Specificity of Minor-Groove and Major-Groove Interactions in a Homeodomain-DNA Complex

Biochemistry ◽  
1995 ◽  
Vol 34 (44) ◽  
pp. 14601-14608 ◽  
Author(s):  
Sarah E. Ades ◽  
Robert T. Sauer
Keyword(s):  
Minor Groove ◽  
Major Groove ◽  
Dna Complex

Cadmium Inhibits BPDE Alkylation of DNA in the Major Groove but Not in the Minor Groove

1998 ◽  
Vol 244 (1) ◽  
pp. 198-203 ◽  
Author(s):  
Arungundrum S. Prakash ◽  
Koyyalamudi S. Rao ◽  
Charles T. Dameron
Keyword(s):  
Minor Groove ◽  
Major Groove

scholarly journals suGF1 binds in the major groove of its oligo(dG).oligo(dC) recognition sequence and is excluded by a positioned nucleosome core.

1994 ◽  
Vol 14 (2) ◽  
pp. 1410-1418 ◽  
Author(s):  
D Patterton ◽  
J Hapgood
Keyword(s):  
Sea Urchin ◽  
Intergenic Region ◽  
Divalent Cations ◽  
Major Groove ◽  
Recognition Sequence ◽  
Nucleosome Core ◽  
Histone Octamer ◽  
Developmental Gene Regulation ◽  
Dna Complex

We have elsewhere reported the purification of a poly(dG).poly(dC)-binding nuclear protein (suGF1) from sea urchin embryos (J. Hapgood and D. Patterton, Mol. Cell. Biol. 14:this issue, 1994). We proposed that suGF1 may be a member of a family of G-string factors involved in developmental gene regulation, possibly via alterations in chromatin structure. In this article, we characterize the binding of purified suGF1 to 11 contiguous Gs in the H1-H4 intergenic region of a sea urchin early histone gene battery in vitro. It is shown that suGF1-DNA binding is dependent on ionic strength and requires divalent cations. Purified suGF1 forms discrete protein-DNA multimers, consistent with suGF1-suGF1 interactions. In a model for the suGF1-DNA complex derived from our footprinting and methylation interference data, suGF1 contacts the Gs in the major groove as well as one of the bordering phosphate backbones. The data are consistent with the direction of curvature of the DNA in the suGF1-DNA complex being the same as that preferred by the free DNA and exhibited by the DNA when bent around a positioned nucleosome core in vitro. However, on the basis of steric considerations, the binding of suGF1 and that of the histone octamer are predicted to be mutually exclusive. We show that suGF1 is indeed unable to bind to the G string when occupied by a histone octamer located in the major in vitro positioning frame in the H1-H4 intergenic region.

Major groove or minor groove?

Nature ◽  
1986 ◽  
Vol 319 (6050) ◽  
pp. 183-184 ◽  
Author(s):  
WANG JIA-HUAI
Keyword(s):  
Minor Groove ◽  
Major Groove

Investigation of changes in the arrangement of water molecules and salt ions surrounding different atoms of the DNA molecule during the melting process: a molecular dynamics simulation study

2015 ◽  
Vol 93 (3) ◽  
pp. 348-361 ◽  
Author(s):  
C. Izanloo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Double Helix ◽  
Melting Process ◽  
Minor Groove ◽  
Dynamics Simulation ◽  
Transition Curve ◽  
Water Molecules ◽  
Major Groove ◽  
Dna Duplex

A molecular dynamics simulation was performed on a B-DNA duplex (CGCGAATTGCGC) at different temperatures. The DNA was immerged in a saltwater medium with 1 mol/L NaCl concentration. The arrangements of water molecules and cations around the different atoms of DNA on the melting pathway were investigated. Almost for all atoms of the DNA by double helix → single-stranded transition, the water molecules released from the DNA duplex and cations were close to single-stranded DNA, but this behavior was not clearly seen at melting temperatures. Therefore, release of water molecules and cations approaching the DNA by the increase of temperature does not have any effect on the sharpness of the transition curve. Most of the water molecules and cations were found to be around the negatively charged phosphate oxygen atoms. The number of water molecules released from the first shell hydration upon melting in the minor groove was higher than in the major groove, and intrusion of cations into the minor groove after melting was higher than into the major groove. The hydrations of imino protons were different from each other and were dependent on DNA bases.

