Linked Life Data

15099741

Source:http://linkedlifedata.com/resource/pubmed/id/15099741

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
4
pubmed:dateCreated
2004-4-21
pubmed:abstractText
DNA supercoiling plays an important role in many genetic processes such as replication, transcription, and recombination. Supercoiling provides energy for helix un-pairing and drives the formation of alternative DNA structural transitions, like cruciforms. Supercoiling also allows distant DNA regions to be brought into close proximity through the formation of inter-wound supercoils. Recently, we showed that the inverted repeat-to-cruciform transition acts as a molecular switch, influencing the global topology of a topological plasmid domain. As alternative DNA structures can affect global topology, a corollary hypothesis might be that the localization of a specific DNA sequence within a topological domain may affect the energetics required for formation of an alternative DNA structure. Here, we test this hypothesis and show that the localization of an inverted repeat to an apical position increases the rate of cruciform formation and reduces the superhelical energy required to drive the transition. For this, we created a series of plasmids containing an inverted repeat and an A-tract bent DNA sequence. The A-tract forms a permanent 180 degrees bend irrespective of DNA topology. The inverted repeat and the bent sequence were placed either at six o'clock or nine o'clock positions with respect to each other. Using 2D agarose gel electrophoresis, we show that the six o'clock construct extrudes the cruciform at a lower superhelical density than a control plasmid without the bend. Atomic force microscopy shows that the nine o'clock construct has the propensity to form branched molecules with the cruciform at the end of one branch. These results demonstrate that the localization of sequences within specific regions of a topological domain can affect the energetics of structural transitions as well as the branching structure of the domain. As structural transitions can be involved in biological processes, localization of alternative conformation-forming sequences to specific locations within a domain provides an additional means for gene regulation.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
May
pubmed:issn
0022-2836
pubmed:author
pubmed:issnType
Print
pubmed:day
7
pubmed:volume
338
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
735-43
pubmed:dateRevised
2007-11-14
pubmed:meshHeading
pubmed:year
2004
pubmed:articleTitle
Influence of global DNA topology on cruciform formation in supercoiled DNA.
pubmed:affiliation
Center for Genome Research, Institute of Biosciences and Technology, Texas A and M University System Health Sciences Center, 2121 W. Holcombe Blvd., Houston, TX 77030, USA.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, P.H.S.