Phosphonoacetic acid as a building block in supramolecular chemistry: salts with organic polyamines

Bowes, Katharine F.; Ferguson, George; Lough, Alan J.; Zakaria, Choudhury M.; Glidewell, Christopher

doi:10.1107/s010876810201858x

Cited by 17 publications

(11 citation statements)

References 7 publications

(4 reference statements)

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“…All biochemical data were collected from analytical, electrophoretic and NMR studies shown in our previously published work [29] and in the present study. Theoretical rationales were derived from the universally accepted principles of the supramolecular chemistry based on the selfassembly by means of weak interactions [47,[55][56][57]. A multistep aggregation plan was developed as follows (a) a cyclic and planar structure representing the single base module, (b) base modules combined in polycyclic planar structures (ladder), (c) the polycyclic modules developed 3D into tunnel-like structures.…”

Section: Methodsmentioning

confidence: 99%

Nuclear aggregates of polyamines are supramolecular structures that play a crucial role in genomic DNA protection and conformation

D’Agostino¹,

Pietro²,

Luccia

2005

The FEBS Journal

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Polyamines interact with DNA phosphate groups by means of nonspecific electrostatic bonds [1]. This interaction has been shown to result in the protection of small DNA molecules from common damaging agents, such as ionizing radiation and reactive oxygen species [2,3]. Polyamines in solution with polynucleotides have also been shown to inhibit the activity of endonucleases, including DNase I [4][5][6][7]. The protective ability of polyamines is attributable not only to the formation of a steric barrier against DNA-damaging agents, but also to their property to condense the DNA. In fact, polyamines, like other cations, induce DNA condensation as a consequence of the inhibition of > 90% of DNA negative charges [8]. Analogous in vivo experiments have demonstrated that spermine and, to a lesser extent, spermidine, prevent DNA fragmentation and the onset of apoptosis. Protection from enzymatic cleavage appears to be the result of a modified chromatin arrangement, rather than inhibition of the endonuclease activity [9].Condensation of DNA in the presence of polyamines has also been proposed to be instrumental in genome packaging [10]. This should be regarded of crucial importance if we consider that the total length of cellular DNA is 1 m, whereas the size of the nucleus is in the range of several micrometers [11]. However, condensation should not be considered as a static state, as the elasticity is a mechanical property of the DNA, indispensable to cellular processes such as replication and transcription [12,13]. For these reasons the DNA strands in vivo, at the same time, must be packaged and protected, but not restrained.The structural impact of polyamines on DNA is also supported by the evidence that these compounds induce, on polynucleotides, a transition from the rightoriented B-form to the left-handed Z-form [14,15]. Such an effect might be important for DNA physiology, as a tight connection occurs between transcriptional activity on DNA and the acquisition of a Z-form [16]. In a previous study we showed that natural polyamines interact in the nuclear environment with phosphate groups to form molecular aggregates [nuclear aggregates of polyamines (NAPs)] with estimated molecular mass values of 8000, 4800 and 1000 Da. NAPs were found to interact with genomic DNA, influence its conformation and interfere with the action of nucleases. In the present work, we demonstrated that NAPs protect naked genomic DNA from DNase I, whereas natural polyamines (spermine, spermidine and putrescine) fail to do so. In the context of DNA protection, NAPs induced noticeable changes in DNA conformation, which were revealed by temperature-dependent modifications of DNA electrophoretic properties. In addition, we presented, for NAPs, a structural model of polyamine aggregation into macropolycyclic compounds. We believe that NAPs are the sole biological forms by which polyamines efficiently protect genomic DNA against DNase I, while maintaining its dynamic structure.Abbreviation NAP, nuclear aggregate of polyamines.

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Section: Methodsmentioning

confidence: 99%

Nuclear aggregates of polyamines are supramolecular structures that play a crucial role in genomic DNA protection and conformation

D’Agostino¹,

Pietro²,

Luccia

2005

The FEBS Journal

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“…In each of (1)±(7) the phosphonate component adopts an extended conformation, with the PÐCÐCÐC torsional angle close to 180 in each case and with the carboxyl or carboxylate group almost normal to the mean plane de®ned by the backbone chain. However, the orientation of the PÐOH bond can vary, as in the analogous salts of phosphonoacetic acid (Bowes et al, 2003). In general, this bond is synclinal to the backbone chain, but in (3) the bond is antiperiplanar.…”

Section: Molecular Conformationsmentioning

confidence: 99%

“…Comparison of phosphonopropionate salts with phosphonoacetate analogues. The adducts formed by phosphonoacetic acid, (HO) 2 P(O)CH 2 COOH, with four of the amines employed in the present study, namely N,N H -dimethylpiperazine, 4,4 H -bipyridyl, 1,2-bis(4-pyridyl)ethane and 2,2 H -dipyridylamine, have recently been structurally characterized (Farrell et al, 2001;Bowes et al, 2003), and it is of interest to compare the structural variation within each of these three pairs of compounds.…”