Allosteric Inhibition of Zinc-Finger Binding in the Major Groove of DNA by Minor-Groove Binding Ligands†

Biochemistry ◽  
2004 ◽  
Vol 43 (13) ◽  
pp. 3880-3890 ◽  
Author(s):  
Doan H. Nguyen-Hackley ◽  
Elizabeth Ramm ◽  
Christina M. Taylor ◽  
J. Keith Joung ◽  
Peter B. Dervan ◽  
...  
Keyword(s):  
Zinc Finger ◽  
Minor Groove ◽  
Minor Groove Binding ◽  
Major Groove ◽  
Groove Binding ◽  
Allosteric Inhibition

Bis-intercalation of a cationic porphyrin dimer linked with trietylene glycol derivative to DNA from the major groove

2012 ◽  
Vol 16 (11) ◽  
pp. 1159-1166 ◽  
Author(s):  
Changyun Lee ◽  
Lindan Gong ◽  
Youngku Shon ◽  
Young Sun Lee ◽  
Suk Joong Lee ◽  
...  
Keyword(s):  
Spectral Properties ◽  
Spectral Characteristics ◽  
Linear Dichroism ◽  
Binding Mode ◽  
Minor Groove ◽  
Major Groove ◽  
Base Pairs ◽  
Absorption Region ◽  
Dna Base ◽  
Porphyrin Dimer

The binding mode of a porphyrin dimer to double stranded native DNA was investigated in this study using normal electric absorption, circular dichroism (CD) and linear dichroism (LD) spectroscopies. At the time of mixing, the spectral properties of the porphyrin dimer upon its association with DNA were characterized by hypochromism and a red shift in the absorption spectrum and by complicated CD and negative LD in the Soret region. As time elapsed, the CD spectrum became a negative single band and the negative LD signal increased. These spectral changes suggested that the majority of both porphyrin moieties of the dimer intercalated between the DNA base-pairs. The changes in the spectral characteristics of the DNA bound porphyrin-dimer were similar when the minor groove of DNA was saturated by 4′,6-diamidino-2-phenylindole (DAPI), which is well-known minor groove binding molecule. The spectral properties of DAPI, which can be summarized by a large positive induced CD in the DAPI absorption region (300~400 nm) and wavelength-independent positive reduced LD, remained intact when the porphyrin dimer was present. These observations indicated that both DAPI and porphyrin bind to DNA simultaneously, and furthermore, the bis-intercalation of the porphyrin dimer occurs in the major groove.

scholarly journals Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine

2019 ◽  
Vol 47 (16) ◽  
pp. 8375-8387 ◽  
Author(s):  
Jie Yang ◽  
John R Horton ◽  
Jia Li ◽  
Yun Huang ◽  
Xing Zhang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Positive Impact ◽  
Minor Groove ◽  
Negative Influence ◽  
Autism Spectrum ◽  
Structural Basis ◽  
Major Groove ◽  
E Box ◽  
Arginine Residues ◽  
Basic Region

