Yuri Lyubchenko
List of publications with links to the article
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Lyubchenko, Y. L., Frank-Kamenetskii, M. D., Vologodskii, A. V., Lazurkin, Y. S.,
and Gause, G. G., Jr. (1976) Fine structure of DNA melting curves, Biopolymers
15, 1019-1036.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=1268312
Lukashin, A. V., Vologodskii, A. V., Frank-Kamenetskii, M. D., and Lyubchenko,
Y. L. (1976) Fluctuational opening of the double helix as revealed by
theoretical and experimental study of DNA interaction with formaldehyde, J
Mol Biol 108, 665-682.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=1018321
Lyubchenko, Y. L., Vologodskii, A. V., and Frank-Kamenetskii, M. D. (1978)
Direct comparison of theoretical and experimental melting profiles for RF II
phiX174 DNA, Nature 271, 28-31.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=625323
Pavlov, V. M., Lyubchenko, Y. L., Borovik, A. S., and Lazurkin, Y. S. (1977)
Specific fragmentation of T7 phage DNA at low-melting sites, Nucleic Acids Res
4, 4053-4062.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=593901
Borovik, A. S., Kalambet, Y. A., Lyubchenko, Y. L., Shitov, V. T., and Golovanov,
E. I. (1980) Equilibrium melting of plasmid ColE1 DNA: electron-microscopic
visualization, Nucleic Acids Res 8, 4165-4184.
http://www.ncbi.nlm.nih.gov/htbinpost/Entrez/query?db=m&form=6&dopt=r&uid=6253910
Amirikyan, B. R., Vologodskii, A. V., and Lyubchenko, Y. L. (1981)
Determination of DNA cooperativity factor, Nucleic Acids Res 9, 5469-5482.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=7029470
Gagua, A. V., Belintsev, B. N., and Lyubchenko, Y. L. (1981) Effect of base-pair
stability on the melting of superhelical DNA, Nature 294, 662-663.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=6458769
Tikchonenko, T. I., Dubichev, A. G., Lyubchenko, Y. L., Kvitko, N. P.,
Chaplygina, N. M., Kalinina, T. I., Dreizin, R. S., and Naroditsky, B. S. (1981)
The distribution of guanine-cytosine pairs in adenovirus DNAs, J Gen Virol 54,
425-429.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=7288411
Lyamichev, V. I., Panyutin, I. G., and Lyubchenko, Y. L. (1982) Gel
electrophoresis of partially denatured DNA. Retardation effect: its analysis
and application, Nucleic Acids Res 10, 4813-4826.
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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=7133999
Lyubchenko, Y. L., Kalambet, Y. A., Lyamichev, V. I., and Borovik, A. S. (1982)
A comparison of experimental and theoretical melting maps for replicative
form of phi X174 DNA, Nucleic Acids Res 10, 1867-1876.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=6210880
Panyutin, I. G., Lyamichev, V. I., and L., L. Y. (1982) A sharp structural
transition in pA03 plasmid DNA caused by increased superhelix density,
FEBS Lett 148, 297-301.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=6295808
Lyamichev, V. I., Panyutin, I. G., Cherny, D. I., and Lyubchenko, Y. L. (1983)
Localization of low-melting regions in phage T7 DNA, Nucleic Acids Res 11,
2165-2176.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=6300796
Kozyavkin, S. A., and Lyubchenko, Y. L. (1984) The nonequilibrium character
of DNA melting: effects of the heating rate on the fine structure of melting
curves, Nucleic Acids Res 12, 4339-4349.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=6328418
Vologodskii, A. V., Amirikyan, B. R., Lyubchenko, Y. L., and Frank-Kamenetskii,
M. D. (1984) Allowance for heterogeneous stacking in the DNA helix-coil
transition theory, J Biomol Struct Dyn 2, 131-148.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=6400927
