Research Groups > Integrative BiologySingle Molecule Imaging

“We develop quantitative single-molecule approaches to investigate mechanisms behind complex biochemical systems”

Single molecule microscopy reveals the structural dynamics of individual molecules, otherwise hidden in ensemble-averaged experiments. This provides us with direct observations of key reaction intermediates, even when present at low levels or for short periods of time, allowing us to characterise reaction mechanisms. We use single-molecule microscopy to study four main areas:

  • RNA folding: the fundamental principles that govern RNA folding from individual folding motifs to large, multidomain, catalytic RNAs. We also study how RNA helicases aid this process under physiological conditions.
  • RNA splicing: the structure and dynamics of two small nuclear RNAs, U2 and U6, that form the active site of the spliceosome – a complex responsible for catalysing RNA splicing.
  • DNA replication: the kinetic intermediates involved in proofreading DNA during replication have not been characterised. We investigate this process by monitoring the movement of E. coli DNA polymerase I on a DNA template during DNA synthesis with single base-pair resolution.
  • ssDNA scanning and deamination: the APOBEC family of enzymes comprise single-stranded DNA cytosine deaminases that are important in eliminating retroviral infectivity and initiating somatic hypermutation. We investigate ssDNA scanning and motif-targeting mechanisms for the APOBEC enzymes, Apo3G and AID

Single Molecule Imaging
Group head

David Rueda

Telephone x31604
Group members

Kathy Chaurasiya (Dr)

Telephone 34154

Amit Gautam (Dr)

Telephone 34154

Bishnu Paudel (Mr)

Telephone 34154

Chandani Warnasooriya (Mrs)

Telephone 34154

Sheila Quingchun Xie (Dr)

Telephone 34154
Admin contact

Tathiana Santana (Ms)

Telephone 38236
Contact details
Telephone: +44 (0)20 8383 1604
Fax: +44 (0)20 8383 2788
Selected publications
Mundigala, H., Michaux, J. B., Feig, A. L., Ennifar, E., Rueda, D., 2014. HIV-1 DIS stem loop forms an obligatory bent kissing intermediate in the dimerization pathway. Nucleic Acids Research. Abstract

G. Senavirathne, M. Jaszczur, P. Auerbach, T. Upton, M. Goodman* and D. Rueda* (2012) Single-stranded DNA scanning and deamination by APOBEC3G at single molecule resolution. The Journal of Biological Chemistry 287:15826-35. Abstract

K. Karunatilaka, A. Solem, A.M. Pyle* and D. Rueda* (2010) Single-molecule analysis of Mss116-mediated group II intron folding. Nature 42:935-39 Abstract

R. Lamichhane, G.M. Daubner, J. Thomas-Crusells, S.D. Auweter, C. Manatchal, K.S. Austin, O. Valniuk, F.H.-T. Allain* and D. Rueda* (2010) RNA Looping by PTB: Evidence Using FRET and NMR Spectroscopy and for a Role in Splicing Repression. Proceedings of the National Academy of Sciences 107:4105-10 Abstract

T.D. Christian, L.J. Romano* and D. Rueda* (2009) Single Molecule Measurements of Synthesis by DNA Polymerase with Base-Pair Resolution. Proceedings of the National Academy of Sciences 106:21109-14 Abstract

Z. Guo, K.S. Karunathilaka and D. Rueda (2009) Single-Molecule Folding of Protein Free U2/U6 snRNAs. Nature Structural & Molecular Biology. 16:1154-59 Abstract

M. Steiner, K.S. Karunathilaka, R.K.O. Sigel and Rueda, D.* (2008) Single-molecule studies of group II intron ribozymes. Proceedings of the National Academy of Sciences 105:13853-8 Abstract

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