Section: Figure 19mentioning

confidence: 99%

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Phosphonopropionic acid as a building block in supramolecular chemistry: salts with organic diamines

Bowes

Ferguson

Lough

et al. 2003

Acta Crystallogr Sect B

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The structures of seven salts formed by phosphonopropionic acid with organic diamines are reported; in these salts, the hydrogen-bonded substructures formed by the anions can be zero-, one- or two-dimensional, while the overall hydrogen-bonded supramolecular structures are three-dimensional. The 1:1 adduct, compound (1), formed between 1,2-bis(4'-pyridyl)ethene and phosphonopropionic acid is a salt, [[(C(12)H(10)N(2))H(2)](2+)].[(C(12)H(10)N(2))].[(C(3)H(6)O(5)P)(-)](2), in which both diamine components lie across centres of inversion in space group P2(1)/c. The anions form hydrogen-bonded head-to-head dimers, and these are linked by the two diamine units into sheets, which are themselves linked by C-H.O hydrogen bonds. With 2,2'-dipyridylamine the acid forms the hydrated salt [[(C(10)H(9)N(3))H](+)].[(C(3)H(6)O(5)P)(-)].H(2)O (2), in which all components are disordered with occupancy 0.5 in space group Fmm2. The anions form head-to-tail dimers, which are linked into sheets by the cations, and the sheets are linked into a three-dimensional framework by the water molecules. The piperazine salt [[(C(4)H(10)N(2))H(2)](2+)].[(C(3)H(5)O(5)P)(2-)] (3) contains simple anion chains linked into a three-dimensional framework by the two independent cations, both of which are centrosymmetric. In the hydrated salt formed by N,N'-dimethylpiperazine, [[(MeNC(4)H(8)NMe)H(2)](2+)].[(C(3)H(6)O(5)P)(-)](2).(H(2)O)(2) (4), head-to-tail anion chains combine with the water molecules to form a three-dimensional framework, which encloses voids that contain the cations. In the 4,4'-bipyridyl adduct [[(C(10)H(8)N(2))H(0.72)](0.72+)].[[(H(0.5)O)(3)PCH(2)CH(2)COOH(0.78)](0.72-)] (5), there is extensive disorder of the H atoms that are bonded to N and O atoms, and the anion chains are linked by the cations into sheets, which are themselves linked by C-H.O hydrogen bonds. In the 1:2 adduct formed with 1,2-bis(4'-pyridyl)ethane, [[(C(12)H(12)N(2))H(2)](2+)].[(C(3)H(6)O(5)P)(-)](2) (6), where the cation lies across an inversion centre, the anions form molecular ladders. These ladders are linked into sheets by the cations, which are themselves linked by C-H.O hydrogen bonds. In the methanol-solvated salt formed with 2,6-dimethylpiperazine, [[(C(6)H(14)N(2))H(2)](2+)].[(C(3)H(6)O(5)P)(-)](2). (CH(4)O)(0.34) (7), the anions form sheets that are linked into a three-dimensional framework by the cations. The supramolecular structures are compared with those of analogous salts formed by phosphonoacetic acid.

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“…cations generally lie across centres of inversion (Gregson et al, 2000;Lough et al, 2000;Burchell et al, 2000;Bowes, Ferguson, Lough, Zakaria & Glidewell, 2003). An exception occurs in the salt formed with 5-hydroxyisophthalic acid, in which the cation lies in a general position in space group P2 1 2 1 2 1 (Burchell et al, 2000).…”

Section: +mentioning

confidence: 99%

meso-5,5,7,12,12,14-Hexamethyl-4,11-diaza-1,8-diazoniacyclotetradecane (S)-malate(2–) methanol disolvate: a chain of rings generated by two pairs of N—H...O hydrogen bonds

et al. 2003

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The title compound is a methanol-solvated salt, C(16)H(38)N(4)(2+).C(4)H(4)O(5)(2-).2CH(3)OH, in which the ionic components are linked into chains by two pairs of N-H.O hydrogen bonds [H.O = 1.78-2.21 A, N.O = 2.702 (14)-3.094 (8) A and N-H.O = 160-179 degrees ]. The methanol molecules are pendent from the chain and are linked to it by O-H.O hydrogen bonds [H.O = 1.86 and 1.89 A, O.O = 2.691 (9) and 2.708 (16) A, and O-H.O = 168 and 165 degrees ].

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Phosphonoacetic acid as a building block in supramolecular chemistry: salts with organic polyamines

Cited by 17 publications

References 7 publications

Nuclear aggregates of polyamines are supramolecular structures that play a crucial role in genomic DNA protection and conformation

Nuclear aggregates of polyamines are supramolecular structures that play a crucial role in genomic DNA protection and conformation

Phosphonopropionic acid as a building block in supramolecular chemistry: salts with organic diamines

meso-5,5,7,12,12,14-Hexamethyl-4,11-diaza-1,8-diazoniacyclotetradecane (S)-malate(2–) methanol disolvate: a chain of rings generated by two pairs of N—H...O hydrogen bonds

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