small. With minor exceptions (X=8-CH(3), 8-F, and 9-NO(2)), both ED and EW substituents increase slightly the DeltaE values of X-A-T derivatives. The individual HB energies (E (HB)s) have been estimated using electron densities that calculated at the hydrogen bond critical points (HBCPs) by the atoms in molecules (AIM) method. Most of changes of individual HBs are in consistent with the ED/EW nature of substituents and the role of atoms entered H-bonding. The remarkable change is observed for NO(2) substituted derivative in each case.

show abstract

Section: Introductionmentioning

confidence: 98%

The effect of CH3, F and NO2 substituents on the individual hydrogen bond energies in the adenine–thymine and guanine–cytosine base pairs

Ebrahimi

Habibi‐Khorassani

Delarami

et al. 2010

J Comput Aided Mol Des

View full text Add to dashboard Cite

show abstract

“…A previous study has shown that the C 4 -N 4 bond of cytosine and its analogs have considerable double-bond character (41), consistent with its slow amino group rotation rate relative to adenine and guanine analogs. We investigated the geometry of the m dC, dC and Cl dC monomers through DFT calculations performed with the 6-31G basis set (B3LYP).…”

Section: Discussionmentioning

confidence: 75%

Comparison of the Structural and Dynamic Effects of 5-Methylcytosine and 5-Chlorocytosine in a CpG Dinucleotide Sequence

et al. 2013

View full text Add to dashboard Cite

Inflammation-mediated reactive molecules can result in an array of oxidized and halogenated DNA damage products including 5-chlorocytosine (ClC). Previous studies have shown that ClC can mimic 5-methylcytosine (mC) and act as a fraudulent epigenetic signal, promoting the methylation of previously unmethylated DNA sequences. Although the 5-halouracils are good substrates for base excision repair, no repair activity has yet been identified for ClC. Due to the apparent biochemical similarities of mC and ClC, we have investigated the effects of mC and ClC substitution on oligonucleotide structure and dynamics. In this study, we have constructed oligonucleotide duplexes containing C, ClC and mC within a CpG dinucleotide. The thermal and thermodynamic stability of these duplexes are found to be experimentally indistinguishable. Crystallographic structures of duplex oligonucleotides containing mC and ClC were determined to 1.2 and 1.9 Å, respectively. Both duplexes are B-form and are superimposable on a previously determined structure of a cytosine-containing duplex with RMSD of approximately 0.25 Å. NMR solution studies indicate that all duplexes containing cytosine or the cytosine analogs are normal B-form, and no structural perturbations are observed surrounding the site of each substitution. The magnitude of the base-stacking induced upfield shifts for non-exchangeable base proton resonances are similar for each of the duplexes examined, indicating that neither mC nor ClC significantly alter base stacking interactions. The ClC analog is paired with G in an apparently normal geometry; however the G-imino proton of the ClC-G base pair resonates to higher field relative to mC-G or C-G, indicating a weaker imino hydrogen bond. Using selective 15N-enrichment and isotope-edited NMR, we observe that the amino group of ClC rotates at roughly half the rate of the corresponding amino groups of the C-G or mC-G base pairs. The altered chemical shifts of hydrogen bonding proton resonances for the ClC-G base pair, as well as the slower rotation of the ClC amino group can be attributed to the electron-withdrawing inductive property of the 5-chloro substituent. The apparent similarity of duplexes containing mC and ClC demonstrated here is in accord with results of previous biochemical studies and further suggests that ClC is likely to be an unusually persistent form of DNA damage.

show abstract

“…In this research, we conducted quantum mechanical computations aiming at quantifying the effects of structural variations in adenine on the hydrogen bonding interaction (pairing) with thymine. As already discussed in the introductory section, derivatives of the nucleobases have been shown to possess biological activities and potential for clinical applications [16][17][18][19][20][21][22][23][24][25][26][27][28]. It was also of interest to analyze the impact of structural changes on the geometries of the formed complexes.…”

Section: Resultsmentioning

confidence: 99%

“…Experimental and theoretical investigations on hydrogen bonding involving structural fragments of biopolymers are the subject of continuing interest [12][13][14][15]. Literature data reveal that structurally modified DNA bases may possess substantial biological activity [16][17][18][19][20][21][22][23][24][25][26][27][28]. For example, halogenated pyrimidines have been shown to possess well-expressed anti-tumor, anti-bacterial and anti-viral effects [20].…”

Section: Introductionmentioning

confidence: 99%

Effects of structural variations on the hydrogen bond pairing between adenine derivatives and thymine

Nikolova¹,

Galabov²

2015

Maced. J. Chem. Chem. Eng.

View full text Add to dashboard Cite

The hydrogen bonding between substituted adenines and thymine was investigated by density functional theory computations at the B3LYP/6-311+G(2d,2p) level. The effect of 20 different polar substituents at position 8 in adenine was examined in detail. Three different theoretical parameters, reflecting the electrostatics at the atoms involved in hydrogen bonding, were applied. An excellent correlation between electrostatic potentials at the bonding atoms in the monomer adenines and interaction energies was derived (Eqn. 2). It can be employed in designing bioactive adenine derivatives that are able to bind with a finely adjusted strength to thymine bioreceptor sites. NBO and Hirshfeld atomic charges are found to be less successful as reactivity predictors in these interactions.Keywords: DNA base pair; adenine; thymine; hydrogen bonding; electrostatic potential; atomic charges ЕФЕКТИ НА СТРУКТУРНИТЕ ВАРИЈАЦИИ ВРЗ СПАРУВАЊЕТО НА АДЕНИНСКИ ДЕРИВАТИ И ТИМИН СО ПОМОШ НА ВОДОРОДНО СВРЗУВАЊЕИстражувано е водородното сврзување помеѓу супституирани аденини и тимин со помош на пресметки според теоријата за функционал на електронската густина на нивото B3LYP/6-311+G(2d,2p). Детално е изучуван ефектот на 20 различни поларни супституенти на аденин во позицијата 8. Применети се три различни теоретски параметри кои ја рефлектираат електростатиката на атомите вклучени во водородното сврзување. Добиена е одлична корелација помеѓу електростатските потенцијали на сврзувачките атоми во мономерните аденини и интеракционите енергии (р-ка 2). Тоа може да се примени при дизајнирање на биоактивни аденински деривати кои можат да се сврзат со фино нагодена јачина со тиминските биорецепторски сајтови. Најдено е дека т.н. NBO и Хиршфилдовите (Hirshfeld) атомски полнежи се помалку успешни како претскажувачи на реактивноста во овие интеракции.Клучни зборови: ДНК базен пар; аденин; тимин; водородно сврзување; електростатски потенцијал; атомски полнежи  Dedicated to Academician Gligor Jovanovski on the occasion of his 70 th birthday.

show abstract

Density functional study of the influence of C5 cytosine substitution in base pairs with guanine

Cited by 19 publications

References 60 publications

The effect of CH3, F and NO2 substituents on the individual hydrogen bond energies in the adenine–thymine and guanine–cytosine base pairs

The effect of CH3, F and NO2 substituents on the individual hydrogen bond energies in the adenine–thymine and guanine–cytosine base pairs

Comparison of the Structural and Dynamic Effects of 5-Methylcytosine and 5-Chlorocytosine in a CpG Dinucleotide Sequence

Effects of structural variations on the hydrogen bond pairing between adenine derivatives and thymine

Contact Info

Product

Resources

About