Jaroslav Malina | Academy of Sciences of the Czech Republic (original) (raw)
Papers by Jaroslav Malina
Chemical Science, 2019
Iron-based self-assembled optically pure compounds mimic the mechanisms of small peptides, accord... more Iron-based self-assembled optically pure compounds mimic the mechanisms of small peptides, according to biophysical, genomic, transcriptomic and other analyses.
Journal of inorganic biochemistry, Jan 21, 2015
Trans diiodido platinum(II) complexes bearing the same as well as different aliphatic amines (mix... more Trans diiodido platinum(II) complexes bearing the same as well as different aliphatic amines (mixed-amines) have interesting biological activity; cytotoxicity and interactions with some important biological models have already been demonstrated. Herein we described the interaction of such compounds with ct-DNA, supercoiled and linearized plasmid DNA and 5-GMP. Interestingly, UV irradiation of these compounds results in an increase in reactivity towards DNA and 5-GMP in such model systems. Additionally, the cytotoxicity of the trans-Pt(II) complexes towards human cancer cells is noticeably increased when treatment is combined for 90min with UVA-irradiation. With this work we provide evidence that trans diiodido compounds can be activated by UV-light over relatively short treatment times.
Nucleic Acids Research, 2022
The design of efficient and safe gene delivery vehicles remains a major challenge for the applica... more The design of efficient and safe gene delivery vehicles remains a major challenge for the application of gene therapy. Of the many reported gene delivery systems, metal complexes with high affinity for nucleic acids are emerging as an attractive option. We have discovered that certain metallohelices—optically pure, self-assembling triple-stranded arrays of fully encapsulated Fe—act as nonviral DNA delivery vectors capable of mediating efficient gene transfection. They induce formation of globular DNA particles which protect the DNA from degradation by various restriction endonucleases, are of suitable size and electrostatic potential for efficient membrane transport and are successfully processed by cells. The activity is highly structure-dependent—compact and shorter metallohelix enantiomers are far less efficient than less compact and longer enantiomers.
Norwegian Archaeological Review, 1983
Chemistry – A European Journal
Angewandte Chemie International Edition
Scientific reports, Jul 12, 2016
The interaction between the HIV-1 transactivator protein Tat and TAR (transactivation responsive ... more The interaction between the HIV-1 transactivator protein Tat and TAR (transactivation responsive region) RNA, plays a critical role in HIV-1 transcription. Iron(II) supramolecular helicates were evaluated for their in vitro activity to inhibit Tat-TAR RNA interaction using UV melting studies, electrophoretic mobility shift assay, and RNase A footprinting. The results demonstrate that iron(II) supramolecular helicates inhibit Tat-TAR interaction at nanomolar concentrations by binding to TAR RNA. These studies provide a new insight into the biological potential of metallosupramolecular helicates.
Biophysical Journal, 2000
Modifications of natural DNA and synthetic oligodeoxyribonucleotide duplexes in a cell-free mediu... more Modifications of natural DNA and synthetic oligodeoxyribonucleotide duplexes in a cell-free medium by analogs of antitumor cisplatin containing enantiomeric amine ligands, such as cis-[PtCl 2 (RR-DAB)] and cis-[PtCl 2 (SS-DAB)] (DAB ϭ 2,3-diaminobutane), were studied by various methods of molecular biophysics and biophysical chemistry. These methods include DNA binding studies by pulse polarography and atomic absorption spectrophotometry, mapping of DNA adducts using transcription assay, interstrand cross-linking assay using gel electrophoresis under denaturing conditions, differential scanning calorimetry, chemical probing, and bending and unwinding studies of the duplexes containing single, site-specific cross-link. The major differences resulting from the modification of DNA by the two enantiomers are the thermodynamical destabilization and conformational distortions induced in DNA by the 1,2-d(GpG) intrastrand cross-link. It has been suggested that these differences are associated with a different biological activity of the two enantiomers observed previously. In addition, the results of the present work are also consistent with the view that formation of hydrogen bonds between the carbonyl oxygen of the guanine residues and the "quasi equatorial" hydrogen of the cis amine in the 1,2-d(GpG) intrastrand cross-link plays an important role in determining the character of the distortion induced in DNA by this lesion.