Kalambet, Y., A., Borovik, A. S., Lyamichev, V. I., and Lyubchenko, Y. L. (1985)
Electron microscopy of the melting of sequenced DNA, Biopolymers 24, 359377.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=2983794
Kozyavkin, S. A., Naritsin, D. B., and Lyubchenko, Y. L. (1986) The kinetics of
DNA helix-coil subtransitions, J Biomol Struct Dyn 3, 689-704.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=3271045
Razlutskii, I. V., Shlyakhtenko, L. S., and Lyubchenko, Y. L. (1987) The effect of
nucleotide substitution on DNA denaturation profiles, Nucleic Acids Res 15,
6665-6676.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=2819824
Lyubchenko, Y. L., and Shlyakhtenko, L. S. (1988) Early melting of supercoiled
DNA, Nucleic Acids Res 16, 3269-3281.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=3375056
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Voloshin, O. N., Shlyakhtenko, L. S., and Lyubchenko, Y. L. (1989) Localization
of melted regions in supercoiled DNA, FEBS Lett 243, 377-380.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=2917657
Livshits, M. A., Amosova, O. A., and Lyubchenko, Y. L. (1990) Flexibility
difference between double-stranded RNA and DNA as revealed by gel
electrophoresis, J Biomol Struct Dyn 7, 1237-1249.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=1973043
Lyubchenko, Y., Shlyakhtenko, L., Chernov, B., and Harrington, R. E. (1991)
DNA bending induced by Cro protein binding as demonstrated by gel
electrophoresis, Proc Natl Acad Sci U S A 88, 5331-5334.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=2052610
Lyubchenko, Y. L., Shlyakhtenko, L. S., Lindsay, S. M., DeRose, J. A., Thundat, T.,
and Harrington, R. E. (1991) STM Studies of Individual DNA Molecules, J.
BIOMOLEC. STRUCT. DYN. 8, A125.
Naritsin, D. B., and Lyubchenko, Y. L. (1991) Melting of oligodeoxynucleotides
with various structures, J Biomol Struct Dyn 8, 813-825.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=2059341
Shlyakhtenko, L., Lyubchenko, Y., Chernov, B. K., and Harrington, R. E. (1991)
Cro Protein Bends DNA. Circularization Experiments and Gel Electrophoresis
Data, J. BIOMOLEC. STRUCT. DYN. 8, A197.
Lindsay, S. M., Tao, N. J., DeRose, J. A., Oden, P. I., Lyubchenko, Y. L.,
Harrington, R. E., and Shlyakhtenko, L. (1992) Potentiostatic deposition of
DNA for scanning probe microscopy, Biophys J 61, 1570-1584.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=1617139
Lindsay, S. M., Lyubchenko, Y. L., Gall, A. A., Shlyakhtenko, L. S., and
Harrington, R. E. (1992) Imaging DNA Molecules Chemically Bound to a Mica
Surface, SPIE PROCEEDINGS 1639, 84-90. http://dx.doi.org/10.1117/12.58177
Lyubchenko, Y. L., Gall, A. A., Shlyakhtenko, L. S., Harrington, R. E., Jacobs, B.
L., Oden, P. I., and Lindsay, S. M. (1992) Atomic force microscopy imaging of
double stranded DNA and RNA, J Biomol Struct Dyn 10, 589-606.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=1492926
Lyubchenko, Y. L., Jacobs, B. L., and Lindsay, S. M. (1992) Atomic force
microscopy of reovirus dsRNA: a routine technique for length measurements,
Nucleic Acids Res 20, 3983-3986.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=1508683
Lyubchenko, Y. L., Lindsay, S. M., Gall, A. A., Shlyakhtenko, L. S., and
Harrington, R. E. (1992) Atomic Force Microscopy Imaging 0f Long Double
Stranded DNA, FASEB J. 6, A149.
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Jing, T. W., Jeffrey, A. M., DeRose, J. A., Lyubchenko, Y. L., Shlyakhtenko, L. S.,
Harrington, R. E., Appella, E., Larsen, J., Vaught, A., Rekesh, D., and et al.
