McKinney SA, Déclais AC, Lilley DM, Ha T.
Nat Struct Biol. 2003 Feb;10(2):93-7.
Single molecule nanometronome.
Buranachai C, McKinney SA, Ha T.
Nano Lett. 2006 Mar;6(3):496-500.
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1. Fluorescence
Lichtman JW, Conchello JA.
Nat Methods. 2005 Dec;2(12):910-9. Review.
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2. Single-molecule fluorescence
Advances in single-molecule fluorescence methods for molecular biology.
Joo C, Balci H, Ishitsuka Y, Buranachai C, Ha T.
Annu Rev Biochem. 2008;77:51-76. doi: 10.1146/annurev.biochem.77.070606.101543. Review.
A practical guide to single-molecule FRET
Rahul Roy, Sungchul Hohng & Taekjip Ha
Nature Methods - 5, 507 - 516 (2008). Review
Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization.
Science. 2012 Aug 31;337(6098):1097-101. doi: 10.1126/science.1224139.
Vafabakhsh R, Ha T
Single-molecule chemical denaturation of riboswitches.
Dalgarno PA, Bordello J, Morris R, St-Pierre P, Dubé A, Samuel ID, Lafontaine DA, Penedo JC.
Nucleic Acids Res. 2013 Apr;41(7):4253-65. doi: 10.1093/nar/gkt128. Epub 2013 Feb 27.
Elastic coupling between RNA degradation and unwinding by an exoribonuclease.
Lee G, Bratkowski MA, Ding F, Ke A, Ha T.
Science. 2012 Jun 29;336(6089):1726-9. doi: 10.1126/science.1216848.
Spring-loaded mechanism of DNA unwinding by hepatitis C virus NS3 helicase.
Myong S1, Bruno MM, Pyle AM, Ha T.
Science. 2007 Jul 27;317(5837):513-6.
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3. Advanced single-molecule FRET techniques
Single-molecule fluorescence resonance energy transfer ***
T. Ha
Methods - Volume 25, Issue 1, September 2001, Pages 78–86
A practical guide to single-molecule FRET ***
Rahul Roy, Sungchul Hohng & Taekjip Ha
Nature Methods - 5, 507 - 516 (2008). Review
Structural dynamics of individual Holliday junctions. *
McKinney SA, Déclais AC, Lilley DM, Ha T.
Nat Struct Biol. 2003 Feb;10(2):93-7.
Immobilization in Surface-Tethered Lipid Vesicles as a New Tool for Single BiomoleculeSpectroscopy**
Erez Boukobza, Alan Sonnenfeld, and Gilad Haran
J. Phys. Chem. B 2001, 105, 12165-12170
Hohng S, Joo C, Ha T.
Biophys J. 2004 Aug;87(2):1328-37.
Single-molecule four-color FRET. ***
Lee J, Lee S, Ragunathan K, Joo C, Ha T, Hohng S.
Angew Chem Int Ed Engl. 2010 Dec 17;49(51):9922-5.
Alternating-Laser Excitation of Single Molecules**
A. Kapanidis, T. Laurence, N.Lee, E. Margeat, X. Kong & S. Weiss
Acc. Chem. Res. 2005, 38, 523-533
Recent Advances in Optical Tweezers*
J.. Moffitt, Y. Chemla, S. Smith and C. Bustamante
Annu. Rev. Biochem. 2008. 77:205–28 (Review)
Detecting force-induced molecular transitions with fluorescence resonant energy transfer. **
P. Tarsa, R. Brau, M. Barch, J. Ferrer, Y. Freyzon, P. Matsudaira, M. Lang
Angew. Chem. Int. Ed. 2007, 46, 1999 –2001
Combined optical trapping and single-molecule fluorescence*
M. Lang, P. Fordyce and S. Block
Journal of Biology 2003, 2:6 doi:10.1186/1475-4924-2-6
Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction. **
Science. 2007 Oct 12;318(5848):279-83.
Hohng S, Zhou R, Nahas MK, Yu J, Schulten K, Lilley DM, Ha T.
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4. Single-molecule kinetics
"Single-Molecule Approach to Enzymology"
Sunney Xie
Single Mol. 2001, 2, 229-236
"Hidden complexity in the isomerization dynamics of Holliday junctions"
C. Hyeon, J. Lee, S. Hohng, D. Thirumalai
Nature Chemistry 2012, 4, 907-914
J. L. Loparo and A. van Oijen
in Handbook of Single-Molecule Biophysics, 2009, (eds. P. Hinterdorfer and A. van Oijen)
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5. I-switch
The first two papers are the most relevant.
A DNA nanomachine that maps spatial and temporal pH changes inside living cells.
Modi S, M G S, Goswami D, Gupta GD, Mayor S, Krishnan Y.
Nat Nanotechnol. 2009 May;4(5):325-30. doi: 10.1038/nnano.2009.83. Epub 2009 Apr 6.
A method to map spatiotemporal pH changes inside living cells using a pH-triggered DNA nanoswitch.
Modi S, Krishnan Y.
Methods Mol Biol. 2011;749:61-77. doi: 10.1007/978-1-61779-142-0_5.
Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell.
Modi S, Nizak C, Surana S, Halder S, Krishnan Y.
Nat Nanotechnol. 2013 Jun;8(6):459-67. doi: 10.1038/nnano.2013.92. Epub 2013 May 26.
Modi S, Halder S, Nizak C, Krishnan Y.
Nanoscale. 2014 Jan 21;6(2):1144-52. doi: 10.1039/c3nr03769j.
pH-induced intramolecular folding dynamics of i-motif DNA.
Choi J, Kim S, Tachikawa T, Fujitsuka M, Majima T.
J Am Chem Soc. 2011 Oct 12;133(40):16146-53. doi: 10.1021/ja2061984. Epub 2011 Sep 15.
Dhakal S, Schonhoft JD, Koirala D, Yu Z, Basu S, Mao H.
J Am Chem Soc. 2010 Jul 7;132(26):8991-7. doi: 10.1021/ja100944j.