Chemistry & Biology, 2002
We examined HMG domain protein recognition of major 1,2-GG intrastrand DNA crosslinks, formed by ... more We examined HMG domain protein recognition of major 1,2-GG intrastrand DNA crosslinks, formed by two bifunctional enantiomeric analogs of antitumor cis-diamminedichloroplatinum(II) (cisplatin), and removal of these crosslinks during in vitro nucleotide excision repair (NER) reactions. Electrophoretic mobility shift assays show that domains A and B of HMGB1 protein bind to (2R,3R)-diaminobutanedichloroplatinum(II)-generated crosslinks with a higher affinity than to those generated by (2S,3S)-diaminobutanedichloroplatinum(II). The crosslinks of both enantiomers are removed by NER with a similar efficiency; however, HMG1B protein significantly inhibits removal of the (2R,3R)-diaminobutaneplatinum(II) adduct, but not that of the (2S,3S) enantiomer. Thus, HMG domain proteins discriminate among different conformations of the 1,2-GG intrastrand crosslinks of the two enantiomeric analogs of cisplatin, which results in different NER of these crosslinks. This observation may provide insight into the mechanisms underlying antitumor activity of cisplatin and its analogs.
Biophysical Journal, 2007
Downstream processes that discriminate between DNA adducts of a third generation platinum antitum... more Downstream processes that discriminate between DNA adducts of a third generation platinum antitumor drug oxaliplatin and conventional cisplatin are believed to be responsible for the differences in their biological effects. These different biological effects are explained by the ability of oxaliplatin to form DNA adducts more efficient in their biological effects. In this work conformation, recognition by HMG domain protein and DNA polymerization across the major 1,2-GG intrastrand cross-link formed by cisplatin and oxaliplatin in three sequence contexts were compared with the aid of biophysical and biochemical methods. The following major differences in the properties of the cross-links of oxaliplatin and cisplatin were found: i), the formation of the cross-link by oxaliplatin is more deleterious energetically in all three sequence contexts; ii), the cross-link of oxaliplatin bends DNA slightly but systematically less in all sequence contexts tested; iii), the affinity of HMG domain protein to the cross-link of oxaliplatin is considerably lower independent of the sequence context; and iv), the Klenow fragment of DNA polymerase I pauses considerably more at the cross-link of oxaliplatin in all sequence contexts tested. We have also demonstrated that the chirality at the carrier ligand of oxaliplatin can affect its biological effects.
Chemistry - A European Journal, 2006
Supporting information for this article is available on the WWW under http://www.chemeurj.org/ or... more Supporting information for this article is available on the WWW under http://www.chemeurj.org/ or from the author: Deconvolution of the film LD spectrum to assign Cu-helicate transition polarisations; calculation of the orientation of Cu-helicate on the DNA; DNAcleavage activity of the cylinders with pBR322 plasmid DNA and hydrogen peroxide; DNA-cleavage activity of the cylinders with ct-DNA and hydrogen peroxide; possible major-groove and minorgroove binding orientations consistent with a 708 binding angle; NMR and ESI-MS data for the copper(i) cylinder.
Environmental Health Perspectives, 2002
In this article we review the biological activity of analogs of the antitumor drug cisplatin that... more In this article we review the biological activity of analogs of the antitumor drug cisplatin that contain chiral amine ligands. Interaction with DNA and formation of cross-links with adjacent purine bases are considered to be the crucial steps in the antitumor activity of this class of complexes. Because double-helical DNA has a chiral structure, interaction with enantiomeric complexes of platinum should lead to diastereomeric adducts. It has been demonstrated that DNA cross-links of platinum complexes with enantiomeric amine ligands not only can exhibit different conformational features but also can be processed differently by the cellular machinery as a consequence of these conformational differences. These results expand the general knowledge of how the stereochemistry of the platinum-DNA adduct can influence the cell response and contribute to understanding the processes that are crucial for antitumor activity. The steric requirements of the chiral ligands, in terms of configuration and flexibility, are also elucidated.