(1993) Structure of hydrated oligonucleotides studied by in situ scanning
tunneling microscopy, Proc Natl Acad Sci U S A 90, 8934-8938.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=8415633
Lindsay, S. M., Lyubchenko, Y. L., Tao, N. J., Li, Y., Oden, P. I., DeRose, J., and
Pan, J. (1993) STM and AFM Studies of Biomaterials at Liquid-Surface
Interface, J. VAC. SCI. TECHNOL. A 11, 808-815.
http://dx.doi.org/10.1116/1.578309
Lyubchenko, Y. L., Shlyakhtenko, L. S., Appella, E., and Harrington, R. E.
(1993) CA runs increase DNA flexibility in the complex of lambda Cro protein
with the OR3 site, Biochemistry 32, 4121-4127.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=8471619
Lyubchenko, Y., Shlyakhtenko, L., Harrington, R., Oden, P., and Lindsay, S.
(1993) Atomic force microscopy of long DNA: imaging in air and under
water, Proc Natl Acad Sci U S A 90, 2137-2140.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=8460119
Lyubchenko, Y. L., Oden, P. I., Lampner, D., Lindsay, S. M., and Dunker, K. A.
(1993) Atomic force microscopy of DNA and bacteriophage in air, water and
propanol: the role of adhesion forces, Nucleic Acids Res 21, 1117-1123.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=8464697
Shlyakhtenko, L. S., Appella, E., Harrington, R. E., Kutyavin, I., and
Lyubchenko, Y. L. (1994) Structure of three-way DNA junctions. 2. Effects of
extra bases and mismatches, J Biomol Struct Dyn 12, 131-143.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=7848563
Shlyakhtenko, L. S., Rekesh, D., Lindsay, S. M., Kutyavin, I., Appella, E.,
Harrington, R. E., and Lyubchenko, Y. L. (1994) Structure of three-way DNA
junctions. 1. Non-planar DNA geometry, J Biomol Struct Dyn 11, 1175-1189.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=7946068
Bezanilla, M., Manne, S., Laney, D. E., Lyubchenko, Y. L., and Hansma, H. G.
(1995) Adsorption of DNA to Mica, Silylated Mica, and Minerals:
Characterization by Atomic Force Microscopy, Langmuir 11, 655-659.
Lyubchenko, Y. L., Jacobs, B. L., Lindsay, S. M., and Stasiak, A. (1995) Atomic
force microscopy of nucleoprotein complexes, Scanning Microsc 9, 705-724;
discussion 724-707.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=7501986
Lyubchenko, Y. L., Blankenship, R. E., Gall, A. A., Lindsay, S. M., Thiemann, O.,
Simpson, L., and Shlyakhtenko, L. S. (1996) Atomic force microscopy of DNA,
nucleoproteins and cellular complexes: the use of functionalized substrates,
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Scanning Microsc Suppl 10, 97-107.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=9601533
Lyubchenko, Y. L., Gall, A.A., Lindsay, S.M. and Shlyakhtenko, L.S. (1996) AFM
imaging of DNA and other biological molecules: use of silylated mica, Biophys.
J. 70, A370.
Rekesh, D., Lyubchenko, Y., Shlyakhtenko, L. S., and Lindsay, S. M. (1996)
Scanning tunneling microscopy of mercapto-hexyl-oligonucleotides attached
to gold, Biophys J 71, 1079-1086.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=8842244
Lyubchenko, Y. L., Shlyakhtenko, L. S., Aki, T., and Adhya, S. (1997) Atomic
force microscopic demonstration of DNA looping by GalR and HU, Nucleic
Acids Res 25, 873-876.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=9016640
Lyubchenko, Y. L., and Shlyakhtenko, L. S. (1997) Visualization of supercoiled
DNA with atomic force microscopy in situ, Proc Natl Acad Sci U S A 94, 496501.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=9012812
Perelroyzen, M. P., Lyamichev, V. I., Kalambet Yu, A., Lyubchenko Yu, L., and
Vologodskii, A. V. (1981) A study of the reversibility of helix-coil transition in
DNA, Nucleic Acids Res 9, 4043-4059.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=7301577
Herbert, A., Schade, M., Lowenhaupt, K., Alfken, J., Schwartz, T., Shlyakhtenko,
L. S., Lyubchenko, Y. L., and Rich, A. (1998) The Zalpha domain from human
ADAR1 binds to the Z-DNA conformer of many different sequences, Nucleic
Acids Res 26, 3486-3493.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=967
Lyubchenko, Y. L., and Lindsay, S. M. (1998) DNA, RNA and Nucleoprotein
Complexes Immobilized on AP-mica and Imaged with AFM, in Procedures in
Scanning Probe Microscopy (Engel, A., Ed.), pp 493-496, Wiley & Sons, Ltd.,
New York, Toronto.