Abstract The psychiatric risk-associated transcription factor 4 (TCF4) is linked to schizophrenia. Rare TCF4 coding variants are found in individuals with Pitt-Hopkins syndrome—an intellectual disability and autism spectrum disorder. TCF4 contains a C-terminal basic-helix-loop-helix (bHLH) DNA binding domain which recognizes the enhancer-box (E-box) element 5′-CANNTG-3′ (where N = any nucleotide). A subset of the TCF4-occupancy sites have the expanded consensus binding specificity 5′-C(A/G)-CANNTG-3′, with an added outer Cp(A/G) dinucleotide; for example in the promoter for CNIH3, a gene involved in opioid dependence. In mammalian genomes, particularly brain, the CpG and CpA dinucleotides can be methylated at the 5-position of cytosine (5mC), and then may undergo successive oxidations to the 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxyl (5caC) forms. We find that, in the context of 5′-0CG-1CA-2CG-3TG-3′(where the numbers indicate successive dinucleotides), modification of the central E-box 2CG has very little effect on TCF4 binding, E-box 1CA modification has a negative influence on binding, while modification of the flanking 0CG, particularly carboxylation, has a strong positive impact on TCF4 binding to DNA. Crystallization of TCF4 in complex with unmodified or 5caC-modified oligonucleotides revealed that the basic region of bHLH domain adopts multiple conformations, including an extended loop going through the DNA minor groove, or the N-terminal portion of a long helix binding in the DNA major groove. The different protein conformations enable arginine 576 (R576) to interact, respectively, with a thymine in the minor groove, a phosphate group of DNA backbone, or 5caC in the major groove. The Pitt-Hopkins syndrome mutations affect five arginine residues in the basic region, two of them (R569 and R576) involved in 5caC recognition. Our analyses indicate, and suggest a structural basis for, the preferential recognition of 5caC by a transcription factor centrally important in brain development.

Nucleic Acid Interactions of Unfused Aromatic Cations:  Evaluation of Proposed Minor-Groove, Major-Groove, and Intercalation Binding Modes

1998 ◽  
Vol 120 (40) ◽  
pp. 10310-10321 ◽  
Author(s):  
W. David Wilson ◽  
Farial A. Tanious ◽  
Daoyuan Ding ◽  
Arvind Kumar ◽  
David W. Boykin ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Minor Groove ◽  
Binding Modes ◽  
Major Groove ◽  
Intercalation Binding ◽  
Nucleic Acid Interactions

scholarly journals Spatial Organization of the Core Region of Yeast TFIIIB-DNA Complexes

1999 ◽  
Vol 19 (7) ◽  
pp. 5218-5234 ◽  
Author(s):  
Jim Persinger ◽  
Sarojini M. Sengupta ◽  
Blaine Bartholomew
Keyword(s):  
Spatial Organization ◽  
Peptide Mapping ◽  
Gene Promoter ◽  
Tata Box ◽  
Cross Linking ◽  
Related Factor ◽  
Start Site ◽  
Major Groove ◽  
Close Proximity ◽  
Dna Complex

ABSTRACT The interaction of yeast TFIIIB with the region upstream of theSUP4 tRNATyr gene was extensively probed by use of photoreactive phosphodiesters, deoxyuridines, and deoxycytidines that are site specifically incorporated into DNA. The TATA binding protein (TBP) was found to be in close proximity to the minor groove of a TATA-like DNA sequence that starts 30 nucleotides upstream of the start site of transcription. TBP was cross-linked to the phosphate backbone of DNA from bp −30 to −20 in the nontranscribed strand and from bp −28 to −24 in the transcribed strand (+1 denotes the start site of transcription). Most of the major groove of DNA in this region was shown not to be in close proximity to TBP, thus resembling the binding of TBP to the TATA box, with one notable exception. TBP was shown to interact with the major groove of DNA primarily at bp −23 and to a lesser degree at bp −25 in the transcribed strand. The stable interaction of TBP with the major groove at bp −23 was shown to require the B" subunit of TFIIIB. The S4 helix and flanking region of TBP were shown to be proximal to the major groove of DNA by peptide mapping of the region of TBP cross-linked at bp −23. Thus, TBP in the TFIIIB-SUP4 gene promoter region is bound in the same direction as TBP bound to the TATA box with respect to the transcription start site. The B" and TFIIB-related factor (BRF) subunits of TFIIIB are positioned on opposite sides of the TBP-DNA core of the TFIIIB complex, as indicated by correlation of cross-linking data to the crystal structure of the TBP-TATA box complex. Evidence is given for BRF binding near the C-terminal stirrup of TBP, similar to that of TFIIB near the TBP-TATA box complex. The protein clamp formed around the TBP-DNA complex by BRF and B" would help explain the long half-life of the TFIIIB-DNA complex and its resistance to polyanions and high salt. The path of DNA traversing the surface of TBP at the 3′ end of the TATA-like element in the SUP4 tRNA gene is not the same as that of TBP bound to a TATA box element, as shown by the cross-linking of TBP at bp −23.

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