A guanine-linked end-effect is a sensitive reporter of charge flow through DNA and RNA double helices

Bergeron, Lucien Junior; Sen, Kaushiki; Sen, Dipankar

doi:10.1016/j.biochi.2008.01.003

Cited by 6 publications

(8 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The subsequent stretches of (A-T) 3 and (T-A) 3 base pairs in the two duplexes shown left and right in Figure A act as insulators, preventing significant charge flow into the (C-G) 3 base pairs distal from the AQ and beyond. Such an insulating behavior of three tandem AT pairs has been reported before. ,, Thus, the 32 P counts at the distal guanine, GGd (Figure A), as a fraction of the total counts in the lane, was measured to be 0.06 ± 0.01% for the Duplex-GTG and 0.29 ± 0.05% for the Duplex-GAG. This difference in conductivity between the two Watson−Crick duplexes is expected, given that duplexes containing all-purine or purine-rich sequence in one strand (such as Duplex-AA) are better hole conductors than those containing mixed purine and pyrimidine sequences (such as Duplex-GTG). ,, …”

Section: Resultssupporting

confidence: 84%

A Contractile Electronic Switch Made of DNA

Huang

Sen

2010

J. Am. Chem. Soc.

Self Cite

View full text Add to dashboard Cite

Double-helical DNA has been shown to conduct both electrons and electron holes, the latter over distances of >20 nm. DNA is thus a material of significant interest for the bottom-up construction of nanocircuitry. Here, we describe a contractile DNA nanoswitch, which can toggle between a structurally extended "off" state and a contracted "on" state, with a 40-fold conductivity difference between the two. To turn on, two short motifs of guanine-guanine mismatches in an otherwise standard double helix synapse to form a conductive G-quadruplex, bypassing an insulating element within the helix. This switch can be turned repeatedly on by treatment with millimolar concentrations of K(+) and turned off by sequestration of the K(+) by a crown ether. Circular dichroism and thymine-thymine photocross-linking experiments reveal that strand orientations within the on state G-quadruplex are wholly antiparallel and that the two conductive double-helices interface with the same face of the quadruplex. Although this DNA nanoswitch is chemically gated, it should be adaptable to other kinds of gating and thus serve as a prototype for increasingly sophisticated and complex electronic devices made of DNA.

show abstract

Section: Resultssupporting

confidence: 84%

A Contractile Electronic Switch Made of DNA

Huang

Sen

2010

J. Am. Chem. Soc.

Self Cite

View full text Add to dashboard Cite

show abstract

“…Damage is also greatest at the 5′-most of the central five guanines (and least in the 3′-most guanine). Under our experimental conditions the presence or absence of a nick in the duplex did not make any difference to the duplex’s charge conduction properties; we have consistently found this to be so for DNA duplexes .…”

Section: Resultssupporting

confidence: 72%

“…To eliminate steric crowding at the duplex−quadruplex junctions, such as was likely found with many of the constructs used by prior investigators in their studies on antiparallel quadruplexes ,, , the junctions in our constructs had a single duplex stacking upon a quadruplex. To minimize the expected helical strain as DNA strands transitioned between two different helical forms, each duplex−quadruplex junction incorporated a strand nick, which does not ordinarily interfere with charge flow but should ensure optimal stacking between the two kinds of helices at each junction.…”

mentioning

confidence: 99%

Charge Conduction Properties of a Parallel-Stranded DNA G-Quadruplex: Implications for Chromosomal Oxidative Damage

Huang¹,

Cheng²,

Yu³

et al. 2009

Biochemistry

Self Cite

View full text Add to dashboard Cite

The charge-flow properties and concomitant guanine damage patterns of a number of intermolecular and wholly parallel-stranded DNA G-quadruplexes were investigated. The DNA constructs were structurally well-defined and consisted of the G-quadruplex sandwiched and stacked between two Watson-Crick base-paired duplexes. Such duplex-quadruplex-duplex constructs were designed to minimize torsional stress as well as steric crowding at the duplex-quadruplex junctions. When anthraquinone was used to induce charge flow within the constructs, it was found that the quadruplex served both as a sink and as a moderately good conductor of electron holes, relative to DNA duplexes. Most strikingly, the quadruplex suffered very little charge-flow generated oxidative damage relative to guanines in the duplex regions and, indeed, to guanines in antiparallel quadruplexes reported in prior studies. It is likely that these differences result from a combination of steric and electronic factors. A biological conclusion that may be drawn from these data is that if, as anticipated, G-quadruplex structures form in vivo at the telomeres and other loci in eukaryotic chromosomes, their ability to serve as protective sinks against chromosomal oxidative damage may depend on their specific character and topology. From a separate perspective, our results on the conduction properties of duplex-quadruplex-duplex DNA composites suggest the utility of G-quadruplexes as junction modules in the construction of DNA-based biosensors and nanocircuitry.

show abstract

“…It is necessary to emphasize that neither the high photostability of single nucleobases [159][160][161][162][163][164][165][288][289][290][291][292][293], nor the even higher stability of their Watson-Crick pairs [164,355,356], nor the aptitude for long-range energy transfer along stacked nucleotides [330,333,360] have anything to do with the current functioning of RNA and DNA in the transfer of genetic information. All these traits, however, support the suggested involvement of UV light as a selecting factor during the initial stages of evolution [105,112,133,159,164].…”

Section: The First Replicators and The Emergence Of Proteins And Enzymesmentioning

confidence: 99%