Shlyakhtenko, L. S., Potaman, V. N., Sinden, R. R., and Lyubchenko, Y. L. (1998)
Structure and dynamics of supercoil-stabilized DNA cruciforms, J Mol Biol
280, 61-72.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=9653031
Engel, A., Lyubchenko, Y., and Muller, D. (1999) Atomic force microscopy: a
powerful tool to observe biomolecules at work, Trends Cell Biol 9, 77-80.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=10087624
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Oussatcheva, E. A., Shlyakhtenko, L. S., Glass, R., Sinden, R. R., Lyubchenko, Y.
L., and Potaman, V. N. (1999) Structure of branched DNA molecules: gel
retardation and atomic force microscopy studies, J Mol Biol 292, 75-86.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=10493858
Shlyakhtenko, L. S., Gall, A. A., Weimer, J. J., Hawn, D. D., and Lyubchenko, Y. L.
(1999) Atomic force microscopy imaging of DNA covalently immobilized on a
functionalized mica substrate, Biophys J 77, 568-576.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=10388781
Yodh, J. G., Lyubchenko, Y. L., Shlyakhtenko, L. S., Woodbury, N., and Lohr, D.
(1999) Evidence for nonrandom behavior in 208-12 subsaturated
nucleosomal array populations analyzed by AFM, Biochemistry 38, 1575615763.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=10625441
Shlyakhtenko, L. S., Potaman, V. N., Sinden, R. R., Gall, A. A., and Lyubchenko,
Y. L. (2000) Structure and dynamics of three-way DNA junctions: atomic
force microscopy studies, Nucleic Acids Res 28, 3472-3477.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=10982865
Shlyakhtenko, L. S., Hsieh, P., Grigoriev, M., Potaman, V. N., Sinden, R. R., and
Lyubchenko, Y. L. (2000) A cruciform structural transition provides a
molecular switch for chromosome structure and dynamics, J Mol Biol 296,
1169-1173.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=10698623
Bash, R. C., Yodh, J., Lyubchenko, Y., Woodbury, N., and Lohr, D. (2001)
Population analysis of subsaturated 172-12 nucleosomal arrays by atomic
force microscopy detects nonrandom behavior that is favored by histone
acetylation and short repeat length, J Biol Chem 276, 48362-48370.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=11583994
Bolshakova, A. V., Kiselyova, O. I., Filonov, A. S., Frolova, O. Y., Lyubchenko, Y.
L., and Yaminsky, I. V. (2001) Comparative studies of bacteria with an atomic
force microscopy operating in different modes, Ultramicroscopy 86, 121-128.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=11215614
Lyubchenko, Y. L., Gall, A. A., and Shlyakhtenko, L. S. (2001) Atomic force
microscopy of DNA and protein-DNA complexes using functionalized mica
substrates, Methods Mol Biol 148, 569-578.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=11357614
Lyubchenko, Y. L., Gall, A. A., and Shlyakhtenko, L. S. (2001) Atomic Force
Microscopy of DNA and Protein-DNA Complexes Using Functionalized Mica
Substrates., in Methods Mol. Biol. DNA-protein interactions; Principles and
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protocols (Moss, T., Ed.), pp 569-578, Humana Press, Totowa, NJ.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=11357614
Tiner, W. J., Sr., Potaman, V. N., Sinden, R. R., and Lyubchenko, Y. L. (2001)
The structure of intramolecular triplex DNA: atomic force microscopy study, J
Mol Biol 314, 353-357.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=11846549
Dahlgren, P. R., and Lyubchenko, Y. L. (2002) Atomic Force Microscopy Study
of the Effects of Mg(2+) and Other Divalent Cations on the End-to-End DNA
Interactions, Biochemistry 41, 11372-11378.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=12234179
Gaillard, C., Shlyakhtenko, L. S., Lyubchenko, Y. L., and Strauss, F. (2002)
Structural analysis of hemicatenated DNA loops, BMC Struct Biol 2, 7.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=12450412
Kato, M., McAllister, C. J., Hokabe, S., Shimizu, N., and Lyubchenko, Y. L. (2002)
Structural heterogeneity of pyrimidine/purine-biased DNA sequence
analyzed by atomic force microscopy, Eur J Biochem 269, 3632-3636.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=12153559
Limansky, A. P., Shlyakhtenko, L. S., S. Schaus, Henderson, E. and Lyubchenko,
Y. L. (2002) Aminomodified probes for atomic force microscopy, Probe
Microscopy 4, 1-6.
