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1hm1

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{{STRUCTURE_1hm1| PDB=1hm1 | SCENE= }}
{{STRUCTURE_1hm1| PDB=1hm1 | SCENE= }}
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'''THE SOLUTION NMR STRUCTURE OF A THERMALLY STABLE FAPY ADDUCT OF AFLATOXIN B1 IN AN OLIGODEOXYNUCLEOTIDE DUPLEX REFINED FROM DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATED ANNEALING, MINIMIZED AVERAGE STRUCTURE'''
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===THE SOLUTION NMR STRUCTURE OF A THERMALLY STABLE FAPY ADDUCT OF AFLATOXIN B1 IN AN OLIGODEOXYNUCLEOTIDE DUPLEX REFINED FROM DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATED ANNEALING, MINIMIZED AVERAGE STRUCTURE===
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==Overview==
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The structure of a formamidopyrimidine (FAPY) adduct arising from imidazole ring opening of the initially formed trans-8, 9-dihydro-8-(N7-guanyl)-9-hydroxyaflatoxin B1 adduct under basic conditions and positioned in the 5'-d(CTATFAPYGATTCA)-3'*5'-d(TGAATCATAG)-3' oligodeoxynucleotide was determined. The FAPY adduct may be a major progenitor of aflatoxin B1-induced mutations in DNA. The freshly prepared sample showed biphasic melting, with transitions at 28 and 56 degreesC. NMR initially showed multiple subspectra. Over a period of several days at 4 degreesC, the sample converted to a single species with a Tm of 56 degreesC, 15 degrees C greater than the unmodified duplex. The deoxyribose was in the beta configuration about the anomeric carbon, evidenced by NOEs between FAPYG5 H3', H2', H2", and H1'. FAPY formation resulted in the loss of the guanine H8 proton, and the introduction of the formyl proton, which showed NOEs to FAPYG5 H1' and A6 N6Ha. A total of 31 NOEs from AFB1 to DNA protons were observed, mostly to the 5'-neighboring base, T4 in the modified strand. Sequential NOEs were interrupted between T4 and FAPYG5 in the modified strand, between C16 and A17 in the complementary strand, and between T4 N3H and FAPYG5 N1H. An NOE between FAPYG5 N1H and C16 N4H showed intact hydrogen bonding at FAPYG5*C16. Upfield chemical shifts were observed for T4 H6 and A17 H8. Molecular dynamics calculations converged with pairwise rmsd differences of &lt;0.9 A. The sixth root residual was 8.7 x 10(-2). The AFB1 moiety intercalated from the major groove between FAPYG5 and T4*A17, and stacked with T4 and FAPYG5 and partially stacked with A17. The base step between T4*A17 and FAPYG5*C16 was increased from 3.4 to 7 A. The duplex unwound by about 15 degrees. The FAPY formyl group was positioned to form a hydrogen bond with A6 N6Ha. Strong stacking involving the AFB1 moiety, and this hydrogen bond explains the thermal stabilization of four base pairs by this adduct, and may be a significant factor in its processing.
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(as it appears on PubMed at http://www.pubmed.gov), where 9521757 is the PubMed ID number.
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{{ABSTRACT_PUBMED_9521757}}
==About this Structure==
==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HM1 OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HM1 OCA].
==Reference==
==Reference==
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[[Category: Nmr]]
[[Category: Nmr]]
[[Category: Solution structure]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 18:59:56 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 08:23:02 2008''

Revision as of 05:23, 1 July 2008

Image:1hm1.png

Template:STRUCTURE 1hm1

THE SOLUTION NMR STRUCTURE OF A THERMALLY STABLE FAPY ADDUCT OF AFLATOXIN B1 IN AN OLIGODEOXYNUCLEOTIDE DUPLEX REFINED FROM DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATED ANNEALING, MINIMIZED AVERAGE STRUCTURE

Template:ABSTRACT PUBMED 9521757

About this Structure

Full experimental information is available from OCA.

Reference

An intercalated and thermally stable FAPY adduct of aflatoxin B1 in a DNA duplex: structural refinement from 1H NMR., Mao H, Deng Z, Wang F, Harris TM, Stone MP, Biochemistry. 1998 Mar 31;37(13):4374-87. PMID:9521757

Page seeded by OCA on Tue Jul 1 08:23:02 2008

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