PDBsum entry 1be5

DNA

PDB id

1be5

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Contents

			DNA/RNA

PDB id:

1be5

Links

Name:

DNA

Title:

Structural studies of a stable parallel-stranded DNA duplex incorporating isoguanine:cytosine and isocytosine:guanine base pairs by nmr, minimized average structure

Structure:

DNA duplex (tgcacggact). Chain: a. Engineered: yes. DNA duplex (tgcacggact). Chain: b. Engineered: yes

Source:

Synthetic: yes. Synthetic: yes

NMR struc:

1 models

Authors:

X.-L.Yang,H.Sugiyama,S.Ikeda,I.Saito,A.H.-J.Wang

Key ref:

X.L.Yang et al. (1998). Structural studies of a stable parallel-stranded DNA duplex incorporating isoguanine:cytosine and isocytosine:guanine basepairs by nuclear magnetic resonance spectroscopy. Biophys J, 75, 1163-1171. PubMed id: 9726918

Date:

19-May-98

Release date:

12-Aug-98

	Headers

	References

DNA/RNA chains

		T-IGU-IMC-A-IMC-IGU-IGU-A-IMC-T 10 bases
		A-C-G-T-G-C-C-T-G-A 10 bases

	Biophys J 75:1163-1171 (1998)
PubMed id: 9726918

Structural studies of a stable parallel-stranded DNA duplex incorporating isoguanine:cytosine and isocytosine:guanine basepairs by nuclear magnetic resonance spectroscopy.
X.L.Yang, H.Sugiyama, S.Ikeda, I.Saito, A.H.Wang.

ABSTRACT

Isoguanine (2-hydroxyladenine) is a product of oxidative damage to DNA and has been shown to cause mutation. It is also a potent inducer of parallel-stranded DNA duplex structure. The structure of the parallel-stranded DNA duplex (PS-duplex) 5'-d(TiGiCAiCiGiGAiCT) + 5'-d(ACGTGCCTGA), containing the isoguanine (iG) and 5-methyl-isocytosine (iC) bases, has been determined by NMR refinement. All imino protons associated with the iG:C, G:iC, and A:T (except the two terminal A:T) basepairs are observed at 2 degrees C, consistent with the formation of a stable duplex suggested by the earlier Tm measurements [Sugiyama, H., S. Ikeda, and I. Saito. 1996. J. Am. Chem. Soc. 118:9994-9995]. All basepairs are in the reverse Watson-Crick configuration. The structural characteristics of the refined PS-duplex are different from those of B-DNA. The PS duplex has two grooves with similar width (7.0 A) and depth (7.7 A), in contrast to the two distinct grooves (major groove width 11.7 A, depth 8.5 A, and minor groove width 5.7 A, depth 7.5 A) of B-DNA. The resonances of the amino protons of iG and C are clearly resolved and observable, but those of the G and iC are very broad and difficult to observe. Several intercalators with different complexities, including ethidium, daunorubicin, and nogalamycin, have been used to probe the flexibility of the backbone of the (iG, iC)-containing PS-duplex. All of them produce drug-induced UV/vis spectra identical to their respective spectra when bound to B-DNA, suggesting that those drugs bind to the (iG, iC)-containing PS-duplex using similar intercalation processes. The results may be useful in the design of intercalator-conjugated oligonucleotides for antisense applications. The study presented in this paper augments our understanding of a growing number of parallel-stranded DNA structures, including the G-quartet, the i-motif, and the unusual homo basepaired parallel-stranded double helix. Their possible relevance is discussed.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20976264

M.Hori, S.Yonekura, T.Nohmi, P.Gruz, H.Sugiyama, S.Yonei, and Q.M.Zhang-Akiyama (2010).
Error-Prone Translesion DNA Synthesis by Escherichia coli DNA Polymerase IV (DinB) on Templates Containing 1,2-dihydro-2-oxoadenine.

J Nucleic Acids, 2010, 807579.

17905816

P.S.Pallan, P.Lubini, M.Bolli, and M.Egli (2007).
Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing.

Nucleic Acids Res, 35, 6611-6624.

14654690

F.Seela, and R.Kröschel (2003).
The base pairing properties of 8-aza-7-deaza-2'-deoxyisoguanosine and 7-halogenated derivatives in oligonucleotide duplexes with parallel and antiparallel chain orientation.

Nucleic Acids Res, 31, 7150-7158.

12685650

L.Lapinski, M.J.Nowak, J.S.Kwiatkowski, and J.Leszczynski (2003).
Photochemical syn-anti isomerization reactions in N2-hydroxyisocytosines--an experimental matrix isolation and theoretical study.

Photochem Photobiol, 77, 243-252.

11504865

J.Kawakami, H.Kamiya, K.Yasuda, H.Fujiki, H.Kasai, and N.Sugimoto (2001).
Thermodynamic stability of base pairs between 2-hydroxyadenine and incoming nucleotides as a determinant of nucleotide incorporation specificity during replication.

Nucleic Acids Res, 29, 3289-3296.

10684930

T.Ohtsubo, K.Nishioka, Y.Imaiso, S.Iwai, H.Shimokawa, H.Oda, T.Fujiwara, and Y.Nakabeppu (2000).
Identification of human MutY homolog (hMYH) as a repair enzyme for 2-hydroxyadenine in DNA and detection of multiple forms of hMYH located in nuclei and mitochondria.

Nucleic Acids Res, 28, 1355-1364.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.