Literature DB >> 1323845

Antiparallel side-by-side dimeric motif for sequence-specific recognition in the minor groove of DNA by the designed peptide 1-methylimidazole-2-carboxamide netropsin.

M Mrksich1, W S Wade, T J Dwyer, B H Geierstanger, D E Wemmer, P B Dervan.   

Abstract

The designed peptide 1-methylimidazole-2-carboxamide netropsin (2-ImN) binds specifically to the sequence 5'-TGACT-3'. Direct evidence from NMR spectroscopy is presented that this synthetic ligand binds DNA as a 2:1 complex, which reveals that the structure is an antiparallel dimer in the minor groove of DNA. This is in contrast to the 1:1 complexes usually seen with most crescent-shaped minor groove binding molecules targeted toward A+T-rich tracts but reminiscent of a dimeric motif found for distamycin at high concentrations. These results suggest that sequence-dependent groove width may play an important role in allowing an expanded set of DNA binding motifs for synthetic peptides.

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Year:  1992        PMID： 1323845      PMCID： PMC49755          DOI： 10.1073/pnas.89.16.7586

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


  18 in total

1.  Molecular recognition between oligopeptides and nucleic acids. Monocationic imidazole lexitropsins that display enhanced GC sequence dependent DNA binding.

Authors:  K Kissinger; K Krowicki; J C Dabrowiak; J W Lown
Journal:  Biochemistry       Date:  1987-09-08       Impact factor: 3.162

2.  Solution structure of the chromomycin-DNA complex.

Authors:  X L Gao; D J Patel
Journal:  Biochemistry       Date:  1989-01-24       Impact factor: 3.162

3.  Structure of an alternating-B DNA helix and its relationship to A-tract DNA.

Authors:  C Yoon; G G Privé; D S Goodsell; R E Dickerson
Journal:  Proc Natl Acad Sci U S A       Date:  1988-09       Impact factor: 11.205

4.  Sequence-specific recognition of B-DNA by oligo(N-methylpyrrolecarboxamide)s.

Authors:  R S Youngquist; P B Dervan
Journal:  Proc Natl Acad Sci U S A       Date:  1985-05       Impact factor: 11.205

5.  The molecular origin of DNA-drug specificity in netropsin and distamycin.

Authors:  M L Kopka; C Yoon; D Goodsell; P Pjura; R E Dickerson
Journal:  Proc Natl Acad Sci U S A       Date:  1985-03       Impact factor: 11.205

6.  A bifurcated hydrogen-bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin.

Authors:  M Coll; C A Frederick; A H Wang; A Rich
Journal:  Proc Natl Acad Sci U S A       Date:  1987-12       Impact factor: 11.205

7.  Structural characterization of a 2:1 distamycin A.d(CGCAAATTGGC) complex by two-dimensional NMR.

Authors:  J G Pelton; D E Wemmer
Journal:  Proc Natl Acad Sci U S A       Date:  1989-08       Impact factor: 11.205

8.  Structural modeling of the distamycin A-d(CGCGAATTCGCG)2 complex using 2D NMR and molecular mechanics.

Authors:  J G Pelton; D E Wemmer
Journal:  Biochemistry       Date:  1988-10-18       Impact factor: 3.162

9.  Structural and dynamic aspects of binding of a prototype lexitropsin to the decadeoxyribonucleotide d(CGCAATTGCG)2 deduced from high-resolution 1H NMR Studies.

Authors:  M Lee; D K Chang; J A Hartley; R T Pon; K Krowicki; J W Lown
Journal:  Biochemistry       Date:  1988-01-12       Impact factor: 3.162

10.  Binding of an antitumor drug to DNA, Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G.

Authors:  M L Kopka; C Yoon; D Goodsell; P Pjura; R E Dickerson
Journal:  J Mol Biol       Date:  1985-06-25       Impact factor: 5.469
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  37 in total

1.  Oligonucleotides with conjugated dihydropyrroloindole tripeptides: base composition and backbone effects on hybridization.

Authors:  I V Kutyavin; E A Lukhtanov; H B Gamper; R B Meyer
Journal:  Nucleic Acids Res       Date:  1997-09-15       Impact factor: 16.971

2.  Binding site size limit of the 2:1 pyrrole-imidazole polyamide-DNA motif.

Authors:  J J Kelly; E E Baird; P B Dervan
Journal:  Proc Natl Acad Sci U S A       Date:  1996-07-09       Impact factor: 11.205

3.  Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin).

Authors:  Graham S Erwin; Matthew P Grieshop; Devesh Bhimsaria; Asuka Eguchi; José A Rodríguez-Martínez; Aseem Z Ansari
Journal:  J Vis Exp       Date:  2016-01-20       Impact factor: 1.355

4.  DNA sequence recognition in the minor groove by crosslinked polyamides: The effect of N-terminal head group and linker length on binding affinity and specificity.

Authors:  C Caroline O'Hare; Darcy Mack; Manju Tandon; Sanjay K Sharma; J William Lown; Mary L Kopka; Richard E Dickerson; John A Hartley
Journal:  Proc Natl Acad Sci U S A       Date:  2001-12-26       Impact factor: 11.205

5.  Investigation of the relative cellular permeability of DNA-binding pyrrole-imidazole polyamides.

Authors:  Bo Liu; Thomas Kodadek
Journal:  J Med Chem       Date:  2009-08-13       Impact factor: 7.446

6.  Designer DNA-binding drugs: the crystal structure of a meta-hydroxy analogue of Hoechst 33258 bound to d(CGCGAATTCGCG)2.

Authors:  G R Clark; C J Squire; E J Gray; W Leupin; S Neidle
Journal:  Nucleic Acids Res       Date:  1996-12-15       Impact factor: 16.971

7.  Variability in DNA minor groove width recognised by ligand binding: the crystal structure of a bis-benzimidazole compound bound to the DNA duplex d(CGCGAATTCGCG)2.

Authors:  A A Wood; C M Nunn; A Czarny; D W Boykin; S Neidle
Journal:  Nucleic Acids Res       Date:  1995-09-25       Impact factor: 16.971

8.  Cyclic polyamides for recognition in the minor groove of DNA.

Authors:  J Cho; M E Parks; P B Dervan
Journal:  Proc Natl Acad Sci U S A       Date:  1995-10-24       Impact factor: 11.205

Review 9.  Binding to the DNA minor groove by heterocyclic dications: from AT-specific monomers to GC recognition with dimers.

Authors:  Rupesh Nanjunda; W David Wilson
Journal:  Curr Protoc Nucleic Acid Chem       Date:  2012-12

10.  Structural basis for cyclic Py-Im polyamide allosteric inhibition of nuclear receptor binding.

Authors:  David M Chenoweth; Peter B Dervan
Journal:  J Am Chem Soc       Date:  2010-10-20       Impact factor: 15.419
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