New Concepts in Protein-DNA Recognition: Sequence-directed DNA Bending and Flexibility

The yeast cell type regulator alpha 1 cooperates with a constitutive factor, MCM1 protein, to recognize the promoter and activate transcription of several alpha-specific genes. I show here that the alpha 1 and MCM1 proteins bind specifically to one of the two strands of their recognition sequence. This single-strand-binding activity shares several characteristics with the duplex-binding properties of these proteins: (i) the MCM1 protein binds alone to single-stranded and duplex sequences of both the alpha-specific (P'Q) and a-specific (P) binding sites; (ii) the alpha 1 protein requires both the MCM1 protein and the Q sequence to bind either single-stranded or duplex DNA; (iii) the alpha 1 protein stimulates binding of the MCM1 protein to both single-stranded and duplex DNAs; and (iv) the affinities of the proteins for single-stranded and duplex DNAs are comparable.

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The yeast alpha 1 and MCM1 proteins bind a single strand of their duplex DNA recognition site.

Molecular and Cellular Biology ◽

10.1128/mcb.12.8.3573 ◽

1992 ◽

Vol 12 (8) ◽

pp. 3573-3582 ◽

Cited By ~ 9

Author(s):

E J Grayhack

Keyword(s):

Yeast Cell ◽

Binding Sites ◽

Dna Recognition ◽

Binding Activity ◽

Single Strand ◽

Duplex Dna ◽

Cell Type ◽

Recognition Sequence ◽

Binding Properties ◽

Constitutive Factor

The yeast cell type regulator alpha 1 cooperates with a constitutive factor, MCM1 protein, to recognize the promoter and activate transcription of several alpha-specific genes. I show here that the alpha 1 and MCM1 proteins bind specifically to one of the two strands of their recognition sequence. This single-strand-binding activity shares several characteristics with the duplex-binding properties of these proteins: (i) the MCM1 protein binds alone to single-stranded and duplex sequences of both the alpha-specific (P'Q) and a-specific (P) binding sites; (ii) the alpha 1 protein requires both the MCM1 protein and the Q sequence to bind either single-stranded or duplex DNA; (iii) the alpha 1 protein stimulates binding of the MCM1 protein to both single-stranded and duplex DNAs; and (iv) the affinities of the proteins for single-stranded and duplex DNAs are comparable.

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DNA Recognition by a .BETA.-sheet. (2) Stereochemical Basis of DNA Bending by the .BETA.-sheets of MetJ and Arc Repressors.

Proceedings of the Japan Academy Series B ◽

10.2183/pjab.71.108 ◽

1995 ◽

Vol 71 (3) ◽

pp. 108-113 ◽

Cited By ~ 1

Author(s):

Masashi SUZUKI ◽

Naoto YAGI

Keyword(s):

Dna Bending ◽

Dna Recognition ◽

Beta Sheets ◽

Beta Sheet

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Assessing the Sequence Dependence of Pyrimidine-Pyrimidone (6-4) Photoproduct in a Duplex Double-Stranded DNA: A Challenge for Microsecond Range Simulation

10.26434/chemrxiv.13404611 ◽

2020 ◽

Author(s):

Natacha Gillet ◽

Alessio Bartocci ◽

Elise Dumont

Keyword(s):

Dna Bending ◽

Dna Recognition ◽

Structural Reorganization ◽

Sequence Dependence ◽

Double Stranded Dna ◽

Conformational Landscape ◽

Non Covalent Interactions ◽

Dynamics Simulations ◽

Close Sequence ◽

Covalent Interactions

Sequence dependence of the (6-4)photoproduct dynamics when embedded in six 25-bp duplexes is evaluated along extensive unbiased and enhanced (replica exchange with solute tempering, REST2) molecular dynamics simulations. The structural reorganization as the central pyrimidines become covalently tethered is traced back in terms of non-covalent interactions, DNA bending and extrusion of adenines of the opposite strands. The close sequence pattern impacts the conformational landscape around the lesion, inducing a different upstream and downstream flexibilities. Moreover, REST2 simulations allow to probe structures possibly important for damaged DNA recognition. <br>

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Differential Histone-DNA Interactions Dictate Nucleosome Recognition of the Pioneer Transcription Factor Sox

10.1101/2021.12.07.471700 ◽

2021 ◽

Author(s):

Burcu Ozden ◽

Ramachandran Boopathi ◽

Ayse Bercin Barlas ◽

Imtiaz N. Lone ◽

Jan Bednar ◽

...

Keyword(s):

Conformational Changes ◽

Dna Recognition ◽

Binding Mode ◽

Chromatin Binding ◽

Dna Interactions ◽

Recognition Sequence ◽

Cellular Processes ◽

Nucleosomal Dna ◽

Pioneer Transcription Factor ◽

Dna Strand

Pioneer transcription factors (PTFs) have the remarkable ability to directly bind to chromatin for stimulating vital cellular processes. Expanding on the recent findings, we aim to unravel the universal binding mode of the famous Sox PTF. Our findings show that the base specific hydrogen bonding (base reading) and the local DNA changes (shape reading) are required for sequence-specific nucleosomal DNA recognition by Sox. Among different nucleosomal positions, base and shape reading can be satisfied at super helical location 2 (SHL2). This indicates that due to distinct histone-DNA interactions, SHL2 acts transparently to Sox binding, where SHL4 permits solely shape reading, and SHL0 (dyad) allows no reading. We also show that at SHL2, Sox binds to its recognition sequence without imposing any major conformational changes, if its consensus DNA sequence is located at the solvent-facing nucleosomal DNA strand. These data explain how Sox have evolved to perfectly adapt for chromatin binding.

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