MersV1, Main, Exploration, bibRecord, 003461

SELEX Selection of High-Affinity Oligonucleotides for Bacteriophage Ff Gene 5 Protein†

Identifieur interne : 003461 ( Main/Exploration ); précédent : 003460; suivant : 003462

SELEX Selection of High-Affinity Oligonucleotides for Bacteriophage Ff Gene 5 Protein†

Auteurs : Jin-Der Wen [États-Unis] ; Carla W. Gray [États-Unis] ; Donald M. Gray [États-Unis]

Source :

Biochemistry [ 0006-2960 ] ; 2001.

RBID : ISTEX:373A64E897640F4570DDCACBFFC388C995F2720C

Descripteurs français

English descriptors

KwdEn :
- Bacteriophage M13 (genetics), Base Sequence, Circular Dichroism, Cloning, Molecular (methods), DNA Primers (genetics), DNA Primers (metabolism), DNA, Single-Stranded (genetics), DNA, Single-Stranded (metabolism), DNA, Viral (genetics), DNA, Viral (metabolism), DNA-Binding Proteins (genetics), DNA-Binding Proteins (metabolism), Electrophoresis, Polyacrylamide Gel, Inovirus (genetics), Ligands, Molecular Sequence Data, Oligonucleotides (genetics), Oligonucleotides (metabolism), Osmolar Concentration, Peptide Chain Initiation, Translational (genetics), Protein Binding (genetics), Salts, Sequence Analysis, DNA (methods), Sequence Deletion, Sodium Chloride, Viral Proteins (genetics), Viral Proteins (metabolism).
MESH :
- chemical , genetics : DNA Primers, DNA, Single-Stranded, DNA, Viral, DNA-Binding Proteins, Oligonucleotides, Viral Proteins.
- genetics : Bacteriophage M13, Inovirus, Peptide Chain Initiation, Translational, Protein Binding.
- chemical , metabolism : DNA Primers, DNA, Single-Stranded, DNA, Viral, DNA-Binding Proteins, Oligonucleotides, Viral Proteins.
- methods : Cloning, Molecular, Sequence Analysis, DNA.
- Base Sequence, Circular Dichroism, Electrophoresis, Polyacrylamide Gel, Ligands, Molecular Sequence Data, Osmolar Concentration, Salts, Sequence Deletion, Sodium Chloride.

Abstract

The Ff gene 5 protein (g5p) is a cooperative ssDNA-binding protein. SELEX was used to identify DNA sequences favorable for g5p binding at physiological ionic strength (200 mM NaCl) and 37 °C. Sequences were selected from a library of 58-mers that contained a central variable segment of 26 nucleotides. DNA sequences selected after eight rounds of SELEX were mostly G-rich, with multiple copies of CPuGGPy, TPuGGGPy, and/or PyPuPuGGGPy motifs. This was unexpected, since g5p has higher binding affinities for polypyrimidine than for polypurine sequences. The most recurrent G-rich sequence, named I-3, was found to have g5p-binding properties that were correlated with a structural transition. At 10 mM NaCl, I-3 existed in a single-stranded form that was saturated by g5p in an all-or-none fashion. At 200 mM NaCl, I-3 existed in a structured form that showed CD spectral features of G-quadruplexes. The g5p binding affinity for this structured form of I-3 was >100-fold higher than for the single-stranded form. Moreover, the structured I-3 was saturated by g5p in two steps, the first of which was the formation of an apparent initiation complex consisting of one I-3 strand and about three g5p dimers. Nuclease S1 footprinting and other experiments showed that g5p molecules in the initiation complex at 200 mM NaCl were bound directly to the G-rich variable segment and that the structure of I-3 was retained after saturation by g5p. Thus, G-rich motifs may form structures favorable for initiation of g5p binding and also provide the actual g5p-binding sites.

Url:

https://api.istex.fr/ark:/67375/TPS-KD58MTD9-V/fulltext.pdf

DOI: 10.1021/bi010109z

Affiliations:

Le document en format XML

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<front><div type="abstract">The Ff gene 5 protein (g5p) is a cooperative ssDNA-binding protein. SELEX was used to identify DNA sequences favorable for g5p binding at physiological ionic strength (200 mM NaCl) and 37 °C. Sequences were selected from a library of 58-mers that contained a central variable segment of 26 nucleotides. DNA sequences selected after eight rounds of SELEX were mostly G-rich, with multiple copies of CPuGGPy, TPuGGGPy, and/or PyPuPuGGGPy motifs. This was unexpected, since g5p has higher binding affinities for polypyrimidine than for polypurine sequences. The most recurrent G-rich sequence, named I-3, was found to have g5p-binding properties that were correlated with a structural transition. At 10 mM NaCl, I-3 existed in a single-stranded form that was saturated by g5p in an all-or-none fashion. At 200 mM NaCl, I-3 existed in a structured form that showed CD spectral features of G-quadruplexes. The g5p binding affinity for this structured form of I-3 was >100-fold higher than for the single-stranded form. Moreover, the structured I-3 was saturated by g5p in two steps, the first of which was the formation of an apparent initiation complex consisting of one I-3 strand and about three g5p dimers. Nuclease S1 footprinting and other experiments showed that g5p molecules in the initiation complex at 200 mM NaCl were bound directly to the G-rich variable segment and that the structure of I-3 was retained after saturation by g5p. Thus, G-rich motifs may form structures favorable for initiation of g5p binding and also provide the actual g5p-binding sites.</div>
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Serveur d'exploration MERS

SELEX Selection of High-Affinity Oligonucleotides for Bacteriophage Ff Gene 5 Protein†

SELEX Selection of High-Affinity Oligonucleotides for Bacteriophage Ff Gene 5 Protein†

Source :

Descripteurs français

English descriptors

Abstract

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