TY - JOUR
T1 - Thermodynamics of forming a parallel DNA crossover
AU - Spink, Charles H.
AU - Ding, Liang
AU - Yang, Qingyi
AU - Sheardy, Richard D.
AU - Seeman, Nadrian C.
N1 - Funding Information:
We believe that the thermodynamic data presented in this study suggest that the PX DNA motif could be used as a model for homology recognition. The results suggest that in relaxed conditions, a system that meets the homology requirements for the PX form would prefer the PX motif relative to juxtaposed duplexes, particularly for the 6:5 structure. It is also important to recognize that we have not yet established the type of PX structure that is formed in superhelical DNA; indeed, the most dramatic results are seen with a 10:5 molecule that is only marginally stable in a four-stranded context (X. Wang, X. Zhang, C. Mao, and N. C. Seeman, unpublished observations). The PX motif is more stable in higher magnesium ion content and the 7:5 and 8:5 structures have a slightly lower tendency to form PX from JX 1 . However, PX 6:5 seems to represent a good model for the formation of fused heteroduplexes that could be a general intermediate in recombination events. Whether there would be kinetic limitations to forming these motifs is an open question. The presence of an apparent thermodynamic driving force for the formation of the paranemic crossover from juxtaposed duplexes indicates there is a potential for this conversion to occur. This work has been supported by the National Institute of General Medical Science (GM-29554), the National Science Foundation (DMI-0210844, EIA-0086015, CCF-0432009, CCF-0523290, CTS-0548774, CTS-0608889), Army Research Office (48681-EL, W911NF-07-1-0439), Department of Education (subcontract from the Research Foundation of the State University of New York; DE-FG02-06ER64281), the office of Naval Research (N000140910181), and the W. M. Keck Foundation (grant to N.C.S.).
PY - 2009
Y1 - 2009
N2 - The process of genetic recombination involves the formation of branched four-stranded DNA structures known as Holliday junctions. The Holliday junction is known to have an antiparallel orientation of its helices, i.e., the crossover occurs between strands of opposite polarity. Some intermediates in this process are known to involve two crossover sites, and these may involve crossovers between strands of identical polarity. Surprisingly, if a crossover occurs at every possible juxtaposition of backbones between parallel DNA double helices, the molecules form a paranemic structure with two helical domains, known as PX-DNA. Model PX-DNA molecules can be constructed from a variety of DNA molecules with five nucleotide pairs in the minor groove and six, seven or eight nucleotide pairs in the major groove. A topoisomer of the PX motif is the juxtaposed JX1 molecule, wherein one crossover is missing between the two helical domains. The JX1 molecule offers an outstanding baseline molecule with which to compare the PX molecule, so as to measure the thermodynamic cost of forming a crossover in a parallel molecule. We have made these measurements using calorimetric and ultraviolet hypochromicity methods, as well as denaturing gradient gel electrophoretic methods. The results suggest that in relaxed conditions, a system that meets the pairing requirements for PX-DNA would prefer to form the PX motif relative to juxtaposed molecules, particularly for the 6:5 structure.
AB - The process of genetic recombination involves the formation of branched four-stranded DNA structures known as Holliday junctions. The Holliday junction is known to have an antiparallel orientation of its helices, i.e., the crossover occurs between strands of opposite polarity. Some intermediates in this process are known to involve two crossover sites, and these may involve crossovers between strands of identical polarity. Surprisingly, if a crossover occurs at every possible juxtaposition of backbones between parallel DNA double helices, the molecules form a paranemic structure with two helical domains, known as PX-DNA. Model PX-DNA molecules can be constructed from a variety of DNA molecules with five nucleotide pairs in the minor groove and six, seven or eight nucleotide pairs in the major groove. A topoisomer of the PX motif is the juxtaposed JX1 molecule, wherein one crossover is missing between the two helical domains. The JX1 molecule offers an outstanding baseline molecule with which to compare the PX molecule, so as to measure the thermodynamic cost of forming a crossover in a parallel molecule. We have made these measurements using calorimetric and ultraviolet hypochromicity methods, as well as denaturing gradient gel electrophoretic methods. The results suggest that in relaxed conditions, a system that meets the pairing requirements for PX-DNA would prefer to form the PX motif relative to juxtaposed molecules, particularly for the 6:5 structure.
UR - http://www.scopus.com/inward/record.url?scp=68949088318&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=68949088318&partnerID=8YFLogxK
U2 - 10.1016/j.bpj.2009.04.054
DO - 10.1016/j.bpj.2009.04.054
M3 - Article
C2 - 19619467
AN - SCOPUS:68949088318
SN - 0006-3495
VL - 97
SP - 528
EP - 538
JO - Biophysical journal
JF - Biophysical journal
IS - 2
ER -