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[[Image:1sls.gif|left|200px]]
{{Seed}}
[[Image:1sls.png|left|200px]]


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{{STRUCTURE_1sls|  PDB=1sls  |  SCENE=  }}  
{{STRUCTURE_1sls|  PDB=1sls  |  SCENE=  }}  


'''IMMOBILE SLIPPED-LOOP STRUCTURE (SLS) OF DNA HOMODIMER IN SOLUTION, NMR, 9 STRUCTURES'''
===IMMOBILE SLIPPED-LOOP STRUCTURE (SLS) OF DNA HOMODIMER IN SOLUTION, NMR, 9 STRUCTURES===




==Overview==
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We report a high-resolution NMR structure of a homodimer formed by a synthetic 25 residue DNA oligonucleotide GCTCCCATGGTTTTTGTGCACGAGC. This structure presents a novel structural motif for single-stranded nucleic acids, called a pseudosquare knot (PSQ). The oligonucleotide was originally designed to mimic a slipped-loop structure (SLS), another "unusual" DNA structure postulated as an alternative conformation for short direct repeats in double-stranded DNA. The design of the sequence is compatible with both SLS and PSQ structures, both of which possess identical sets of base-paired and unpaired nucleotides but different tertiary folds. We used deuteration of the H8 positions of purines to ascertain that the PSQ is actually formed under the conditions used. The PSQ structure was solved based on homonuclear proton nuclear Overhauser effect data using complete relaxation matrix methods. The structure essentially consists of two side-by-side helices connected by single-stranded loops. Each of the helices is well-defined; however, the relative orientation of the two remains undetermined by the NMR data. The sequences compatible with the PSQ formation are frequent in single-stranded genomes; this structure may play a role as a dimerization motif.
The line below this paragraph, {{ABSTRACT_PUBMED_9737848}}, adds the Publication Abstract to the page
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{{ABSTRACT_PUBMED_9737848}}


==About this Structure==
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLS OCA].  
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLS OCA].  


==Reference==
==Reference==
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[[Category: Slipped-loop structure]]
[[Category: Slipped-loop structure]]
[[Category: Unusual structure]]
[[Category: Unusual structure]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 08:51:47 2008''
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 17:07:31 2008''

Revision as of 14:07, 27 July 2008

File:1sls.png

Template:STRUCTURE 1sls

IMMOBILE SLIPPED-LOOP STRUCTURE (SLS) OF DNA HOMODIMER IN SOLUTION, NMR, 9 STRUCTURES

Template:ABSTRACT PUBMED 9737848

About this Structure

Full experimental information is available from OCA.

Reference

A pseudosquare knot structure of DNA in solution., Ulyanov NB, Ivanov VI, Minyat EE, Khomyakova EB, Petrova MV, Lesiak K, James TL, Biochemistry. 1998 Sep 15;37(37):12715-26. PMID:9737848

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