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Moiseeva ED, Bazhulina NP, Gursky YG, Grokhovsky SL, Surovaya AN, Gursky GV. Targeting Holliday junctions by origin DNA-binding protein of herpes simplex virus type 1. J Biomol Struct Dyn 2016; 35:704-723. [PMID: 26987269 DOI: 10.1080/07391102.2016.1161561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
In the present paper, the interactions of the origin binding protein (OBP) of herpes simplex virus type 1 (HSV1) with synthetic four-way Holliday junctions (HJs) were studied using electrophoresis mobility shift assay and the FRET method and compared with the interactions of the protein with duplex and single-stranded DNAs. It has been found that OBP exhibits a strong preference for binding to four-way and three-way DNA junctions and possesses much lower affinities to duplex and single-stranded DNAs. The protein forms three types of complexes with HJs. It forms complexes I and II which are reminiscent of the tetramer and octamer complexes with four-way junction of HJ-specific protein RuvA of Escherichia coli. The binding approaches saturation level when two OBP dimers are bound per junction. In the presence of Mg2+ ions (≥2 mM) OBP also interacts with HJ in the stacked arm form (complex III). In the presence of 5 mM ATP and 10 mM Mg2+ ions OBP catalyzes processing of the HJ in which one of the annealed oligonucleotides has a 3'-terminal tail containing 20 unpaired thymine residues. The observed preference of OBP for binding to the four-way DNA junctions provides a basis for suggestion that OBP induces large DNA structural changes upon binding to Box I and Box II sites in OriS. These changes involve the bending and partial melting of the DNA at A+T-rich spacer and also include the formation of HJ containing Box I and Box II inverted repeats and flanking DNA sequences.
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Affiliation(s)
- E D Moiseeva
- a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , ul. Vavilova 32, 119991 Moscow , Russia
| | - N P Bazhulina
- a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , ul. Vavilova 32, 119991 Moscow , Russia
| | - Y G Gursky
- b Russian Cardiology Research-and-Production Complex , 3ya Cherepkovskaya ul. 15a, 121552 Moscow , Russia
| | - S L Grokhovsky
- a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , ul. Vavilova 32, 119991 Moscow , Russia
| | - A N Surovaya
- a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , ul. Vavilova 32, 119991 Moscow , Russia
| | - G V Gursky
- a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , ul. Vavilova 32, 119991 Moscow , Russia
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Bazhulina NP, Surovaya AN, Gursky YG, Andronova VL, Moiseeva ED, Nikitin CACM, Golovkin MV, Galegov GА, Grokhovsky SL, Gursky GV. Complex of the herpes simplex virus type 1 origin binding protein UL9 with DNA as a platform for the design of a new type of antiviral drugs. J Biomol Struct Dyn 2013; 32:1456-73. [PMID: 23879454 PMCID: PMC4066892 DOI: 10.1080/07391102.2013.820110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The herpes simplex virus type 1 origin-binding protein, OBP, is a DNA helicase encoded by the UL9 gene. The protein binds in a sequence-specific manner to the viral origins of replication, two OriS sites and one OriL site. In order to search for efficient inhibitors of the OBP activity, we have obtained a recombinant origin-binding protein expressed in Escherichia coli cells. The UL9 gene has been amplified by PCR and inserted into a modified plasmid pET14 between NdeI and KpnI sites. The recombinant protein binds to Box I and Box II sequences and possesses helicase and ATPase activities. In the presence of ATP and viral protein ICP8 (single-strand DNA-binding protein), the initiator protein induces unwinding of the minimal OriS duplex (≈80 bp). The protein also binds to a single-stranded DNA (OriS*) containing a stable Box I-Box III hairpin and an unstable AT-rich hairpin at the 3'-end. In the present work, new minor groove binding ligands have been synthesized which are capable to inhibit the development of virus-induced cytopathic effect in cultured Vero cells. Studies on binding of these compounds to DNA and synthetic oligonucleotides have been performed by fluorescence methods, gel mobility shift analysis and footprinting assays. Footprinting studies have revealed that Pt-bis-netropsin and related molecules exhibit preferences for binding to the AT-spacer in OriS. The drugs stabilize structure of the AT-rich region and inhibit the fluctuation opening of AT-base pairs which is a prerequisite to unwinding of DNA by OBP. Kinetics of ATP-dependent unwinding of OriS in the presence and absence of netropsin derivatives have been studied by measuring the efficiency of Forster resonance energy transfer (FRET) between fluorophores attached to 5'- and 3'- ends of an oligonucleotide in the minimal OriS duplex. The results are consistent with the suggestion that OBP is the DNA Holiday junction (HJ) binding helicase. The protein induces conformation changes (bending and partial melting) of OriS duplexes and stimulates HJ formation in the absence of ATP. The antiviral activity of bis-netropsins is coupled with their ability to inhibit the fluctuation opening of АТ base pairs in the А + Т cluster and their capacity to stabilize the structure of the АТ-rich hairpin in the single-stranded oligonucleotide corresponding to the upper chain in the minimal duplex OriS. The antiviral activities of bis-netropsins in cell culture and their therapeutic effects on HSV1-infected laboratory animals have been studied.