![Research paper thumbnail of DNA-protein cross-linking by trans-[PtCl2(E-iminoether)2]. A concept for activation of the trans geometry in platinum antitumor complexes](https://attachments.academia-assets.com/44462285/thumbnails/1.jpg)
](Nucleic Acids Research
The structure±pharmacological activity relationships generally accepted for antitumor platinum co... more The structure±pharmacological activity relationships generally accepted for antitumor platinum compounds stressed the necessity for the cis-[PtX 2 (amine) 2 ] structure while the trans-[PtX 2 (amine) 2 ] structure was considered inactive. However, more recently, several trans-platinum complexes have been identi®ed which are potently toxic, antitumor-active and demonstrate activity distinct from that of conventional cisplatin (cis-[PtCl 2 (NH 3 ) 2 ]). We have shown in the previous report that the replacement of ammine ligands by iminoether in transplatin (trans-[PtCl 2 (NH 3 ) 2 ]) results in a marked enhancement of its cytotoxicity so that it is more cytotoxic than its cis congener and exhibits signi®cant antitumor activity, including activity in cisplatin-resistant tumor cells. In addition, we have also shown previously that this new trans compound (trans-[PtCl 2 (E-iminoether) 2 ]) forms mainly monofunctional adducts at guanine residues on DNA, which is generally accepted to be the cellular target of platinum drugs. In order to shed light on the mechanism underlying the antitumor activity of trans-[PtCl 2 (E-iminoether) 2 ] we examined oligodeoxyribonucleotide duplexes containing a single, site-speci®c, monofunctional adduct of this transplatin analog by the methods of molecular biophysics. The results indicate that major monofunctional adducts of trans-[PtCl 2 (E-iminoether) 2 ] locally distort DNA, bend the DNA axis by 21 o toward the minor groove, are not recognized by HMGB1 proteins and are readily removed from DNA by nucleotide excision repair (NER). In addition, the monofunctional adducts of trans-[PtCl 2 (E-iminoether) 2 ] readily cross-link proteins, which markedly enhances the ef®ciency of this adduct to terminate DNA polymerization by DNA polymerases in vitro and to inhibit removal of this adduct from DNA by NER. It is suggested that DNA±protein ternary cross-links produced by trans-[PtCl 2 (E-iminoether) 2 ] could persist considerably longer than the non-cross-linked monofunctional adducts, which would potentiate toxicity of this antitumor platinum compound toward tumor cells sensitive to this drug. Thus, trans-[PtCl 2 (E-iminoether) 2 ] represents a quite new class of platinum antitumor drugs in which activation of trans geometry is associated with an increased ef®ciency to form DNA±protein ternary cross-links thereby acting by a different mechanism from`classical' cisplatin and its analogs.
Dalton transactions (Cambridge, England : 2003), Jan 11, 2015
Bulged structures have been identified in nucleic acids and have been shown to be linked to biomo... more Bulged structures have been identified in nucleic acids and have been shown to be linked to biomolecular processes involved in numerous diseases. Thus, chemical agents with affinity for bulged nucleic acids are of general biological significance. Herein, the mechanism of specific recognition and stabilization of bulged DNA and RNA by helical bimetallic species was established through detailed molecular biophysics and biochemistry assays. These agents, known as 'flexicates', are potential mimetics of α-helical peptides in cancer treatment, exhibiting antimicrobial and antitumor effects. The flexicates have positive impacts on the thermal stability of DNA duplexes containing bulges, which means that the flexicates interact with the duplexes containing bulges, and that these interactions stabilize the secondary structures of these duplexes. Notably, the stabilising effect of the flexicates increases with the size of the bulge, the maximal stabilization is observed for the duple...