Lyubchenko, Y. L., Shlyakhtenko, L. S., Binus, M., Gaillard, C., and Strauss, F.
(2002) Visualization of hemiknot DNA structure with an atomic force
microscope, Nucleic Acids Res 30, 4902-4909.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=12433993
Lyubchenko, Y. L., Shlyakhtenko, L. S., Potaman, V. P. and Sinden, R. R. (2002)
Global and Local DNA Structure and Dynamics. Single molecule studies with
AFM, Microsc. Microanal. 8, 170-171.
Potaman, V. N., Lushnikov, A. Y., Sinden, R. R., and Lyubchenko, Y. L. (2002)
Site-specific labeling of supercoiled DNA at the a+t rich sequences,
Biochemistry 41, 13198-13206.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=11927777
Sinden, R. R., Potaman, V. N., Oussatcheva, E. A., Pearson, C. E., Lyubchenko, Y.
L., and Shlyakhtenko, L. S. (2002) Triplet repeat DNA structures and human
genetic disease: dynamic mutations from dynamic DNA, J Biosci 27 Suppl 1,
53-65.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=11927777
Yodh, J. G., Woodbury, N., Shlyakhtenko, L. S., Lyubchenko, Y. L., and Lohr, D.
(2002) Mapping nucleosome locations on the 208-12 by AFM provides clear
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evidence for cooperativity in array occupation, Biochemistry 41, 3565-3574.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=11888272
Kato, M., Hokabe, S., Itakura, S., Minoshima, S., Lyubchenko, Y. L., Gurkov, T.
D., Okawara, H., Nagayama, K., and Shimizu, N. (2003) Interarm interaction of
DNA cruciform forming at a short inverted repeat sequence, Biophys J 85,
402-408.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
&dopt=Citation&list_uids=12829494
Lushnikov, A. Y., Bogdanov, A., and Lyubchenko, Y. L. (2003) DNA
recombination: Holliday junctions dynamics and branch migration, J Biol
Chem 278, 43130-43134.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
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Shlyakhtenko, L. S., Lyubchenko, Y. L., Matsuura, T., Ashizawa, T., Leffak, M.,
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Lyubchenko, Y. L., Hinterdorfer, P., and Gruber, H. J. (2003) A Simple Test
System for Single Molecule Recognition Force Microscopy, Analytica Chimica
Acta 479, 59–75.
Shlyakhtenko, L. S., Gall, A. A., Filonov, A., Cerovac, Z., Lushnikov, A., and
Lyubchenko, Y. L. (2003) Silatrane-based surface chemistry for
immobilization of DNA, protein-DNA complexes and other biological
materials, Ultramicroscopy 97, 279-287.
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Shlyakhtenko, L. S., Miloseska, L., Potaman, V. N., Sinden, R. R., and
Lyubchenko, Y. L. (2003) Intersegmental interactions in supercoiled DNA:
atomic force microscope study, Ultramicroscopy 97, 263-270.
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Virnik, K., Lyubchenko, Y. L., Karymov, M. A., Dahlgren, P., Tolstorukov, M. Y.,
Semsey, S., Zhurkin, V. B., and Adhya, S. (2003) "Antiparallel" DNA loop in gal
repressosome visualized by atomic force microscopy, J Mol Biol 334, 53-63.
