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Cyanine dyes in biophysical research: the photophysics of polymethine fluorescent dyes in biomolecular environments.

Levitus M, Ranjit S.

Q Rev Biophys. 2011 Feb;44(1):123-51. doi: 10.1017/S0033583510000247. Epub 2010 Nov 26. Review.


Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance.

Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD, Cherepanov P.

Proc Natl Acad Sci U S A. 2010 Nov 16;107(46):20057-62. doi: 10.1073/pnas.1010246107. Epub 2010 Oct 28.


Signal/noise analysis of FRET-based sensors.

Woehler A, Wlodarczyk J, Neher E.

Biophys J. 2010 Oct 6;99(7):2344-54. doi: 10.1016/j.bpj.2010.07.053.


Structure-based modeling of the functional HIV-1 intasome and its inhibition.

Krishnan L, Li X, Naraharisetty HL, Hare S, Cherepanov P, Engelman A.

Proc Natl Acad Sci U S A. 2010 Sep 7;107(36):15910-5. doi: 10.1073/pnas.1002346107. Epub 2010 Aug 23.


Retroviral intasome assembly and inhibition of DNA strand transfer.

Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov P.

Nature. 2010 Mar 11;464(7286):232-6. doi: 10.1038/nature08784. Epub 2010 Jan 31.


Comparison of metal-dependent catalysis by HIV-1 and ASV integrase proteins using a new and rapid, moderate throughput assay for joining activity in solution.

Andrake MD, Ramcharan J, Merkel G, Zhao XZ, Burke TR Jr, Skalka AM.

AIDS Res Ther. 2009 Jun 29;6:14. doi: 10.1186/1742-6405-6-14.


Oligonucleotide-based assays for integrase activity.

Merkel G, Andrake MD, Ramcharan J, Skalka AM.

Methods. 2009 Apr;47(4):243-8. doi: 10.1016/j.ymeth.2008.10.024. Epub 2008 Nov 14. Review.


SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling.

Wang Q, Canutescu AA, Dunbrack RL Jr.

Nat Protoc. 2008;3(12):1832-47. doi: 10.1038/nprot.2008.184.


Integration of rous sarcoma virus DNA: a CA dinucleotide is not required for integration of the U3 end of viral DNA.

Oh J, Chang KW, Hughes SH.

J Virol. 2008 Nov;82(22):11480-3. doi: 10.1128/JVI.01353-08. Epub 2008 Sep 3.


Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids.

Iqbal A, Arslan S, Okumus B, Wilson TJ, Giraud G, Norman DG, Ha T, Lilley DM.

Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11176-81. doi: 10.1073/pnas.0801707105. Epub 2008 Aug 1.


The structure of cyanine 5 terminally attached to double-stranded DNA: implications for FRET studies.

Iqbal A, Wang L, Thompson KC, Lilley DM, Norman DG.

Biochemistry. 2008 Jul 29;47(30):7857-62. doi: 10.1021/bi800773f. Epub 2008 Jul 3.


Rous sarcoma virus (RSV) integration in vivo: a CA dinucleotide is not required in U3, and RSV linear DNA does not autointegrate.

Oh J, Chang KW, Wierzchoslawski R, Alvord WG, Hughes SH.

J Virol. 2008 Jan;82(1):503-12. Epub 2007 Oct 24.


Fluorescence measurements of duplex DNA oligomers under conditions conducive for forming M-DNA (a metal-DNA complex).

Spring BQ, Clegg RM.

J Phys Chem B. 2007 Aug 23;111(33):10040-52. Epub 2007 Aug 1.


Site-specific dynamics of strands in ss- and dsDNA as revealed by time-domain fluorescence of 2-aminopurine.

Ramreddy T, Rao BJ, Krishnamoorthy G.

J Phys Chem B. 2007 May 24;111(20):5757-66. Epub 2007 May 1.


Molecular mechanisms of HIV integration and therapeutic intervention.

Vandegraaff N, Engelman A.

Expert Rev Mol Med. 2007 Feb 26;9(6):1-19. Review.


Crystal structures of oligonucleotides including the integrase processing site of the Moloney murine leukemia virus.

Montaño SP, Coté ML, Roth MJ, Georgiadis MM.

Nucleic Acids Res. 2006;34(19):5353-60. Epub 2006 Sep 26.


Integration requires a specific interaction of the donor DNA terminal 5'-cytosine with glutamine 148 of the HIV-1 integrase flexible loop.

Johnson AA, Santos W, Pais GC, Marchand C, Amin R, Burke TR Jr, Verdine G, Pommier Y.

J Biol Chem. 2006 Jan 6;281(1):461-7. Epub 2005 Oct 27.


Processing of viral DNA ends channels the HIV-1 integration reaction to concerted integration.

Li M, Craigie R.

J Biol Chem. 2005 Aug 12;280(32):29334-9. Epub 2005 Jun 14.


MollDE: a homology modeling framework you can click with.

Canutescu AA, Dunbrack RL Jr.

Bioinformatics. 2005 Jun 15;21(12):2914-6. Epub 2005 Apr 21.


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