Nucleic acids research, Jan 4, 2015
Loss of a base in DNA leading to creation of an abasic (AP) site leaving a deoxyribose residue in... more Loss of a base in DNA leading to creation of an abasic (AP) site leaving a deoxyribose residue in the strand, is a frequent lesion that may occur spontaneously or under the action of various physical and chemical agents. Progress in the understanding of the chemistry and enzymology of abasic DNA largely relies upon the study of AP sites in synthetic duplexes. We report here on interactions of diastereomerically pure metallo-helical 'flexicate' complexes, bimetallic triple-stranded ferro-helicates [Fe2(NN-NN)3](4+) incorporating the common NN-NN bis(bidentate) helicand, with short DNA duplexes containing AP sites in different sequence contexts. The results show that the flexicates bind to AP sites in DNA duplexes in a shape-selective manner. They preferentially bind to AP sites flanked by purines on both sides and their binding is enhanced when a pyrimidine is placed in opposite orientation to the lesion. Notably, the Λ-enantiomer binds to all tested AP sites with higher affi...
Chemistry (Weinheim an der Bergstrasse, Germany), 2014
Loss of a base in DNA and the creation of an abasic (apurinic/apyrimidinic, AP) site is a frequen... more Loss of a base in DNA and the creation of an abasic (apurinic/apyrimidinic, AP) site is a frequent lesion that may occur spontaneously, or as a consequence of the action of DNA-damaging agents. The AP lesion is mutagenic or lethal if not repaired. We report a systematic thermodynamic investigation by differential scanning calorimetry on the evolution, during primer extension, of a model AP site in chemically simulated DNA translesion synthesis. Incorporation of dAMP (deoxyadenosine monophosphate), as well as dTMP (deoxythymidine monophosphate), opposite an AP site is enthalpically unfavorable, although incorporation of dTMP is more enthalpically unfavorable than that of dAMP. This finding is in a good agreement with experimental data showing that AP sites block various DNA polymerases of eukaryotic and prokaryotic origin and that, if bypassed, dAMP is preferentially inserted, whereas insertion of dTMP is less likely. The results emphasize the importance of thermodynamic contributions to the insertion of nucleotides opposite an AP site by DNA polymerases.
Chemical Science, 2019
Iron-based self-assembled optically pure compounds mimic the mechanisms of small peptides, accord... more Iron-based self-assembled optically pure compounds mimic the mechanisms of small peptides, according to biophysical, genomic, transcriptomic and other analyses.
Journal of inorganic biochemistry, Jan 21, 2015
Trans diiodido platinum(II) complexes bearing the same as well as different aliphatic amines (mix... more Trans diiodido platinum(II) complexes bearing the same as well as different aliphatic amines (mixed-amines) have interesting biological activity; cytotoxicity and interactions with some important biological models have already been demonstrated. Herein we described the interaction of such compounds with ct-DNA, supercoiled and linearized plasmid DNA and 5-GMP. Interestingly, UV irradiation of these compounds results in an increase in reactivity towards DNA and 5-GMP in such model systems. Additionally, the cytotoxicity of the trans-Pt(II) complexes towards human cancer cells is noticeably increased when treatment is combined for 90min with UVA-irradiation. With this work we provide evidence that trans diiodido compounds can be activated by UV-light over relatively short treatment times.
Nucleic Acids Research, 2022
The design of efficient and safe gene delivery vehicles remains a major challenge for the applica... more The design of efficient and safe gene delivery vehicles remains a major challenge for the application of gene therapy. Of the many reported gene delivery systems, metal complexes with high affinity for nucleic acids are emerging as an attractive option. We have discovered that certain metallohelices—optically pure, self-assembling triple-stranded arrays of fully encapsulated Fe—act as nonviral DNA delivery vectors capable of mediating efficient gene transfection. They induce formation of globular DNA particles which protect the DNA from degradation by various restriction endonucleases, are of suitable size and electrostatic potential for efficient membrane transport and are successfully processed by cells. The activity is highly structure-dependent—compact and shorter metallohelix enantiomers are far less efficient than less compact and longer enantiomers.