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Emadi, S., Liu, R., Yuan, B., Schulz, P., McAllister, C., Lyubchenko, Y., Messer, A.,
and Sierks, M. R. (2004) Inhibiting aggregation of alpha-synuclein with
human single chain antibody fragments, Biochemistry 43, 2871-2878.
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Liu, R., McAllister, C., Lyubchenko, Y., and Sierks, M. R. (2004) Residues 17-20
and 30-35 of beta-amyloid play critical roles in aggregation, J Neurosci Res 75,
162-171.
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Liu, R., Yuan, B., Emadi, S., Zameer, A., Schulz, P., McAllister, C., Lyubchenko,
Y., Goud, G., and Sierks, M. R. (2004) Single chain variable fragments against
beta-amyloid (Abeta) can inhibit Abeta aggregation and prevent abetainduced neurotoxicity, Biochemistry 43, 6959-6967.
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Liu, R., McAllister, C., Lyubchenko, Y., and Sierks, M. R. (2004) Proteolytic
antibody light chains alter beta-amyloid aggregation and prevent
cytotoxicity, Biochemistry 43, 9999-10007.
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Lushnikov, A. Y., Brown, B. A., 2nd, Oussatcheva, E. A., Potaman, V. N., Sinden,
R. R., and Lyubchenko, Y. L. (2004) Interaction of the Zalpha domain of
human ADAR1 with a negatively supercoiled plasmid visualized by atomic
force microscopy, Nucleic Acids Res 32, 4704-4712.
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Lyubchenko, Y. L. (2004) DNA structure and dynamics: an atomic force
microscopy study, Cell Biochem Biophys 41, 75-98.
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Oussatcheva, E. A., Pavlicek, J., Sankey, O. F., Sinden, R. R., Lyubchenko, Y. L.,
and Potaman, V. N. (2004) Influence of global DNA topology on cruciform
formation in supercoiled DNA, J Mol Biol 338, 735-743.
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Pavlicek, J. W., Oussatcheva, E. A., Sinden, R. R., Potaman, V. N., Sankey, O. F.,
and Lyubchenko, Y. L. (2004) Supercoiling-induced DNA bending,
Biochemistry 43, 10664-10668.
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&dopt=Citation&list_uids=15311927
Potaman, V. N., Oussatcheva, E. A., Lyubchenko, Y. L., Shlyakhtenko, L. S.,
Bidichandani, S. I., Ashizawa, T., and Sinden, R. R. (2004) Length-dependent
structure formation in Friedreich ataxia (GAA)n*(TTC)n repeats at neutral
pH, Nucleic Acids Res 32, 1224-1231.
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Sankey, O. F., Potaman, V. N., Sinden, R. R., and Lyubchenko, Y. L. (2004)
Thermodynamic and kinetic modeling of cruciform formation, J Mol Biol
suplement to J Mol Biol, 2004. 338(4): p. 735-743.
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Dahlgren, P. R., Karymov, M. A., Bankston, J., Holden, T., Thumfort, P., Ingram,
V. M., and Lyubchenko, Y. L. (2005) Atomic force microscopy analysis of the
Huntington protein nanofibril formation, Nanomedicine: Nanotechnology,
Biology, and Medicine 1, 52-57.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
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Dahlgren, P. R., Karymov, M. A., Bankston, J., Holden, T., Thumfort, P., Ingram,
V. M., and Lyubchenko, Y. L. (2005) Atomic force microscopy analysis of the
Huntington protein nanofibril formation, Dis Mon 51, 374-385.
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Karymov, M., Daniel, D., Sankey, O. F., and Lyubchenko, Y. L. (2005) Holliday
junction dynamics and branch migration: single-molecule analysis, Proc Natl
Acad Sci U S A 102, 8186-8191.
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Kransnoslobodtsev, A. V., Shlyakhtenko, L. S., Ukraintsev, E., Zaikova, T. O.,
Keana, J. F., and Lyubchenko, Y. L. (2005) Nanomedicine and Protein
Misfolding Diseases, Nanomedicine 1, 300-305.
