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Borisova, O. A.; Romanenkov, A. S.; Metelev, Valeri; Кубарева, Е. А.; Zubin, E. M.; Timchenko, Maria; Oretskaya, Tatiana S.

doi:10.1023/a:1024203830741

Cited by 3 publications

(6 citation statements)

References 21 publications

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“…These reactive groups either modified the 2′ position of a nucleotide unit (2′ aldehyde (Fig. 3a) and 2′ iodoacet amide [30] groups) or substituted the natural phosphodi ester bond (internucleotide phosphoryldisulfide (Fig. 3b) and modified pyrophosphate groups [28,29]).…”

Section: Resultsmentioning

confidence: 99%

“…Only DNA duplexes XVI and XVIII can effectively form conju gates with p50 (the yields of reaction products were 25 and 21%, respectively) [30]. Formation of conjugate between the (Id κ κB) containing duplex XVIII and p50 homodimer can be explained from a close proximity of Cys59 to the iodoacetamide group (Fig.…”

Section: ′ G a G C C T T T C A G G G G A G A 5′mentioning

confidence: 99%

“…These groups interact with sulfhydryl group of cysteine: the first one due to thiol disulfide exchange (Fig. 3b), and the second due to alkylation [30].…”

Section: ′ G a G C C T T T C A G G G G A G A 5′mentioning

confidence: 99%

“…Modification can distort the DNA structure, thus influencing the pat tern of contacts with protein amino acid residues. Earlier, we used 2′ iodoacetamide containing DNA duplexes for affinity modification of the transcription fac tor NF κB p50 homodimer [30]. These modified DNAs interacted with Cys residues of the protein in buffer sys tems with pH 8.3 for no more than 15 min.…”

Section: ′ G a G C C T T T C A G G G G A G A 5′mentioning

confidence: 99%

“…To study the interaction of a given modified DNA type with the transcription factor NF κB p50 homo dimer, we constructed oligonucleotide duplexes XV XVIII [30] containing 2′ deoxy 2′ iodoacetamidouridine (U) residues in Ig κ κB and Id κ κB sites (Table 2). Only DNA duplexes XVI and XVIII can effectively form conju gates with p50 (the yields of reaction products were 25 and 21%, respectively) [30].…”

Section: ′ G a G C C T T T C A G G G G A G A 5′mentioning

confidence: 99%

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Analysis of DNA-Protein Interactions in Complexes of Transcription Factor NF-κB with DNA

Romanenkov

Ustyugov

Zatsepin

et al. 2005

Biochemistry (Moscow)

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We have applied bioinformatic analysis of X-ray 3D structures of complexes of transcription factor NF-kappaB with DNAs. We determined the number of possible Van der Waals contacts and hydrogen bonds between amino acid residues and nucleotides. Conservative contacts in the NF-kappaB dimer-DNA complex composed of p50 and/or p65 NF-kappaB subunit and DNA sequences like 5 -GGGAMWTTCC-3 were revealed. Based on these results, we propose a novel scheme for interactions between NF-kappaB p50 homodimer and the kappaB region of the immunoglobulin light chain gene enhancer (Ig-kappaB). We applied a chemical cross-linking technique to study the proximity of some Lys and Cys residues of NF-kappaB p50 subunit with certain reactive nucleotides into its recognition site. In all cases, the experimentally determined protein-DNA contacts were in good agreement with the predicted ones.

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Section: Resultsmentioning

confidence: 99%

Section: ′ G a G C C T T T C A G G G G A G A 5′mentioning

confidence: 99%

“…These groups interact with sulfhydryl group of cysteine: the first one due to thiol disulfide exchange (Fig. 3b), and the second due to alkylation [30].…”

Section: ′ G a G C C T T T C A G G G G A G A 5′mentioning

confidence: 99%

Section: ′ G a G C C T T T C A G G G G A G A 5′mentioning

confidence: 99%

Section: ′ G a G C C T T T C A G G G G A G A 5′mentioning

confidence: 99%

See 3 more Smart Citations

Analysis of DNA-Protein Interactions in Complexes of Transcription Factor NF-κB with DNA

Romanenkov

Ustyugov

Zatsepin

et al. 2005

Biochemistry (Moscow)

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Identification of base-specific contacts in protein–DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII

Pingoud

Geyer

et al. 2005

Mol. BioSyst.

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Specific protein-nucleic acid interactions are of paramount importance for the propagation, maintenance and expression of genetic information. Restriction endonucleases serve as model systems to study the mechanisms of DNA recognition by proteins. SsoII is a Type II restriction endonuclease that recognizes the double stranded sequence downward arrow CCNGG and cleaves it in the presence of Mg(2+)-ions, as indicated. SsoII shows sequence similarity over a stretch of approximately 70 amino acid residues with several other restriction endonucleases that recognize a similar sequence as SsoII (Cfr10I, EcoRII, NgoMIV, PspGI). In NgoMIV this stretch is involved in DNA recognition and cleavage, as shown by the crystal structure analysis of an enzyme-product complex. To find out whether the presumptive DNA recognition region in SsoII is indeed in contact with DNA we have photocrosslinked SsoII with an oligodeoxyribonucleotide in which the first guanine of the recognition sequence was replaced by 5-iodouracil. Following digestion by trypsin, the peptide-oligodeoxyribonucleotide conjugate was purified by Fe(3+)-IMAC and then incubated with hydrogen fluoride, which hydrolyzes the oligodeoxyribonucleotide to yield the peptide-deoxyuridine conjugate. The site of photocrosslinking was identified by MALDI-TOF-MS and MALDI-TOF-MS/MS to be Trp189, adjacent to Arg188, which aligns with Arg194 in NgoMIV, involved in recognition of the second guanine in the NgoMIV recognition sequence G downward arrow CCGGC. This result confirms previously published conclusions drawn on the basis of a mutational analysis of SsoII. The methodology that was employed here can be used in principle to identify the DNA binding site of any protein.

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Design and Synthesis of 2-Functionalised Oligonucleotides. Their Application for Covalent Trapping the Protein – DNA Complexes

Dolinnaya¹,

Zubin²,

Кубарева³

et al. 2009

COC

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Untitled

Cited by 3 publications

References 21 publications

Analysis of DNA-Protein Interactions in Complexes of Transcription Factor NF-κB with DNA

Analysis of DNA-Protein Interactions in Complexes of Transcription Factor NF-κB with DNA

Identification of base-specific contacts in protein–DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII

Design and Synthesis of 2-Functionalised Oligonucleotides. Their Application for Covalent Trapping the Protein – DNA Complexes

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