Norwegian Archaeological Review, 1983
Chemistry – A European Journal
Angewandte Chemie International Edition
Scientific reports, Jul 12, 2016
The interaction between the HIV-1 transactivator protein Tat and TAR (transactivation responsive ... more The interaction between the HIV-1 transactivator protein Tat and TAR (transactivation responsive region) RNA, plays a critical role in HIV-1 transcription. Iron(II) supramolecular helicates were evaluated for their in vitro activity to inhibit Tat-TAR RNA interaction using UV melting studies, electrophoretic mobility shift assay, and RNase A footprinting. The results demonstrate that iron(II) supramolecular helicates inhibit Tat-TAR interaction at nanomolar concentrations by binding to TAR RNA. These studies provide a new insight into the biological potential of metallosupramolecular helicates.
Biophysical Journal, 2000
Modifications of natural DNA and synthetic oligodeoxyribonucleotide duplexes in a cell-free mediu... more Modifications of natural DNA and synthetic oligodeoxyribonucleotide duplexes in a cell-free medium by analogs of antitumor cisplatin containing enantiomeric amine ligands, such as cis-[PtCl 2 (RR-DAB)] and cis-[PtCl 2 (SS-DAB)] (DAB ϭ 2,3-diaminobutane), were studied by various methods of molecular biophysics and biophysical chemistry. These methods include DNA binding studies by pulse polarography and atomic absorption spectrophotometry, mapping of DNA adducts using transcription assay, interstrand cross-linking assay using gel electrophoresis under denaturing conditions, differential scanning calorimetry, chemical probing, and bending and unwinding studies of the duplexes containing single, site-specific cross-link. The major differences resulting from the modification of DNA by the two enantiomers are the thermodynamical destabilization and conformational distortions induced in DNA by the 1,2-d(GpG) intrastrand cross-link. It has been suggested that these differences are associated with a different biological activity of the two enantiomers observed previously. In addition, the results of the present work are also consistent with the view that formation of hydrogen bonds between the carbonyl oxygen of the guanine residues and the "quasi equatorial" hydrogen of the cis amine in the 1,2-d(GpG) intrastrand cross-link plays an important role in determining the character of the distortion induced in DNA by this lesion.
Chemistry & Biology, 2002
We examined HMG domain protein recognition of major 1,2-GG intrastrand DNA crosslinks, formed by ... more We examined HMG domain protein recognition of major 1,2-GG intrastrand DNA crosslinks, formed by two bifunctional enantiomeric analogs of antitumor cis-diamminedichloroplatinum(II) (cisplatin), and removal of these crosslinks during in vitro nucleotide excision repair (NER) reactions. Electrophoretic mobility shift assays show that domains A and B of HMGB1 protein bind to (2R,3R)-diaminobutanedichloroplatinum(II)-generated crosslinks with a higher affinity than to those generated by (2S,3S)-diaminobutanedichloroplatinum(II). The crosslinks of both enantiomers are removed by NER with a similar efficiency; however, HMG1B protein significantly inhibits removal of the (2R,3R)-diaminobutaneplatinum(II) adduct, but not that of the (2S,3S) enantiomer. Thus, HMG domain proteins discriminate among different conformations of the 1,2-GG intrastrand crosslinks of the two enantiomeric analogs of cisplatin, which results in different NER of these crosslinks. This observation may provide insight into the mechanisms underlying antitumor activity of cisplatin and its analogs.