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Lonskaya, I., Potaman, V. N., Shlyakhtenko, L. S., Oussatcheva, E. A.,
Lyubchenko, Y. L., and Soldatenkov, V. A. (2005) Regulation of poly(ADPribose) polymerase-1 by DNA structure-specific binding, J Biol Chem 280,
17076-17083.
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McAllister, C., Karymov, M. A., Kawano, Y., Lushnikov, A. Y., Mikheikin, A.,
Uversky, V. N., and Lyubchenko, Y. L. (2005) Protein Interactions and
Misfolding Analyzed by AFM Force Spectroscopy, J Mol Biol 354, 1028-1042.
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Potaman, V. N., Shlyakhtenko, L. S., Oussatcheva, E. A., Lyubchenko, Y. L., and
Soldatenkov, V. A. (2005) Specific Binding of Poly(ADP-ribose) Polymerase-1
to Cruciform Hairpins, J Mol Biol 348, 609-615.
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Spagnoli, C., Korniakov, A., Ulman, A., Balazs, E. A., Lyubchenko, Y. L., and
Cowman, M. K. (2005) Hyaluronan conformations on surfaces: effect of
surface charge and hydrophobicity, Carbohydr Res 340, 929-941.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
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Uversky, V. N., Yamin, G., Munishkina, L. A., Karymov, M. A., Millett, I. S.,
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Brain Res Mol Brain Res 134, 84-102.
Watson, D., Castano, E., Kokjohn, T. A., Kuo, Y. M., Lyubchenko, Y., Pinsky, D.,
Connolly, E. S., Jr., Esh, C., Luehrs, D. C., Stine, W. B., Rowse, L. M., Emmerling,
M. R., and Roher, A. E. (2005) Physicochemical characteristics of soluble
oligomeric Abeta and their pathologic role in Alzheimer's disease, Neurol Res
27, 869-881.
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Yamin, G., Munishkina, L. A., Karymov, M. A., Lyubchenko, Y. L., Uversky, V. N.,
and Fink, A. L. (2005) Forcing Nonamyloidogenic beta-Synuclein To
Fibrillate, Biochemistry 44, 9096-9107.
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Lushnikov, A. Y., Potaman, V. N., Oussatcheva, E. A., Sinden, R. R., and
Lyubchenko, Y. L. (2006) DNA Strand Arrangement within the SfiI-DNA
Complex: Atomic Force Microscopy Analysis, Biochemistry 45, 152-158.
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Lushnikov, A. Y., Potaman, V. N., and Lyubchenko, Y. L. (2006) Site-specific
labeling of supercoiled DNA, Nucleic Acids Res 34, e111 (111-117).
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Lyubchenko, Y. L., Sherman, S., Shlyakhtenko, L. S., and Uversky, V. N. (2006)
Nanoimaging for protein misfolding and related diseases, J Cell Biochem 99,
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Mikheikin, A. L., Lushnikov, A. Y., and Lyubchenko, Y. L. (2006) The effect of
DNA supercoiling on geometry of Holliday junctions, Biochemistry 45,1299813006.
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Uversky, V. N., Kabanov, A. V., and Lyubchenko, Y. L. (2006) Nanotools for
Megaproblems: Probing Protein Misfolding Diseases Using Nanomedicine
Modus Operandi, J Proteome Res 5, 2505-2522.
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Vetcher, A. A., Lushnikov, A. Y., Navarra-Madsen, J., Scharein, R. G.,
Lyubchenko, Y. L., Darcy, I. K., and Levene, S. D. (2006) DNA topology and
geometry in Flp and Cre recombination, J Mol Biol 357, 1089-1104.
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Dynamics of synaptic SfiI-DNA complex: single-molecule fluorescence
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Krasnoslobodtsev, A. V., Shlyakhtenko, L. S., and Lyubchenko, Y. L. (2007)
Probing Interactions within the synaptic DNA-SfiI complex by AFM force
spectroscopy, J Mol Biol 365, 1407-1416.
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Shlyakhtenko, L. S., Gilmore, J., Portillo, A., Tamulaitis, G., Siksnys, V., and
Lyubchenko, Y. L. (2007) Direct visualization of the EcoRII-DNA triple
synaptic complex by atomic force microscopy, Biochemistry 46, 1112811136.
