Literature DB >> 12011426

Looped out and perpendicular: deformation of Watson-Crick base pair associated with actinomycin D binding.

Shan-Ho Chou1, Ko-Hsin Chin, Fu-Ming Chen.   

Abstract

Many anticancer drugs interact directly with DNA to exert their biological functions. To date, all noncovalent, intercalating drugs interact with DNA exclusively by inserting their chromophores into base steps to form elongated and unwound duplex structures without disrupting the flanking base pairs. By using actinomycin D (ActD)-5'-GXC/CYG-5' complexes as examples, we have found a rather unusual interaction mode for the intercalated drug; the central Watson-Crick X/Y base pairs are looped out and displaced by the ActD chromophore. The looped-out bases are not disordered but interact perpendicularly with the base/chromophore and form specific H bonds with DNA. Such a complex structure provides intriguing insights into how ligand interacts with DNA and enlarges the repertoires for sequence-specific DNA recognition.

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Year:  2002        PMID： 12011426      PMCID： PMC124453          DOI： 10.1073/pnas.102580399

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


  30 in total

1.  Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog.

Authors:  K Goedecke; M Pignot; R S Goody; A J Scheidig; E Weinhold
Journal:  Nat Struct Biol       Date:  2001-02

2.  CH/pi interactions in the crystal structure of TATA-box binding protein/DNA complexes.

Authors:  Y Umezawa; M Nishio
Journal:  Bioorg Med Chem       Date:  2000-11       Impact factor: 3.641

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Authors:  S H Chou; K H Chin
Journal:  J Mol Biol       Date:  2001-11-16       Impact factor: 5.469

4.  Zipper-like Watson-Crick base-pairs.

Authors:  S H Chou; K H Chin
Journal:  J Mol Biol       Date:  2001-09-28       Impact factor: 5.469

5.  Crystallographic analysis of a novel complex of actinomycin D bound to the DNA decamer CGATCGATCG.

Authors:  H Robinson; Y G Gao; X Yang ; R Sanishvili; A Joachimiak; A H Wang
Journal:  Biochemistry       Date:  2001-05-15       Impact factor: 3.162

6.  Binding of actinomycin D to DNA: evidence for a nonclassical high-affinity binding mode that does not require GpC sites.

Authors:  J G Snyder; N G Hartman; B L D'Estantoit; O Kennard; D P Remeta; K J Breslauer
Journal:  Proc Natl Acad Sci U S A       Date:  1989-06       Impact factor: 11.205

7.  Non-Watson-Crick G.C and A.T base pairs in a DNA-antibiotic complex.

Authors:  G J Quigley; G Ughetto; G A van der Marel; J H van Boom; A H Wang; A Rich
Journal:  Science       Date:  1986-06-06       Impact factor: 47.728

8.  Determination of the preferred conformations constrained along the C-4'-C-5' and C-5'-O-5' bonds of beta-5'-nucleotides in solution. Four-bond 31P-1H coupling.

Authors:  R H Sarma; R T Mynott; D J Wood; F E Hruska
Journal:  J Am Chem Soc       Date:  1973-09-19       Impact factor: 15.419

9.  Binding specificities of actinomycin D to self-complementary tetranucleotide sequences -XGCY-.

Authors:  F M Chen
Journal:  Biochemistry       Date:  1988-08-23       Impact factor: 3.162

10.  Assignment of the 31P and 1H resonances in oligonucleotides by two-dimensional NMR spectroscopy.

Authors:  V Sklenár; H Miyashiro; G Zon; H T Miles; A Bax
Journal:  FEBS Lett       Date:  1986-11-10       Impact factor: 4.124
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  11 in total

1.  Crystal structure of actinomycin D bound to the CTG triplet repeat sequences linked to neurological diseases.

Authors:  Ming-Hon Hou; Howard Robinson; Yi-Gui Gao; Andrew H-J Wang
Journal:  Nucleic Acids Res       Date:  2002-11-15       Impact factor: 16.971

Review 2.  Unusual DNA duplex and hairpin motifs.

Authors:  Shan-Ho Chou; Ko-Hsin Chin; Andrew H-J Wang
Journal:  Nucleic Acids Res       Date:  2003-05-15       Impact factor: 16.971

3.  The nature of actinomycin D binding to d(AACCAXYG) sequence motifs.

Authors:  Fu-Ming Chen; Feng Sha; Ko-Hsin Chin; Shan-Ho Chou
Journal:  Nucleic Acids Res       Date:  2004-01-09       Impact factor: 16.971

4.  The Mechanism of Action of (-)-Lomaiviticin A.

Authors:  Seth B Herzon
Journal:  Acc Chem Res       Date:  2017-09-28       Impact factor: 22.384

5.  Structural basis for DNA cleavage by the potent antiproliferative agent (-)-lomaiviticin A.

Authors:  Christina M Woo; Zhenwu Li; Eric K Paulson; Seth B Herzon
Journal:  Proc Natl Acad Sci U S A       Date:  2016-02-29       Impact factor: 11.205

6.  Solution structure of the ActD-5'-CCGTT3GTGG-3' complex: drug interaction with tandem G.T mismatches and hairpin loop backbone.

Authors:  Ko-Hsin Chin; Fu-Ming Chen; Shan-Ho Chou
Journal:  Nucleic Acids Res       Date:  2003-05-15       Impact factor: 16.971

7.  Unique actinomycin D binding to self-complementary d(CXYGGCCY'X'G) sequences: duplex disruption and binding to a nominally base-paired hairpin.

Authors:  Fu-Ming Chen; Feng Sha; Ko-Hsin Chin; Shan-Ho Chou
Journal:  Nucleic Acids Res       Date:  2003-07-15       Impact factor: 16.971

8.  Binding of actinomycin D to single-stranded DNA of sequence motifs d(TGTCT(n)G) and d(TGT(n)GTCT).

Authors:  Fu-Ming Chen; Feng Sha; Ko-Hsin Chin; Shan-Ho Chou
Journal:  Biophys J       Date:  2003-01       Impact factor: 4.033

9.  XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins.

Authors:  Srdan D Stojanović; Vesna B Medaković; Goran Predović; Milos Beljanski; Snezana D Zarić
Journal:  J Biol Inorg Chem       Date:  2007-07-21       Impact factor: 3.862

10.  The structural basis of actinomycin D-binding induces nucleotide flipping out, a sharp bend and a left-handed twist in CGG triplet repeats.

Authors:  Yu-Sheng Lo; Wen-Hsuan Tseng; Chien-Ying Chuang; Ming-Hon Hou
Journal:  Nucleic Acids Res       Date:  2013-02-13       Impact factor: 16.971
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