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Affiliation(s)
- N P Bazhulina
- a V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , ul. Vavilova 32, 119991 , Moscow , Russia
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Fornander LH, Wu L, Billeter M, Lincoln P, Nordén B. Minor-Groove Binding Drugs: Where Is the Second Hoechst 33258 Molecule? J Phys Chem B 2013; 117:5820-30. [DOI: 10.1021/jp400418w] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Louise H. Fornander
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Lisha Wu
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Martin Billeter
- Department of Chemistry and
Molecular Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Per Lincoln
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Bengt Nordén
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, S-41296 Gothenburg, Sweden
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Bazhulina NP, Nikitin AM, Rodin SA, Surovaya AN, Kravatsky YV, Pismensky VF, Archipova VS, Martin R, Gursky GV. Binding of Hoechst 33258 and its derivatives to DNA. J Biomol Struct Dyn 2009; 26:701-18. [PMID: 19385699 DOI: 10.1080/07391102.2009.10507283] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In the present work, we employed UV-VIS spectroscopy, fluorescence methods, and circular dichroism spectroscopy (CD) to study the interaction of dye Hoechst 33258, Hoechst 33342, and their derivatives to poly[d(AT)].poly[d(AT)], poly(dA).poly(dT), and DNA dodecamer with the sequence 5'-CGTATATATACG-3'. We identified three types of complexes formed by Hoechst 33258, Hoechst 33342, and methylproamine with DNA, corresponding to the binding of each drug in monomer, dimer, and tetramer forms. In a dimer complex, two dye molecules are sandwiched in the same place of the minor DNA groove. Our data show that Hoechst 33258, Hoechst 33342, and methylproamine also form complexes of the third type that reflects binding of dye associates (probably tetramers) to DNA. Substitution of a hydrogen atom in the ortho position of the phenyl ring by a methyl group has a little effect on binding of monomers to DNA. However it reduces strength of binding of tetramers to DNA. In contrast, a Hoechst derivative containing the ortho-isopropyl group in the phenyl ring exhibits a low affinity to poly(dA).poly(dT) and poly[d(AT)].poly[d(AT)] and binds to DNA only in the monomer form. This can be attributed to a sterical hindrance caused by the ortho-isopropyl group for side-by-side accommodation of two dye molecules in the minor groove. Our experiments show that mode of binding of Hoechst 33258 derivatives and their affinity for DNA depend on substituents in the ortho position of the phenyl ring of the dye molecule. A statistical mechanical treatment of binding of Hoechst 33258 and its derivatives to a polynucleotide lattice is described and used for determination of binding parameters of Hoechst 33258 and its derivatives to poly[d(AT)].poly[d(AT)] and poly(dA).poly(dT).