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Shlyakhtenko, L. S., Yuan, B., Emadi, S., Lyubchenko, Y. L., and Sierks, M. R.
(2007) Single-molecule selection and recovery of structure-specific
antibodies using atomic force microscopy, Nanomedicine 3, 192-197.
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Walker, J. R., Gnanam, A. J., Blinkova, A. L., Hermandson, M. J., Karymov, M. A.,
Lyubchenko, Y. L., Graves, P. R., Haystead, T. A., and Linse, K. D. (2007)
Clostridium taeniosporum spore ribbon-like appendage structure,
composition and genes, Mol Microbiol 63, 629-643.
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Wang, D., Miller, S. C., Shlyakhtenko, L. S., Portillo, A. M., Liu, X. M.,
Papangkorn, K., Kopeckova, P., Lyubchenko, Y., Higuchi, W. I., and Kopecek, J.
(2007) Osteotropic Peptide that differentiates functional domains of the
skeleton, Bioconjug Chem 18, 1375-1378.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed
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Wei, C., Liu, N., Xu, P., Heller, M., Tomalia, D. A., Haynie, D. T., Chang, E. H.,
Wang, K., Lee, Y. S., Lyubchenko, Y. L., Bawa, R., Tian, R., Hanes, J., Pun, S.,
Meiners, J. C., and Guo, P. (2007) From bench to bedside: successful
translational nanomedicine: highlights of the Third Annual Meeting of the
American Academy of Nanomedicine, Nanomedicine 3, 322-331.
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Karymov, M. A., Chinnaraj, M., Bogdanov, A., Srinivasan, A. R., Zheng, G., Olson,
W. K., and Lyubchenko, Y. L. (2008) Structure, dynamics, and branch
migration of a DNA Holliday junction: a single-molecule fluorescence and
modeling study, Biophys J 95, 4372-4383.
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sequence, Biophys J 95, 1239-1247.
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Nazarov, I. B., Shlyakhtenko, L. S., Lyubchenko, Y. L., Zalenskaya, I. A., and
Zalensky, A. O. (2008) Sperm chromatin released by nucleases, Syst Biol
Reprod Med 54, 37-46.
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Pavlicek, J. W., Lyubchenko, Y. L., and Chang, Y. (2008) Quantitative analyses
of RAG-RSS interactions and conformations revealed by atomic force
microscopy, Biochemistry 47, 11204-11211.
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Yu, J., Malkova, S., and Lyubchenko, Y. L. (2008) alpha-Synuclein misfolding:
single molecule AFM force spectroscopy study, J Mol Biol 384, 992-1001.
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Lyubchenko, Y. L., and Shlyakhtenko, L. S. (2009) AFM for analysis of
structure and dynamics of DNA and protein-DNA complexes, Methods 47,
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Lyubchenko, Y. L., Shlyakhtenko, L. S., and Gall, A. A. (2009) Atomic force
microscopy imaging and probing of DNA, proteins, and protein DNA
complexes: silatrane surface chemistry, Methods Mol Biol 543, 337-351.
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Rubinstein, A., Lyubchenko, Y. L., and Sherman, S. (2009) Dynamic properties
of pH-dependent structural organization of the amyloidogenic beta-protein
(1-40), Prion 3, 31-43.
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Shlyakhtenko, L. S., Lushnikov, A. Y., and Lyubchenko, Y. L. (2009) Dynamics
of nucleosomes revealed by time-lapse atomic force microscopy,
Biochemistry 48, 7842-7848.
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Shlyakhtenko, L. S., Gilmore, J., Kriatchko, A. N., Kumar, S., Swanson, P. C., and
Lyubchenko, Y. L. (2009) Molecular Mechanism Underlying RAG1/RAG2
Synaptic Complex Formation, J Biol Chem 284, 20956-20965.
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Yu, J., and Lyubchenko, Y. L. (2009) Early stages for Parkinson's
development: alpha-synuclein misfolding and aggregation, J Neuroimmune
Pharmacol 4, 10-16.
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