Biophysical Journal, 2007
Downstream processes that discriminate between DNA adducts of a third generation platinum antitum... more Downstream processes that discriminate between DNA adducts of a third generation platinum antitumor drug oxaliplatin and conventional cisplatin are believed to be responsible for the differences in their biological effects. These different biological effects are explained by the ability of oxaliplatin to form DNA adducts more efficient in their biological effects. In this work conformation, recognition by HMG domain protein and DNA polymerization across the major 1,2-GG intrastrand cross-link formed by cisplatin and oxaliplatin in three sequence contexts were compared with the aid of biophysical and biochemical methods. The following major differences in the properties of the cross-links of oxaliplatin and cisplatin were found: i), the formation of the cross-link by oxaliplatin is more deleterious energetically in all three sequence contexts; ii), the cross-link of oxaliplatin bends DNA slightly but systematically less in all sequence contexts tested; iii), the affinity of HMG domain protein to the cross-link of oxaliplatin is considerably lower independent of the sequence context; and iv), the Klenow fragment of DNA polymerase I pauses considerably more at the cross-link of oxaliplatin in all sequence contexts tested. We have also demonstrated that the chirality at the carrier ligand of oxaliplatin can affect its biological effects.
Chemistry - A European Journal, 2006
Supporting information for this article is available on the WWW under http://www.chemeurj.org/ or... more Supporting information for this article is available on the WWW under http://www.chemeurj.org/ or from the author: Deconvolution of the film LD spectrum to assign Cu-helicate transition polarisations; calculation of the orientation of Cu-helicate on the DNA; DNAcleavage activity of the cylinders with pBR322 plasmid DNA and hydrogen peroxide; DNA-cleavage activity of the cylinders with ct-DNA and hydrogen peroxide; possible major-groove and minorgroove binding orientations consistent with a 708 binding angle; NMR and ESI-MS data for the copper(i) cylinder.
Environmental Health Perspectives, 2002
In this article we review the biological activity of analogs of the antitumor drug cisplatin that... more In this article we review the biological activity of analogs of the antitumor drug cisplatin that contain chiral amine ligands. Interaction with DNA and formation of cross-links with adjacent purine bases are considered to be the crucial steps in the antitumor activity of this class of complexes. Because double-helical DNA has a chiral structure, interaction with enantiomeric complexes of platinum should lead to diastereomeric adducts. It has been demonstrated that DNA cross-links of platinum complexes with enantiomeric amine ligands not only can exhibit different conformational features but also can be processed differently by the cellular machinery as a consequence of these conformational differences. These results expand the general knowledge of how the stereochemistry of the platinum-DNA adduct can influence the cell response and contribute to understanding the processes that are crucial for antitumor activity. The steric requirements of the chiral ligands, in terms of configuration and flexibility, are also elucidated.
Nucleic Acids Research
The structure±pharmacological activity relationships generally accepted for antitumor platinum co... more The structure±pharmacological activity relationships generally accepted for antitumor platinum compounds stressed the necessity for the cis-[PtX 2 (amine) 2 ] structure while the trans-[PtX 2 (amine) 2 ] structure was considered inactive. However, more recently, several trans-platinum complexes have been identi®ed which are potently toxic, antitumor-active and demonstrate activity distinct from that of conventional cisplatin (cis-[PtCl 2 (NH 3 ) 2 ]). We have shown in the previous report that the replacement of ammine ligands by iminoether in transplatin (trans-[PtCl 2 (NH 3 ) 2 ]) results in a marked enhancement of its cytotoxicity so that it is more cytotoxic than its cis congener and exhibits signi®cant antitumor activity, including activity in cisplatin-resistant tumor cells. In addition, we have also shown previously that this new trans compound (trans-[PtCl 2 (E-iminoether) 2 ]) forms mainly monofunctional adducts at guanine residues on DNA, which is generally accepted to be the cellular target of platinum drugs. In order to shed light on the mechanism underlying the antitumor activity of trans-[PtCl 2 (E-iminoether) 2 ] we examined oligodeoxyribonucleotide duplexes containing a single, site-speci®c, monofunctional adduct of this transplatin analog by the methods of molecular biophysics. The results indicate that major monofunctional adducts of trans-[PtCl 2 (E-iminoether) 2 ] locally distort DNA, bend the DNA axis by 21 o toward the minor groove, are not recognized by HMGB1 proteins and are readily removed from DNA by nucleotide excision repair (NER). In addition, the monofunctional adducts of trans-[PtCl 2 (E-iminoether) 2 ] readily cross-link proteins, which markedly enhances the ef®ciency of this adduct to terminate DNA polymerization by DNA polymerases in vitro and to inhibit removal of this adduct from DNA by NER. It is suggested that DNA±protein ternary cross-links produced by trans-[PtCl 2 (E-iminoether) 2 ] could persist considerably longer than the non-cross-linked monofunctional adducts, which would potentiate toxicity of this antitumor platinum compound toward tumor cells sensitive to this drug. Thus, trans-[PtCl 2 (E-iminoether) 2 ] represents a quite new class of platinum antitumor drugs in which activation of trans geometry is associated with an increased ef®ciency to form DNA±protein ternary cross-links thereby acting by a different mechanism from`classical' cisplatin and its analogs.