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Affiliation(s)
- N P Bazhulina
- V. A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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Surovaya AN, Grokhovskii SL, Bazhulina NP, Gurskii GV. DNA-Binding activity of bis-netropsin containing a cis-diaminoplatinum group between two netropsin fragments. Biophysics (Nagoya-shi) 2009. [DOI: 10.1134/s0006350908050047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Andronova VL, Grokhovsky SL, Surovaya AN, Arkhipova VS, Gursky GV, Galegov GA. Antiviral and cytotoxic activity of netropsin derivatives in vero cells infected with vaccinia virus and herpes simplex virus type I. DOKL BIOCHEM BIOPHYS 2008; 422:296-301. [PMID: 19024561 DOI: 10.1134/s1607672908050116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- V L Andronova
- Ivanovsky Research Institute of Virology, Russian Academy of Medical Sciences, ul. Gamalei 16, Moscow, 123098 Russia
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Grokhovsky SL, Il’icheva IA, Nechipurenko DY, Panchenko LA, Polozov RV, Nechipurenko YD. Ultrasonic cleavage of DNA: Quantitative analysis of sequence specificity. Biophysics (Nagoya-shi) 2008. [DOI: 10.1134/s0006350908030159] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Boutorine AS, Halby L, Simon P, Perrouault L, Giovannangeli C, Gursky GV, Surovaya AN, Grokhovsky SL, Ryabinin VA, Sinyakov AN. Sequence-specific recognition of double-stranded DNA by synthetic minor groove binder conjugates. toward the construction of artificial site-specific deoxyribonucleases. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:1559-63. [PMID: 18066826 DOI: 10.1080/15257770701545549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Bis-conjugates of hairpin N-methylpyrrole/N-methylimidazole oligocarboxamide minor groove binders (MGB) possessing enhanced affinity and sequence-specificity for dsDNA were synthesized. Two hairpin MGBs were connected by their N-termini via an aminodiacetate linker. The binding of bis-MGB conjugates to the target DNA was studied by gel mobility retardation, footprinting, and circular dichroism; their affinity and binding mode in the DNA minor groove were determined. In order to functionalize the bis-MGB conjugates, DNA-cleaving agents such as phenanthroline or bipyridine were attached. Effective site-specific cleavage of target DNA in the presence of Cu(2+) ions was observed.
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Halby L, Ryabinin VA, Sinyakov AN, Novopashina DS, Venyaminova AG, Grokhovsky SL, Surovaya AN, Gursky GV, Boutorine AS. Head-to-head bis-hairpin polyamide minor groove binders and their conjugates with triplex-forming oligonucleotides: studies of interaction with target double-stranded DNA. J Biomol Struct Dyn 2007; 25:61-76. [PMID: 17676939 DOI: 10.1080/07391102.2007.10507156] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Two hairpin hexa(N-methylpyrrole)carboxamide DNA minor groove binders (MGB) were linked together via their N-termini in head-to-head orientation. Complex formation between these bis-MGB conjugates and target DNA has been studied using DNase I footprinting, circular dichroism, thermal dissociation, and molecular modeling. DNase I footprint revealed binding of these conjugates to all the sites of 492 b.p. DNA fragment containing (A/T)(n)X(m)(A/T)(p) sequences, where n>3, p>3; m=1,2; X = A,T,G, or C. Binding affinity depended on the sequence context of the target. CD experiments and molecular modeling showed that oligo(N-methylpyrrole)carboxamide moieties in the complex form two short antiparallel hairpins rather than a long parallel head-to-head hairpin. Binding of bis-MGB also stabilized a target duplex thermodynamically. Sequence specificity of bis-MGB/DNA binding was validated using bis-conjugates of sequence-specific hairpin (N-methylpyrrole)/(N-methylimidazole) carboxamides. In order to increase the size of recognition sequence, the conjugates of bis-MGB with triplex-forming oligonucleotides (TFO) were synthesized and compared to TFO conjugated with single MGB hairpin unit. Bis-MGB-oligonucleotide conjugates also bind to two blocks of three and more A.T/T.A pairs similarly to bis-MGB alone, independently of the oligonucleotide moiety, but with lower affinity. However, the role of TFO in DNA recognition was demonstrated for mono-MGB-TFO conjugate where the binding was detected mainly in the area of the target sequence consisting of both MGB and TFO recognition sites. Basing on the molecular modeling, three-dimensional models of both target DNA/bis-MGB and target DNA/TFO-bis-MGB complexes were built, where bis-MGB forms two antiparallel hairpins. According to the second model, one MGB hairpin is in the minor groove of 5'-adjacent A/T sequence next to the triplex-forming region, whereas the other one occupies the minor groove of the TFO binding polypurine tract. All these data together give a key information for the construction of MGB-MGB and MGB-oligonucleotide conjugates possessing high specificity and affinity for the target double-stranded DNA.
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Affiliation(s)
- Ludovic Halby
- Museum National d'Histoire Naturelle, RDDM, USM 0503, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231 France
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Andronova VL, Grokhovskii SL, Surovaya AN, Gurskii GV, Galegov GA. Effect of dimeric derivatives of netropsin and their combinations with acyclovir on herpes simplex virus type 1 infection in mice. DOKL BIOCHEM BIOPHYS 2007; 413:79-82. [PMID: 17546959 DOI: 10.1134/s1607672907020111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- V L Andronova
- Ivanovskv Research Institute of Virology, Russian Academy of Medical Sciences, ul. Gamalei 16, Moscow, 123098, Russia
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