313d: Difference between revisions

Revision as of 20:15, 4 May 2008

Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE HOOGSTEEN BASE PAIR

OverviewOverview

We have solved the structures of the homoduplex d(Gm5CGCGCG)2, and the heteroduplexes d(GCGCGCG)/d(TCGCGCG) and d(GCGCGCG)/d(CCGCGCG). The structures form six base-pairs of identical Z-DNA duplexes with single nucleotides overhanging at the 5'-ends. The overhanging nucleotide from one strand remains stacked and sandwiched between the blunt-ends of two adjacent Z-DNA duplexes, while the overhanging base of the opposing strand is extra-helical. The stacked and the extra-helical bases from adjacent duplexes pair to form a distorted d(G x G) reverse Hoogsteen base-pair in the d(Gm5CGCGCG)2 homoduplex, and d(G x T) reverse wobble and d(G x C) reverse Watson-Crick base-pairs in the d(GCGCGCG)/d(TCGCGCG) and d(GCGCGCG)/d(CCGCGCG) heteroduplexes, respectively. Interestingly, only the d(G,T) and d(G x C) base-pairs were observed in the heteroduplexes, suggesting that both the d(G x T) reverse wobble and d(G x C) reverse Watson-Crick base-pairs are more stable in this crystal environment than the d(G x G) reverse Hoogsteen base-pair. To estimate the relative stability of the three types of reverse base-pairs, crystals were grown using various mixtures of sequences and their strand compositions analyzed by mass spectrometry. The d(G x C) reverse Watson-Crick base-pair was estimated to be more stable by approximately 1.5 kcal/mol and the d(G x T) reverse wobble base-pair more stable by approximately 0.5 kcal/mol than the d(G x G) reverse Hoogsteen base-pair. The step during crystallization responsible for discriminating between the strands in the crystal is highly cooperative, suggesting that it occurs during the initial nucleating event of crystal growth.

About this StructureAbout this Structure

Full crystallographic information is available from OCA.

ReferenceReference

The structures and relative stabilities of d(G x G) reverse Hoogsteen, d(G x T) reverse wobble, and d(G x C) reverse Watson-Crick base-pairs in DNA crystals., Mooers BH, Eichman BF, Ho PS, J Mol Biol. 1997 Jun 27;269(5):796-810. PMID:9223642 Page seeded by OCA on Sun May 4 20:15:13 2008

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OCA

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 [[Image:313d.gif|left|200px]]
- {{Structure
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-}}
 '''Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE HOOGSTEEN BASE PAIR'''
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 ==About this Structure==
-D is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=313D OCA].
+Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=313D OCA].
 ==Reference==
 The structures and relative stabilities of d(G x G) reverse Hoogsteen, d(G x T) reverse wobble, and d(G x C) reverse Watson-Crick base-pairs in DNA crystals., Mooers BH, Eichman BF, Ho PS, J Mol Biol. 1997 Jun 27;269(5):796-810. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9223642 9223642]
-[[Category: Protein complex]]
 [[Category: Eichman, B F.]]
 [[Category: Ho, P S.]]
 [[Category: Mooers, B H.M.]]
-[[Category: double helix]]
+[[Category: Double helix]]
-[[Category: flipped-out base]]
+[[Category: Flipped-out base]]
-[[Category: modified]]
+[[Category: Modified]]
-[[Category: overhanging base]]
+[[Category: Overhanging base]]
-[[Category: z-dna]]
+[[Category: Z-dna]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 20:15:13 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:21:15 2008''