Dalton transactions (Cambridge, England : 2003), Jan 11, 2015
Bulged structures have been identified in nucleic acids and have been shown to be linked to biomo... more Bulged structures have been identified in nucleic acids and have been shown to be linked to biomolecular processes involved in numerous diseases. Thus, chemical agents with affinity for bulged nucleic acids are of general biological significance. Herein, the mechanism of specific recognition and stabilization of bulged DNA and RNA by helical bimetallic species was established through detailed molecular biophysics and biochemistry assays. These agents, known as 'flexicates', are potential mimetics of α-helical peptides in cancer treatment, exhibiting antimicrobial and antitumor effects. The flexicates have positive impacts on the thermal stability of DNA duplexes containing bulges, which means that the flexicates interact with the duplexes containing bulges, and that these interactions stabilize the secondary structures of these duplexes. Notably, the stabilising effect of the flexicates increases with the size of the bulge, the maximal stabilization is observed for the duple...
Nucleic acids research, Jan 4, 2015
Loss of a base in DNA leading to creation of an abasic (AP) site leaving a deoxyribose residue in... more Loss of a base in DNA leading to creation of an abasic (AP) site leaving a deoxyribose residue in the strand, is a frequent lesion that may occur spontaneously or under the action of various physical and chemical agents. Progress in the understanding of the chemistry and enzymology of abasic DNA largely relies upon the study of AP sites in synthetic duplexes. We report here on interactions of diastereomerically pure metallo-helical 'flexicate' complexes, bimetallic triple-stranded ferro-helicates [Fe2(NN-NN)3](4+) incorporating the common NN-NN bis(bidentate) helicand, with short DNA duplexes containing AP sites in different sequence contexts. The results show that the flexicates bind to AP sites in DNA duplexes in a shape-selective manner. They preferentially bind to AP sites flanked by purines on both sides and their binding is enhanced when a pyrimidine is placed in opposite orientation to the lesion. Notably, the Λ-enantiomer binds to all tested AP sites with higher affi...
Chemistry (Weinheim an der Bergstrasse, Germany), 2014
Loss of a base in DNA and the creation of an abasic (apurinic/apyrimidinic, AP) site is a frequen... more Loss of a base in DNA and the creation of an abasic (apurinic/apyrimidinic, AP) site is a frequent lesion that may occur spontaneously, or as a consequence of the action of DNA-damaging agents. The AP lesion is mutagenic or lethal if not repaired. We report a systematic thermodynamic investigation by differential scanning calorimetry on the evolution, during primer extension, of a model AP site in chemically simulated DNA translesion synthesis. Incorporation of dAMP (deoxyadenosine monophosphate), as well as dTMP (deoxythymidine monophosphate), opposite an AP site is enthalpically unfavorable, although incorporation of dTMP is more enthalpically unfavorable than that of dAMP. This finding is in a good agreement with experimental data showing that AP sites block various DNA polymerases of eukaryotic and prokaryotic origin and that, if bypassed, dAMP is preferentially inserted, whereas insertion of dTMP is less likely. The results emphasize the importance of thermodynamic contributions to the insertion of nucleotides opposite an AP site by DNA polymerases.