Publications
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RECENT PUBLICATIONS:
DNA TRANSCRIPTION
Basu U, Mishra N, Farooqui M, Shen J, Johnson LC, Patel SS.
The C-terminal tails of the mitochondrial transcription factors Mtf1 and TFB2M are part of an auto-inhibitory mechanism that regulates DNA binding.
J Biol Chem. 2020 Apr 2. PMID: 32241911
Basu U, Lee SW, Deshpande A, Shen J, Sohn BK, Cho H, Kim H, Patel SS.
The C-terminal tail of the yeast mitochondrial transcription factor Mtf1 coordinates template strand alignment, DNA scrunching and timely transition into elongation.
Nucleic Acids Res. 2020 Mar 18 PMID: 31980825
Chang HW, Hsieh FK, Patel SS, Studitsky VM.
Time-resolved analysis of transcription through chromatin.
Methods. 2019 Apr 15;159-160:90-95. PMID: 30707952
Bird JG, Basu U, Kuster D, Ramachandran A, Grudzien-Nogalska E, Towheed A, Wallace DC, Kiledjian M, Temiakov D, Patel SS, Ebright RH, Nickels BE.
Highly efficient 5' capping of mitochondrial RNA with NAD+ and NADH by yeast and human mitochondrial RNA polymerase.
Elife. 2018 Dec 12;7. PMID: 30526856
Koh HR, Roy R, Sorokina M, Tang GQ, Nandakumar D, Patel SS, Ha T.
Correlating Transcription Initiation and Conformational Changes by a Single-Subunit RNA Polymerase with Near Base-Pair Resolution.
Mol Cell. 2018 May 17;70(4):695-706. PMID: 29775583
Sultana S, Solotchi M, Ramachandran A, Patel SS.
Transcriptional fidelities of human mitochondrial POLRMT, yeast mitochondrial Rpo41, and phage T7 single-subunit RNA polymerases.
J Biol Chem. 2017 Nov 3;292(44):18145-18160. PMID: 28882896
Ramachandran A, Basu U, Sultana S, Nandakumar D, Patel SS.
Human mitochondrial transcription factors TFAM and TFB2M work synergistically in promoter melting during transcription initiation.
Nucleic Acids Res. 2016 Nov 29. PMID:27903899
Ramachandran A, Nandakumar D, Deshpande A, Lucas TP, Bhojappa RR, Tang GQ, Raney K, Yin YW, Patel SS.
The yeast mitochondrial RNA polymerase and transcription factor complex catalyzes efficient priming of DNA synthesis on single-stranded DNA.
J Biol Chem. 2016 Jun 16. PMID:27311715
DNA REPLICATION
Singh A, Pandey M, Nandakumar D, Raney KD, Yin YW, Patel SS.
Excessive excision of correct nucleotides during DNA synthesis explained by replication hurdles.
EMBO J. 2020 Mar 16;39(6):e103367. PMID: 32037587
Sun B, Singh A, Sultana S, Inman JT, Patel SS, Wang MD
Helicase promotes replication re-initiation from an RNA transcript.
Nat Commun. 2018 Jun 13;9(1):2306. PMID: 29899338
Chang HW, Pandey M, Kulaeva OI, Patel SS, Studitsky VM.
Overcoming a nucleosomal barrier to replication.
Sci Adv. 2016 Nov 11;2(11):e1601865. PMID:27847876
Brennan LD, Forties RA, Patel SS, Wang MD.
DNA looping mediates nucleosome transfer.
Nat Commun. 2016 Nov 3;7:13337. PMID:27808093
Nandakumar D, Patel SS.
Methods to study the coupling between replicative helicase and leading-strand DNA polymerase at the replication fork.
Methods. 2016 May 9. S1046-2023(16)30126-8. Review. PMID:27173619
Sen D, Patel G, Patel SS.
Homologous DNA strand exchange activity of the human mitochondrial DNA helicase TWINKLE.
Nucleic Acids Res. 2016 May 19;44(9):4200-10. PMID:26887820
Szymanski MR, Kuznetsov VB, Shumate C, Meng Q, Lee YS, Patel G, Patel S, Yin YW.
Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase.
EMBO J. 2015 Jul 14;34(14):1959-70. PMID:26056153
Sun B, Pandey M, Inman JT, Yang Y, Kashlev M, Patel SS, Wang MD.
T7 replisome directly overcomes DNA damage.
Nat Commun. 2015 Dec 17;6:10260. doi: 10.1038/ncomms10260.PMID:26675048
Pandey M, Elshenawy MM, Jergic S, Takahashi M, Dixon NE, Hamdan SM, Patel SS.
Two mechanisms coordinate replication termination by the Escherichia coli Tus-Ter complex.
Nucleic Acids Res. 2015 Jul 13;43(12):5924-35. PMID:26007657
Nandakumar D, Pandey M, Patel SS.
Cooperative base pair melting by helicase and polymerase positioned one nucleotide from each other.
Elife. 2015 May 13;4. doi: 10.7554/eLife.06562. PMID: 25970034
Nandakumar D, Patel SS.
Finding the right match fast.
Cell. 2015 Feb 26;160(5):809-11. doi: 10.1016/j.cell.2015.02.007.PMID:25723158
INNATE IMMUNITY
Zheng J, Wang C, Chang MR, Devarkar SC, Schweibenz B, Crynen GC, Garcia-Ordonez RD, Pascal BD, Novick SJ, Patel SS, Marcotrigiano J, Griffin PR.
HDX-MS reveals dysregulated checkpoints that compromise discrimination against self RNA during RIG-I mediated autoimmunity.
Nat Commun. 2018 Dec 18;9(1):5366. PMID: 30560918
Devarkar SC, Schweibenz B, Wang C, Marcotrigiano J, Patel SS.
RIG-I Uses an ATPase-Powered Translocation-Throttling Mechanism for Kinetic Proofreading of RNAs and Oligomerization.
Mol Cell. 2018 Oct 18;72(2):355-368. PMID: 30270105
Devarkar SC, Wang C, Miller MT, Ramanathan A, Jiang F, Khan AG, Patel SS, Marcotrigiano J.
Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I.
Proc Natl Acad Sci U S A. 2016 Jan 19;113(3):596-601. PMID:26733676
Ramanathan A, Devarkar SC, Jiang F, Miller MT, Khan AG, Marcotrigiano J, Patel SS.
The autoinhibitory CARD2-Hel2i Interface of RIG-I governs RNA selection.
Nucleic Acids Res. 2016 Jan 29;44(2):896-909. PMID:26612866