Blinking statistics of a molecular beacon triggered by end-denaturation of DNA

被引：5

作者：

Ambjörnsson, T ^{[1
]}

Metzler, R ^{[1
]}

机构：

[1] NORDITA, Nord Inst Theoret Phys, DK-2100 Copenhagen O, Denmark

来源：

JOURNAL OF PHYSICS-CONDENSED MATTER | 2005年 / 17卷 / 49期

关键词：

D O I：

10.1088/0953-8984/17/49/022

中图分类号：

O469 [凝聚态物理学];

学科分类号：

070205 ;

摘要：

We use a master equation approach based on the Poland-Scheraga free energy for DNA denaturation to investigate the (un)zipping dynamics of a denaturation wedge in a stretch of DNA that is clamped at one end. In particular, we quantify the blinking dynamics of a fluorophore-quencher pair mounted within the denaturation wedge. We also Study the behavioural changes in the presence of proteins that selectively bind to single-stranded DNA. We show that Such a set-up could be well Suited as an easy-to-implement nanodevice for sensing environmental conditions in small volumes.

引用

页码：S4305 / S4316

页数：12

共 27 条

[1] Bubble dynamics in double-stranded DNA [J].

Altan-Bonnet, G ;

Libchaber, A ;

Krichevsky, O .

PHYSICAL REVIEW LETTERS, 2003, 90 (13)

[2] Chaperone-assisted translocation [J].

Ambjörnsson, T ;

Metzler, R .

PHYSICAL BIOLOGY, 2004, 1 (1-2) :77-88

[3] Binding dynamics of single-stranded DNA binding proteins to fluctuating bubbles in breathing DNA [J].

Ambjörnsson, T ;

Metzler, R .

JOURNAL OF PHYSICS-CONDENSED MATTER, 2005, 17 (20) :S1841-S1869

[4]

AMBJORNSSON T, 2005, IN PRESS PHYS REV E

[5]

AMBJORNSSON T, UNPUB

[6]

AMBJORNSSON T, 2005, IN PRESS J COMPUT TH

[7]

ANIK SK, 2005, EUROPHYS LETT, V71, P852

[8] Statistical mechanical simulation of polymeric DNA melting with MELTSIM [J].

Blake, RD ;

Bizzaro, JW ;

Blake, JD ;

Day, GR ;

Delcourt, SG ;

Knowles, J ;

Marx, KA ;

SantaLucia, J .

BIOINFORMATICS, 1999, 15 (05) :370-375

[9] Entropy-driven translational isomerism:: A tristable molecular shuttle [J].

Bottari, G ;

Dehez, F ;

Leigh, DA ;

Nash, PJ ;

Pérez, EM ;

Wong, JKY ;

Zerbetto, F .

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 2003, 42 (47) :5886-5889

[10]

EIFERT U, 2005, PHYS REV LETT, P602

← 1 2 3 →