Two-Domain DNA Strand Displacement
نویسنده
چکیده
We investigate the computing power of a restricted class of DNA strand displacement structures: those that are made of double strands with nicks (interruptions) in the top strand. To preserve this structural invariant, we impose restrictions on the single strands they interact with: we consider only two-domain single strands consisting of one toehold domain and one recognition domain. We study fork and join signal processing gates based on these structures, and we show that these systems are amenable to formalization and to mechanical verification.
منابع مشابه
Modular Verification of DNA Strand Displacement Networks via Serializability Analysis
DNA strand displacement gates can be used to emulate arbitrary chemical reactions, and a number of different schemes have been proposed to achieve this. Here we develop modular correctness proofs for strand displacement encodings of chemical reaction networks and show how they may be applied to two-domain strand displacement systems. Our notion of correctness is serializability of interleaved r...
متن کاملA specific subdomain in phi29 DNA polymerase confers both processivity and strand-displacement capacity.
Recent crystallographic studies of phi29 DNA polymerase have provided structural insights into its strand displacement and processivity. A specific insertion named terminal protein region 2 (TPR2), present only in protein-primed DNA polymerases, together with the exonuclease, thumb, and palm subdomains, forms two tori capable of interacting with DNA. To analyze the functional role of this inser...
متن کاملDNA-Binding Proteins Essential for Protein-Primed Bacteriophage Φ29 DNA Replication
Bacillus subtilis phage Φ29 has a linear, double-stranded DNA 19 kb long with an inverted terminal repeat of 6 nucleotides and a protein covalently linked to the 5' ends of the DNA. This protein, called terminal protein (TP), is the primer for the initiation of replication, a reaction catalyzed by the viral DNA polymerase at the two DNA ends. The DNA polymerase further elongates the nascent DNA...
متن کاملActivity of Herpes Simplex Virus Type 1 DNA Polymerase Modulates Its Strand Displacement Activity
Using a minicircle DNA primer-template, the wild-type catalytic subunit of herpes simplex virus type 1 (HSV-1) DNA polymerase (pol) was shown to lack significant strand displacement activity with or without its processivity factor, UL42. However, an exonuclease-deficient (exo ) pol (D368A) was capable of slow strand displacement. Although UL42 increased the rate (2/s) and processivity of strand...
متن کامل3' to 5' exonuclease activity of herpes simplex virus type 1 DNA polymerase modulates its strand displacement activity.
Using a minicircle DNA primer-template, the wild-type catalytic subunit of herpes simplex virus type 1 (HSV-1) DNA polymerase (pol) was shown to lack significant strand displacement activity with or without its processivity factor, UL42. However, an exonuclease-deficient (exo(-)) pol (D368A) was capable of slow strand displacement. Although UL42 increased the rate (2/s) and processivity of stra...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
دوره شماره
صفحات -
تاریخ انتشار 2013