Multi-helical DNA-binding domains: Their structures and modes of DNA-binding

Suzuki, Masashi; Suckow, Jörg Michael; Kisters‐Woike, Brigitte; Aramaki, Hironori; Marino, Kozo

doi:10.1016/0065-227x(96)84740-x

Cited by 11 publications

(5 citation statements)

References 58 publications

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“…[23] b-Lactam mesylate 1, easily accessible from l-aspartic acid, [24] was alkylated with adenine in presence of 1,8-diazabicyclo[5. 4.0]undec-7-ene (DBU) providing nucleo-b-lactam 2 exclusively as its N9-regioisomer in 62 % yield. By using NaH or K 2 CO 3 as base a mixture of N9 and N7 regioisomers was obtained.…”

Section: Resultsmentioning

confidence: 99%

“…[2,3] Furthermore, de novo design of artificial molecules capable of forming structurally well-defined and predictable structures offers new possibilities in the field of molecular recognition, catalysis, and protein folding. [4,5] In recent years, considerable effort has been devoted to the construction of artificial tertiary structures. [6] With this contribution we introduce selective and reversible organization into b-peptide helical secondary structures based on nucleobase recognition.…”

Section: Introductionmentioning

confidence: 99%

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Three‐Dimensional Organization of Helices: Design Principles for Nucleobase‐Functionalized β‐Peptides

Chakraborty

Diederichsen

2005

Chemistry A European J

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The construction and molecular recognition of various three-dimensional biomimetic structures is based on the predictable de novo design of artificial molecules. In this regard beta-peptides are especially interesting, since stable secondary structures are obtained already with short sequences; one of them is the 14-helix in which every third residue has the same orientation. The covalent functionalization of every third 14-helix side chain with nucleobases was used for a reversible organization of two helices based on nucleobase pairing. A series of beta-peptides with various nucleobase sequences was synthesized and the stability of double strand formation was investigated. As few as four nucleobases are sufficient for considerable duplex stability. The stability of base pairing was examined by temperature-dependent UV spectroscopy and the formation of the 14-helix was confirmed by circular dichroism (CD) spectroscopy. The preferred strand orientation of complementary-nucleobase-modified beta-peptide helices was investigated as well as the influence of helix content on the duplex stability. The preorganization of a 14-helix in regard to double-strand recognition was tuned by the sequential order of polar beta-amino acids or by the amount of 2-aminocyclohexanecarboxylic acid units incorporated, which are known to facilitate 14-helix formation, respectively.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Three‐Dimensional Organization of Helices: Design Principles for Nucleobase‐Functionalized β‐Peptides

Chakraborty

Diederichsen

2005

Chemistry A European J

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“…More importhese transcription factors bind to their cognate setantly, the resulting conjugate, which would grasp DNA quences as noncovalent dimers or multimers, with key through both the major and the minor groove, should DNA contacts responsible for the recognition estabexhibit higher affinity for its target composite DNA site lished by ␣-helical regions of the protein inserted into the than either of its individual components. Indeed, we DNA major groove [3][4][5][6][7][8][9]. This multimerization strategy have recently found that appropriate crosslinking of a ensures tight affinity and high specificity while providing slightly modified basic region of GCN4 to a tripyrrole for diversity in target recognition [10][11][12][13].…”

Section: Introduction By the Mode Of Dna Recognition Of Monomeric Homeodomain Proteins We Envisaged That Suitable Tetheringmentioning

confidence: 99%

A Synthetic Miniprotein that Binds Specific DNA Sequences by Contacting Both the Major and the Minor Groove

Blanco

Vázquez

Martı́nez-Costas

et al. 2003

Chemistry & Biology

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Attachment of a slightly modified basic region of a bZIP protein (GCN4) to a distamycin-related tripyrrole provides a bivalent system capable of binding with high affinity to specific DNA sequences. Appropriate adjustment of the linker between the two units has led to a hybrid that binds a 9 base-pair-long DNA site (TTTTATGAC) with low nanomolar affinity at 4 degrees C. Circular dichroism and gel retardation studies indicate that the binding occurs by simultaneous insertion of the bZIP basic region into the DNA major groove and the tripyrrole moiety into the minor groove of the flanking sequence. Analysis of hybrids bearing alternative linkers revealed that tight, specific binding is strongly dependent on the length and nature of the connecting unit.

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“…Helical secondary structures are the most important recognition elements in biological processes for specific protein–protein or peptide/protein–nucleic acid recognition 1–3. Examples are the leucine zipper binding to DNA or the organization of helices in bundles forming transmembrane channels 4.…”

Section: Introductionmentioning

confidence: 99%

Organization of nucleobase‐functionalized β‐peptides investigated by soft electrospray ionization mass spectrometry

et al. 2009

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The development and validation of analytical methods is a key to succeed in investigating noncovalent interactions between biomolecules or between small molecules and biomolecules. Electrospray ionization mass spectrometry (ESI-MS) was applied with a Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS) as well as a quadrupole/time-of-flight tandem mass spectrometer (QqToF-MS) for a systematic investigation of noncovalent complexes based on nucleobase pairing in an artificial and noncharged backbone topology. Synthetical beta-peptide helices covalently modified with nucleobases were organized by recognition of a sequence of four nucleobases. Specific duplexes of beta-peptide helices were obtained on the basis of hydrogen bonding base pair complementarity. Oligomer interactions were detected with defined stoichiometry and sensitivity for the respective duplex stability. FTICR-MS and QqToF-MS were used equally well to indicate double strand stabilities in agreement with the dissociation data determined by UV spectroscopy. Furthermore, the dissociation energies of gas phase ions of the noncovalent complexes were analyzed with collision induced dissociation (CID)-MS/MS and infrared multiphoton dissociation (IRMPD)-MS/MS. The CID conditions turned out to be too harsh for a differentiation of the duplex stabilities, whereas IRMPD might be developed as a technique to detect even small interaction energy differences.

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Multi-helical DNA-binding domains: Their structures and modes of DNA-binding

Cited by 11 publications

References 58 publications

Three‐Dimensional Organization of Helices: Design Principles for Nucleobase‐Functionalized β‐Peptides

Three‐Dimensional Organization of Helices: Design Principles for Nucleobase‐Functionalized β‐Peptides

A Synthetic Miniprotein that Binds Specific DNA Sequences by Contacting Both the Major and the Minor Groove

Organization of nucleobase‐functionalized β‐peptides investigated by soft electrospray ionization mass spectrometry

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